Team:ETH Zurich/project/background/biotoolssimple

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Revision as of 14:17, 13 October 2014

Biological Tools

Integrases – Molecules working as scissors on the DNA

Integrases are proteins that work like scissors on two specific sites on the DNA.

Within those two sites they can invert the sequence or they can completely remove it. The genes coding for those integrase-scissors and their corresponding specific sites can easily be inserted into bacteria.

This way you can control which genes are expressed by defining integrases present in your system.

In our project integrases working as scissors for DNA is one of the core components we tried to implement in Mosaicoli.

Specific sites for the binding of integrases

Quorum sensing – Communication using signal molecules

Bacteria can interact with their surroundings and neighboring cells via cell-to-cell communication. Using this communication they can coordinate the expression of genes and thus the overall behavior of their population.

Quorum sensing describes a system including a stimulus and a response. It is the synthesis and diffusion of small molecules, which are able to trigger a response. One of these small molecules is called N-(3-oxohexanoyl)-L-homoserine lactones, which we will just call AHL here, and is produced by the enzyme LuxI (Please consider the figure below for the flow of AHL between cells).

The AHL produced in one cell can then diffuse out of the cell and reach other cells. In those other cells it binds and activates a protein called LuxR. This activated LuxR protein binds the DNA in the receiver cells and triggers the production of LuxI, which will itself trigger the production of more AHL diffusing to the next cells.

There are also ther systems of AHLs corresponding to the LuxR/LuxI system. These additional systems are called LasR/LasI and RhlR/RhlI.

Simplified Quorum Sensing System

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 ==='''Quorum sensing – Communication using signal molecules'''===
-Bacteria can interact with their surroundings and neighboring cells via cell-to-cell communication. Using this communication they can coordinate the expression of genes and thus the overall behavior of the population of bacteria.
+Bacteria can interact with their surroundings and neighboring cells via cell-to-cell communication. Using this communication they can coordinate the expression of genes and thus the overall behavior of their population.
-Quorum sensing describes a system including a stimulus and a response. It is the synthesis, secretion and diffusion of small molecules, which are able to trigger a response.
+Quorum sensing describes a system including a stimulus and a response. It is the synthesis and diffusion of small molecules, which are able to trigger a response. One of these small molecules is called N-(3-oxohexanoyl)-L-homoserine lactones, which we will just call AHL here, and is produced by the enzyme LuxI (Please consider the figure below for the flow of AHL between cells).
-Already in the early 1980s by investigating a specific strain of bacteria it was found that depending on the cell density and the concentration of signal molecules, bacteria were able to communicate.
+The AHL produced in one cell can then diffuse out of the cell and reach other cells. In those other cells it binds and activates a protein called LuxR. This activated LuxR protein binds the DNA in the receiver cells and triggers the production of LuxI, which will itself trigger the production of more AHL diffusing to the next cells.
-<br>
-The communication was visualized by bioluminescence, which is the production and emission of light by a living organism.
-It was then found that the molecule inducing this bioluminescence is N-(3-oxohexanoyl)-L-homoserine lactone, which we will just call AHL here and is produced by the enzyme Luxl (Please consider the figure below for the flow of AHL between cells).
-Another enzyme named LuxI produces this AHL. The AHL produced in one cell can then diffuse out of the cell and reach other cells. In those other cells it binds and activates a protein called LuxR. This LuxR protein regulates the gene transcription (first step on the way from DNA to proteins).
+There are also ther systems of AHLs corresponding to the LuxR/LuxI system. These additional systems are called LasR/LasI and RhlR/RhlI.
-Further research on such signal molecules was conducted and other systems of AHLs corresponding to the LuxR/LuxI system were found. These additional systems are called LasR/LasI and RhlR/RhlI.
 [[File:ETH Zurich 2014 Simplified biotools QS.png|center|600px|thumb|Simplified Quorum Sensing System]]