Team:Bielefeld-Germany/Project/Appoach

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{{Team:Bielefeld/Head}}
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              Approach
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__TOC__
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The conventional methods of sewage treatment plants in order to take care of waste water are insufficient. This appears to be the case because most common microcontaminants like synthetic estrogen, bisphenol A, diclofenac ''etc.'' are very difficult to break down.
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The goal of Bielefeld's iGEM team is to develop a biological filter-system using immobilized laccases for the purification of municipal and industrial waste water to get rid of these synthetic estrogens and other aromatic compounds. Laccases are copper-containing oxidase enzymes found in many organisms. One of their properties is the ability to degrade a wide range of aromatic and phenolic compounds. For this purpose, genes of various bacterial and eukaryotic laccases were isolated and expressed in ''Escherichia coli'' and ''Pichia pastoris'' (see Fig. 1). The choice of the expression system was meanwhile dependent on the enzyme's glycosylation status.
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[[File:File-Bielefeld2012_Approach_Isolation_Production_Purification.JPG|center|thumb|700px|'''Figure 1:''' The first steps of our project included the cloning, production and purification of the selected laccases from different organisms.]]
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=Approach=
 
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The conventional methods of sewage treatment plants to take care of waste water are insufficient. This is, because the most common micro contaminants like synthetic estrogen, Bisphenol A, Dicolfenac ''etc.'' are very difficult to break down.
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==Isolation of laccase genes and generation of new BioBricks==
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The goal of Bielefeld’s iGEM team is to develop a biological filter-system using immobilized laccases to purify municipal and industrial waste water from these synthetic estrogens and other aromatic compounds. Laccases are copper-containing oxidase enzymes found in many organisms. One of their properties is the ability to break down a wide range of aromatic and phenolic compounds. For this purpose, genes of various bacterial and eukaryotic laccases will be isolated and expressed in Escherichia coli and Pichia pastoris. The choice of the expression-system depends on the glycosylation status of the enzyme.
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==Isolation and Generating of new BioBricks==
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The first step of our project was to isolate the specific laccase gene sequences and to generate new BioBricks for the iGEM competition.
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The first step of our project is to isolate the specific gene sequences and to generate new BioBricks for the iGEM competition.
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The laccases of the following organisms have been isolated:
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The Laccases of the following organisms are isolated:
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'''bacterial laccases:'''[[File:Bielefeld2012_Approach_Isolation_Production_Purification.JPG|right|thumb|1200px|First steps of our Project]]
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'''Bacterial laccases from:'''
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#Escherichia Coli
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#''Escherichia coli''
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#Bacillus Halodurans
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#''Bacillus halodurans''
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#Bacillus Pumilus
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#''Bacillus pumilus''
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#Streptomyces griseus
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#''Streptomyces griseus''
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#Streptomyces lavendulae
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#''Streptomyces lavendulae''
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#Thermus thermophilus
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#''Thermus thermophilus''
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#Xanthomonas campestris
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#''Xanthomonas campestris''
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''' Eukaryota laccases:'''
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'''Eukaryotic laccases from:'''
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#Arabidopsis thaliana
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#''Arabidopsis thaliana''
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#Trametes versicolor
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#''Pycnoporus cinnabarinus''
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#Trametes villosa
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#''Trametes versicolor''
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#''Trametes villosa''
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For more information about the organisms [https://2012.igem.org/Team:Bielefeld-Germany/Project/Background#4 click here].
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For more information about the Organisms [[Team:Bielefeld-Germany/Project/Background/Organisms |click here]].
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The essential parts which were used to design our functional plasmids and a new shuttle-vector-system are listed in the following table:
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The additional and essential BioBricks and characteristics, which are used to design our functional plasmids and a new shuttle-vector-system are shown in the following table:
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<center>
<center>
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'''Parts of the ''E.coli'' Expressionvector and the ''P.Pastoris'' Shuttle-Vector'''
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'''Parts of the ''E. coli'' expression vector and the ''P. pastoris'' shuttle vector'''
{|class="wikitable" style="text-align: center; width: 300px: height: 300px;" border=0}
{|class="wikitable" style="text-align: center; width: 300px: height: 300px;" border=0}
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! Plasmid Characteristics  
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! Plasmid characteristics  
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! Shuttlevector Characteristics
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! Shuttle vector characteristics
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|T7 Promotorregion
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|T7 promoter region
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|AOX-Promotor
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|AOX1 promoter
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|His-Tag-Sequence
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|His-Tag sequence
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|alpha-factor
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|Mating factor alpha 1
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|Chloramphenicol Resistance
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|Chloramphenicol resistance
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|Zeocin Resistance
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|Histidine auxotrophic complementation
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Which expression system is used is determined by the folding and glycosylation of the individual laccase.   
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The choice of the expression system was determined by the folding and glycosylation status of the individual laccase.   
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The resulting genetically modified organisms produce the laccases for our approach. Further down the line, these laccases are isolated and purified.
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The resulting genetically modified organisms produced the laccases for our approach. In order to characterize the different laccases these enzymes have been isolated and purified.
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== Determining Activity and Potential of The Different Laccases ==
 
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== Determining activity and potential of the different laccases ==
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{|
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The next step to generate an efficient filter system was to characterize the purified laccases. To identify the potential of the laccases, each of the enzymes was examined for its activity and potential to degrade several substances. The degradation potential of the manufactured laccases was determined representatively for substances that originate from different chemical groups, such as analgesics, endocrine substances, pesticides, polycyclic aromatic hydrocarbons and bleaching agents (see Fig. 2).
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|The next step to generate a effeciantally filter system is to characterize different produced and purified laccases. To identify the potential of different laccases, the enzyme are examined on their activity and the potential to degrade different substances. The degradation potential of different laccases are investigate for representative substances from different chemical areas like analgetics, endocrine substances, pesticides, poly aromatic hydrocarbons and bleaching agents.
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In our case, we analyzed the specific laccases for their degradation efficiency while varying different parameters like temperature, pH value and buffer system. A great concern of our team is to guarantee [https://2012.igem.org/Team:Bielefeld-Germany/Safety the safety] of the generated filter system. Besides the degradation potential, a very important aspect to us is the analysis of the degraded substances to ensure the harmlessness of the degradation result of an individual laccase. This was investigated and verified by HPLC-masspectroscopy (LC-ESI-qTOF-MS). With this knowledge, our aim was to identify the one laccase which shows the highest potential for a safe and highly functional filter system.
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In this case we analyses the efficiency of the laccase degradation and investigate different parameters like temperature, pH, and Buffer-systems. A great concern of our team is to guarantee the Safety of the generated filter system. Besides the degradation potential, a very important aspect is an analyzing of the degradated substances to guarantee, that the degradation with laccases don't generate any toxic or dangerous substances. These analyses realized by HPLC-massspectorscopy. With this knowledge we want to identify these laccase which show the highes potential for a functional filter system.
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|[[File:Bielefeld2012_Substrates.png|right|thumb|450px|'''Representative substances''' from different chemical areas: Endocrine Substances (''Estradiol,Ethynylestradiol,Estrone''), Pesticides (''Lindane''), Bleaching Agent (''Violuracid''), Poly-Aromatic-Hydrocarbons and Analgetics(''Diclofenac, Naproxen, Ibuprofen'')]]
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== Immobilization and the final Development of the Filter==
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[[File:Bielefeld2012_Substrates.png|center|thumb|450px|'''Figure 2:''' Representative substances from different chemical areas: endocrine substances (''estradiol, ethynyl estradiol, estrone''), pesticides (''lindane''), bleaching agent (''violuracid''), polycyclic aromatic hydrocarbons and analgesics (''diclofenac, naproxen, ibuprofen'')]]
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The last step to realize our project is to immobilize the produced lacasses with the highest potentials. To generate a filter-system with a high yield of active and immobilized enzymes, different approaches are tested. On the one hand we try to immobilize the enzymes with a chemical immobilization protocol to bind covalent the laccases on specific silica-beads, and on the other hand we try to generate a natural immobilization protocols with different binding proteins like the ''cellulose-binding-protein'' or the ''chitin-binding-protein''. By generating the new natural immobilization protocol two different ''cellulose-binding-protein'' are inverstigated ot the organisms ''Cellulomonas fimi'', ''Clostridium josui '' and ''Clostridium cellulovorans''. To investigate the bindicapacity and the bond strength of the different proteins at first the binding-proteins are linked with GFP (Green fluorescens Protein) and in the end with the lacasses.
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== Immobilization and the final development of a degradation system==
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The last step for the realization of our project was to immobilize the produced laccase with the highest degradation potential. To generate a filter-system with a high yield of active and immobilized enzymes, different approaches were tested. On one hand, we tried to immobilize the enzymes with a chemical immobilization protocol to bind the laccases covalently on special silica-beads (CPC silica beads). On the other hand, we tried to generate an immobilization protocol by fusing the laccases to natural binding domains, such as the cellulose binding domain, the ceratin binding domain or the chitin binding domain. By establishing a new protocol, three different cellulose binding domains from the organisms ''Cellulomonas fimi'', ''Clostridium josui '' and ''Clostridium cellulovorans'' were investigated (see Fig. 3). In a first step, the binding-domains were linked to GFP (green fluorescent protein) in order to examine the strength of the binding and the binding-capacity. In the end, the domains will be fused to the laccases.
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[[File:Bielefeld2012_Immobilisierung_Approach.JPG|center|thumb|1200px|Immobilization-strategies]]
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[[File:Bielefeld2012_Immobilisierung_Approach.JPG|center|thumb|650px|'''Figure 3:''' Immobilization strategies]]
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The goal of the iGEM-Team Bielefeld was to generate a functional filter system with a high efficiency to degrade a high number of different microcontaminants. This filter system will be able to reduce the environmental pollution and improve the quality of waterbodies for the safety of animals and Mankind.
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</div>
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<html>
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  </div>
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</html>
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The goal of the iGEM-Team Bielefeld is to generate a functional filter system with a high efficiency to degrade a high number of micro contaminants. If we are able to generate this filter systems, this system is able to reduce the environmental pollution and to improve the waterbody quality for animals and the mankind.
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{{Team:Bielefeld/Sponsoren}}

Latest revision as of 23:54, 2 December 2012

Approach

Contents

The conventional methods of sewage treatment plants in order to take care of waste water are insufficient. This appears to be the case because most common microcontaminants like synthetic estrogen, bisphenol A, diclofenac etc. are very difficult to break down. The goal of Bielefeld's iGEM team is to develop a biological filter-system using immobilized laccases for the purification of municipal and industrial waste water to get rid of these synthetic estrogens and other aromatic compounds. Laccases are copper-containing oxidase enzymes found in many organisms. One of their properties is the ability to degrade a wide range of aromatic and phenolic compounds. For this purpose, genes of various bacterial and eukaryotic laccases were isolated and expressed in Escherichia coli and Pichia pastoris (see Fig. 1). The choice of the expression system was meanwhile dependent on the enzyme's glycosylation status.

Figure 1: The first steps of our project included the cloning, production and purification of the selected laccases from different organisms.


Isolation of laccase genes and generation of new BioBricks

The first step of our project was to isolate the specific laccase gene sequences and to generate new BioBricks for the iGEM competition. The laccases of the following organisms have been isolated:

Bacterial laccases from:

  1. Escherichia coli
  2. Bacillus halodurans
  3. Bacillus pumilus
  4. Streptomyces griseus
  5. Streptomyces lavendulae
  6. Thermus thermophilus
  7. Xanthomonas campestris


Eukaryotic laccases from:

  1. Arabidopsis thaliana
  2. Pycnoporus cinnabarinus
  3. Trametes versicolor
  4. Trametes villosa

For more information about the organisms click here.

The essential parts which were used to design our functional plasmids and a new shuttle-vector-system are listed in the following table:

Parts of the E. coli expression vector and the P. pastoris shuttle vector

Plasmid characteristics Shuttle vector characteristics
T7 promoter region AOX1 promoter
His-Tag sequence Mating factor alpha 1
Chloramphenicol resistance Histidine auxotrophic complementation

The choice of the expression system was determined by the folding and glycosylation status of the individual laccase. The resulting genetically modified organisms produced the laccases for our approach. In order to characterize the different laccases these enzymes have been isolated and purified.


Determining activity and potential of the different laccases

The next step to generate an efficient filter system was to characterize the purified laccases. To identify the potential of the laccases, each of the enzymes was examined for its activity and potential to degrade several substances. The degradation potential of the manufactured laccases was determined representatively for substances that originate from different chemical groups, such as analgesics, endocrine substances, pesticides, polycyclic aromatic hydrocarbons and bleaching agents (see Fig. 2).

In our case, we analyzed the specific laccases for their degradation efficiency while varying different parameters like temperature, pH value and buffer system. A great concern of our team is to guarantee the safety of the generated filter system. Besides the degradation potential, a very important aspect to us is the analysis of the degraded substances to ensure the harmlessness of the degradation result of an individual laccase. This was investigated and verified by HPLC-masspectroscopy (LC-ESI-qTOF-MS). With this knowledge, our aim was to identify the one laccase which shows the highest potential for a safe and highly functional filter system.

Figure 2: Representative substances from different chemical areas: endocrine substances (estradiol, ethynyl estradiol, estrone), pesticides (lindane), bleaching agent (violuracid), polycyclic aromatic hydrocarbons and analgesics (diclofenac, naproxen, ibuprofen)

Immobilization and the final development of a degradation system

The last step for the realization of our project was to immobilize the produced laccase with the highest degradation potential. To generate a filter-system with a high yield of active and immobilized enzymes, different approaches were tested. On one hand, we tried to immobilize the enzymes with a chemical immobilization protocol to bind the laccases covalently on special silica-beads (CPC silica beads). On the other hand, we tried to generate an immobilization protocol by fusing the laccases to natural binding domains, such as the cellulose binding domain, the ceratin binding domain or the chitin binding domain. By establishing a new protocol, three different cellulose binding domains from the organisms Cellulomonas fimi, Clostridium josui and Clostridium cellulovorans were investigated (see Fig. 3). In a first step, the binding-domains were linked to GFP (green fluorescent protein) in order to examine the strength of the binding and the binding-capacity. In the end, the domains will be fused to the laccases.

Figure 3: Immobilization strategies

The goal of the iGEM-Team Bielefeld was to generate a functional filter system with a high efficiency to degrade a high number of different microcontaminants. This filter system will be able to reduce the environmental pollution and improve the quality of waterbodies for the safety of animals and Mankind.

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