Team:TU Darmstadt/Project

From 2012.igem.org

(Difference between revisions)

Revision as of 16:20, 24 September 2012

Overview

Since the discovery of [http://en.wikipedia.org/wiki/Polyethylene_terephthalate Polyethylene terephthalate] ([http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET]) in the 1940s, it has become the most widely manufactured synthetic. In 2010, global annual production exceeded 100 million tons. Its popularity also creates the issue of PET waste. In Western countries today, less than 70% of [http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET] produced are recovered by conventional means of recycling. Biological processes currently play no role, as its chemical properties make [http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET] inert to biological degradation. As a solution to this, we suggest the development of a bacterial recycling system, transforming PET waste into harmless, environmentally benign compounds which then can be used further in a wide range of applications. This will help to turn [http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET] into a useful secondary raw material that is just too valuable to throw away.

How would such a bacterial recycling system look like and what features are required?

The bacterial recycling system we aim for is based on an easy to cultivate microorganism. This is then enhanced by inserting enzymes that are tailored to handle a specific task. This will ultimately enable the microorganism to recycle [http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET]. The recycling itself will be done in fermenters, thus preventing any release of process products or organisms. We named the microorganism containing all the enzymes PET.er ([http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET] terminator). First of all, our genetically modified organism (GMO) shall be able to digest the PET, decomposing it into its [http://en.wikipedia.org/wiki/Terephthalic_acid terephtalic acid] ([http://en.wikipedia.org/wiki/Terephthalic_acid TPA]) subunits. Due to its chemical properties, [http://en.wikipedia.org/wiki/Terephthalic_acid TPA] uptake by diffusion is not possible at pH values higher than 3.0. Under such conditions, [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli Escherichia coli] ([http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]), the most common microorganism in genetics, cannot be cultivated. If one still wants to use [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli], it is necessary to implement a specialised TPA uptake system in order to make it work at pH 7.0. There are multiple reasons for using [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli] as our host bacteria. It is easy to cultivate, secure to handle and literally tons of different strains and materials are available. Most important is the circumstance that the genome of [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli] is well-known and characterised. This enables us to modify and insert proteins as we please. Yet there is a challenge: Even if an unmodified [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli] were able to absorb [http://en.wikipedia.org/wiki/Terephthalic_acid TPA], it could not use it in its metabolism. Therefore, we need to insert additional enzymes to ‘tweak’ the metabolic pathway, thus enabling [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli] to use the [http://en.wikipedia.org/wiki/Terephthalic_acid TPA] as an energy source. So, obviously, information about the [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli genome] is essential for this task. In brief, we need to insert enzymes for degradation, transport (uptake) and metabolism. This may sound easy, but it isn't. First of all, [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli] is a living system. It may repel, mutate or modify [http://en.wikipedia.org/wiki/DNA DNA] that it doesn't tolerate or may simply die after transformation. Secondly, even if enzymes are proven to work in other microorganisms, it doesn't necessarily mean that they'll work after insertion into [http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]. Therefore, a whole variety of tests is required to evaluate the project and to verify successful implementation. Testing involves material science (physical testing) and modeling.

How did we handle the task?

We were able to recruit numerous team members, so we split our project into a number of tasks by their respective objectives:

In addition to these sub-projects we invited students from other departments to contribute to our project. This involves:

The information provided in this overview is just a brief introduction. Want to learn more? Continue with 1. Degradation.

@@ Line 48: / Line 48: @@
 The bacterial recycling system we aim for is based on an easy to cultivate microorganism. This is then enhanced by inserting enzymes that are tailored to handle a specific task. This will ultimately enable the microorganism to recycle [http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET]. The recycling itself will be done in fermenters, thus preventing any release of process products or organisms.
 We named the microorganism containing all the enzymes PET.er ([http://en.wikipedia.org/wiki/Polyethylene_terephthalate PET] terminator).
-First of all, our genetically modified organism (GMO) shall be able to [https://2012.igem.org/Team:TU_Darmstadt/Project/Degradation digest] the PET, decomposing it into its [http://en.wikipedia.org/wiki/Terephthalic_acid terephtalic acid] ([http://en.wikipedia.org/wiki/Terephthalic_acid TPA]) subunits. Due to its chemical properties, [http://en.wikipedia.org/wiki/Terephthalic_acid TPA] uptake by diffusion is not possible at pH values higher than 3.0. Under such conditions, ''Escherichia coli'' (''E. coli''), the most common microorganism in genetics, cannot be cultivated. If one still wants to use E. coli, it is necessary to implement a specialised TPA uptake system in order to make it work at pH 7.0. There are multiple reasons for using E. coli as our host bacteria. It is easy to cultivate, secure to handle and literally tons of different strains and materials are available. Most important is the circumstance that the genome of E. coli is well-known and characterised. This enables us to modify and insert proteins as we please. Yet there is a challenge: Even if an unmodified E. coli were able to absorb TPA, it could not use it in its metabolism. Therefore, we need to insert additional enzymes to ‘tweak’ the metabolic pathway, thus enabling E. coli to use the TPA as an energy source. So, obviously, information about the E. coli genome is essential for this task.
+First of all, our genetically modified organism (GMO) shall be able to [https://2012.igem.org/Team:TU_Darmstadt/Project/Degradation digest] the PET, decomposing it into its [http://en.wikipedia.org/wiki/Terephthalic_acid terephtalic acid] ([http://en.wikipedia.org/wiki/Terephthalic_acid TPA]) subunits. Due to its chemical properties, [http://en.wikipedia.org/wiki/Terephthalic_acid TPA] [https://2012.igem.org/Team:TU_Darmstadt/Project/Transport uptake] by diffusion is not possible at pH values higher than 3.0. Under such conditions, ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli Escherichia coli]'' (''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]''), the most common microorganism in genetics, cannot be cultivated. If one still wants to use ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]'', it is necessary to implement a specialised [https://2012.igem.org/Team:TU_Darmstadt/Project/Transport TPA uptake system] in order to make it work at pH 7.0. There are multiple reasons for using ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]'' as our host bacteria. It is easy to cultivate, secure to handle and literally tons of different [https://2012.igem.org/Team:TU_Darmstadt/Materials#Strains strains] and [https://2012.igem.org/Team:TU_Darmstadt/Materials materials] are available. Most important is the circumstance that the genome of ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]'' is well-known and characterised. This enables us to modify and insert proteins as we please. Yet there is a challenge: Even if an unmodified ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]'' were able to absorb [http://en.wikipedia.org/wiki/Terephthalic_acid TPA], it could not use it in its metabolism. Therefore, we need to insert additional enzymes to ‘tweak’ the [https://2012.igem.org/Team:TU_Darmstadt/Project/Metabolism metabolic pathway], thus enabling ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]'' to use the [http://en.wikipedia.org/wiki/Terephthalic_acid TPA] as an energy source. So, obviously, information about the ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli genome]'' is essential for this task.
-In brief, we need to insert enzymes for [https://2012.igem.org/Team:TU_Darmstadt/Project/Degradation degradation], [https://2012.igem.org/Team:TU_Darmstadt/Project/Transport transport (uptake)] and [https://2012.igem.org/Team:TU_Darmstadt/Project/Metabolism metabolism]. This may sound easy, but it isn't. First of all, E. coli is a living system. It may repel, mutate or modify DNA that it doesn't tolerate or may simply die after insertion. Secondly, even if enzymes are proven to work in other microorganisms, it doesn't necessarily mean that they'll work after insertion into E. coli. Therefore, a whole variety of tests is required to evaluate the project and to verify successful implementation. Testing involves [https://2012.igem.org/Team:TU_Darmstadt/Project/Material_Science material science] (physical testing) and [https://2012.igem.org/Team:TU_Darmstadt/Project/Simulation modeling].
+In brief, we need to insert enzymes for [https://2012.igem.org/Team:TU_Darmstadt/Project/Degradation degradation], [https://2012.igem.org/Team:TU_Darmstadt/Project/Transport transport (uptake)] and [https://2012.igem.org/Team:TU_Darmstadt/Project/Metabolism metabolism]. This may sound easy, but it isn't. First of all, ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]'' is a living system. It may repel, mutate or modify [http://en.wikipedia.org/wiki/DNA DNA] that it doesn't tolerate or may simply die after transformation. Secondly, even if enzymes are proven to work in other microorganisms, it doesn't necessarily mean that they'll work after insertion into ''[http://ecoliwiki.net/colipedia/index.php/Escherichia_coli E. coli]''. Therefore, a whole variety of tests is required to evaluate the project and to verify successful implementation. Testing involves [https://2012.igem.org/Team:TU_Darmstadt/Project/Material_Science material science] (physical testing) and [https://2012.igem.org/Team:TU_Darmstadt/Project/Simulation modeling].
 '''How did we handle the task?'''