Team:University College London/Module 4

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Latest revision as of 02:43, 27 September 2012

Description

The Buoyancy module is key to both the Degradation and the Aggregation systems. Buoyancy is required to position our bacteria in the water column, and also to enable them to buoy the plastic aggregates.

This module requires driving the expression of a gas vesicle gene cluster. Gas vesicles are formed within the cell, and are hollow spaces surrounded by a wall of hydrophobic protein. These gas vesicles are permeable to gases, which diffuse into the gas vesicles, increasing its partial pressure, thereby increasing buoyancy.

Gas vesicles are found largely in cyanobacteria and halophillicarchea, where they are necessary to access oxygen and light. Their formation is driven by a number of genes required for production and regulation. We are using the gas vesicle gene to attribute buoyancy to our cells so that they float on to the surface of the ocean. Our particular cluster -known as GVP is extracted from Bacillus Megaterium which contains 14 putative gens gvp-A,-P,-Q,-B,-R,-N,-F,-G,-L,-S,-K,-J,-T and -U of which the last 11 genes, in a 5.7-kb gene cluster are the maximum required for gas vesicle synthesis and function in E. coli.

The Buoyancy system is subject to the control of a glucose-repressible promoter, cstA (BBa_K118011). During carbon starvation, ATP is transformed into cAMP and then it binds the cAMP receptor protein, this complex activates the cstA promoter. Studies suggest that cstA promoter can be used to induce the expression of reporter genes in cultures with different glucose concentrations (1). Free glucose concentration varies in the upper 300 m of the seawater (2), so this gives us a gradient of activation which allows us to control the transcription of gas vesicle genes in different glucose concentrations. Since the plastic particles are mostly found in the upper 25 m, bacteria needs to be positioned in this water column. This is very important for our system therefore we designed a mechanism to amplify the expression of gene under the control of the cstA promoter, such design includes T7 RNA polymerase and a second promoter (pT7). Hence we believe that this will produce larger amounts of gas vesicle gene cluster. In order to test this module we used GFP as a reporter gene instead of the gas vesicle gene cluster.

References

1. Schultz JE, Matin A. (1991) Molecular and functional characterization of a carbon starvation gene of Escherichia coli. J Mol Biol.; 218(1):129-40.

2. Skoog, A., Biddanda B, Benner R. (1999) Bacterial utilization of dissolved glucose in the upper water column of the Gulf of Mexico. Limnol. Oceanogr. 44:1625-1633.

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+{{:Team:University_College_London/templates/headnocover}}<html><iframe width="990" height="500" src="http://www.plasticrepublic.org/wikianimations/module4desc.html"></iframe></html>
-= Module 4: Buoyancy=
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 == Description==
 The '''Buoyancy module''' is key to both the Degradation and the Aggregation systems. Buoyancy is required to '''position''' our bacteria in the water column, and also to enable them to buoy the plastic '''aggregates'''.
 This module requires driving the expression of a '''gas vesicle gene cluster'''. Gas vesicles are formed within the cell, and are hollow spaces surrounded by a wall of '''hydrophobic''' protein. These gas vesicles are '''permeable''' to gases, which diffuse into the gas vesicles, increasing its '''partial pressure''', thereby increasing buoyancy.
-The Buoyancy system is subject to the control of a '''glucose-repressible''' promoter, '''PcstA''' (BBa_K118011). As a '''starvation''' promoter, production of gas vesicles will be limited in '''high cell nutrient''' environments, but increase as carbon sources become scarce. This gives us a '''gradient''' of activation which allows us to control the transcription of gas vesicle genes in different conditions. In our project, we expect this to occur as cells sink to greater depths in the ocean, thereby up regulating buoyancy as resources decrease, buoying our cells back to the targeted ocean surface.
+Gas vesicles are found largely in cyanobacteria and halophillicarchea, where they are necessary to access oxygen and light. Their  formation is driven by a number of genes required for production and regulation. We are using the gas vesicle gene to attribute buoyancy to our cells so that they float on to the surface of the ocean. Our particular cluster -known as GVP is extracted from Bacillus Megaterium which contains 14 putative gens gvp-A,-P,-Q,-B,-R,-N,-F,-G,-L,-S,-K,-J,-T and -U of which the last 11 genes, in a 5.7-kb gene cluster are the maximum required for gas vesicle synthesis and function in ''E. coli''.
+The Buoyancy system is subject to the control of a '''glucose-repressible promoter, cstA''' (BBa_K118011). During carbon starvation, ATP is transformed into cAMP and then it binds the cAMP receptor protein, this complex activates the cstA promoter. Studies suggest that cstA promoter can be used to induce the expression of reporter genes in cultures with different '''glucose concentrations''' (1).
+Free glucose concentration varies in the upper 300 m of the seawater (2), so this gives us a gradient of activation which allows us to control the transcription of gas vesicle genes in different glucose concentrations.
+Since the plastic particles are mostly found in the upper 25 m, bacteria needs to be positioned in this water column. This is very important for our system therefore we designed a mechanism to amplify the expression of gene under the control of the cstA promoter, such design includes '''T7 RNA polymerase''' and a second promoter '''(pT7)'''. Hence we believe that this will produce larger amounts of gas vesicle gene cluster.
+In order to test this module we used '''GFP''' as a reporter gene instead of the gas vesicle gene cluster.
+==References==
+. Schultz JE, Matin A. (1991) Molecular and functional characterization of a carbon starvation gene of Escherichia coli. J Mol Biol.; 218(1):129-40.
+. Skoog, A., Biddanda B, Benner R. (1999) Bacterial utilization of dissolved glucose in the upper water column of the Gulf of Mexico. Limnol. Oceanogr. 44:1625-1633.
 {{:Team:University_College_London/templates/foot}}