Team:ETH Zurich/project/background/biotoolssimple

From 2014.igem.org

(Difference between revisions)
(Biological Tools)
(Integrases – Molecules working as scissors on the DNA)
 
(30 intermediate revisions not shown)
Line 1: Line 1:
== Biological Tools ==
== Biological Tools ==
-
===Integrases Molecules working as scissors on the DNA===
+
==='''Quorum sensing Communication using signal molecules'''===
-
Integrases are molecules that work like scissors on specific sites on the DNA (DNA is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms).
+
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.  
-
There are two sites in the genome needed for the scissors to act. Within those sites they can in a unidirectional way invert the sequence or they can completely remove it. Inversion or removals only depend on the orientation of the sites where the scissors recognize and act.
+
<br>
-
The genes coding for those integrase-scissors can easily be expressed in bacteria. So we can basically encode scissors that will then act on a target plasmid (a plasmid is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently) in bacteria.
+
<br>
-
There exist various kinds of these integrase-scissors that are specific for some target sites in the genome.  
+
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 different integrases just described can then be combined in a system. This system is then used for engineering Boolean logic gates. A logic gate is a system where we have an input and inside a decision is taken. We have inputs in the form of yes or no and the output again is yes or no. The same accounts for on versus off states. Depending on the kind of the logic gate, the inputs are interpreted differently.
+
<br>
 +
<br>
 +
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. This way, the sensor cells will also act as a producer cell and trasnfer the signal to the following cells.
 +
<br>
 +
<br>
 +
There are also ther systems of AHLs corresponding to the LuxR/LuxI system. These additional systems are called LasR/LasI and RhlR/RhlI.
-
In our project integrases working as scissors for DNA is one of the core components we tried to implement in Mosaicoli.
 
 +
[[File:ETH Zurich 2014 Simplified biotools QS.png|center|600px|thumb|'''Figure 4''' Simplified Quorum Sensing System]]
-
===Quorum sensing Communication using signal molecules===
+
==='''Integrases Molecules working as scissors on the DNA'''===
-
Bacteria can interact with their surroundings and neighboring cells via cell-to-cell communication. Using this coordination they can coordinate the expression of genes (a gene is the molecular unit of heredity of a living organism) and thus coordinate the overall behavior of the population of bacteria living together.  
+
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. 
-
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.
 
-
 
-
By investigating a specific strain of bacteria already in the early 1980s it was found that depending on the cell density and the concentration of signal molecules, bacteria were able to communicate. 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 is part of the N-acyl homoserine lactone (AHL) family.
 
-
For reasons of simplicity we just call this molecule AHL here.
 
-
Another enzyme named LuxI synthesizes this AHL. The AHL can then diffuse out of a cell and reach other cells. In those other cells it binds and activates a protein called LuxR which regulates the gene transcription (first step on the way from DNA to proteins).
 
-
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.
 
-
 
-
=Integrases – Molecules working as scissors on the DNA=
 
-
 
-
Integrases are molecules that work like scissors on specific sites on the DNA (DNA is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms).
 
-
There are two sites in the genome needed for the scissors to act. Within those sites they can in a unidirectional way invert the sequence or they can completely remove it. Inversion or removals only depend on the orientation of the sites where the scissors recognize and act.
 
-
The genes coding for those integrase-scissors can easily be expressed in bacteria. So we can basically encode scissors that will then act on a target plasmid (a plasmid is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently) in bacteria. 
 
-
There exist various kinds of these integrase-scissors that are specific for some target sites in the genome.
 
-
The different integrases just described can then be combined in a system. This system is then used for engineering Boolean logic gates. A logic gate is a system where we have an input and inside a decision is taken. We have inputs in the form of yes or no and the output again is yes or no. The same accounts for on versus off states. Depending on the kind of the logic gate, the inputs are interpreted differently.
 
In our project integrases working as scissors for DNA is one of the core components we tried to implement in Mosaicoli.
In our project integrases working as scissors for DNA is one of the core components we tried to implement in Mosaicoli.
-
=Quorum sensing – Communication using signal molecules=
+
[[File:ETHZ Integrasesites.png|center|300px|thumb|'''Figure 5''' Specific sites for the binding of integrases]]
-
 
+
-
Bacteria can interact with their surroundings and neighboring cells via cell-to-cell communication. Using this coordination they can coordinate the expression of genes (a gene is the molecular unit of heredity of a living organism) and thus coordinate the overall behavior of the population of bacteria living together.
+
-
 
+
-
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.
+
-
 
+
-
By investigating a specific strain of bacteria already in the early 1980s it was found that depending on the cell density and the concentration of signal molecules, bacteria were able to communicate. 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 is part of the N-acyl homoserine lactone (AHL) family.
+
-
For reasons of simplicity we just call this molecule AHL here.
+
-
Another enzyme named LuxI synthesizes this AHL. The AHL can then diffuse out of a cell and reach other cells. In those other cells it binds and activates a protein called LuxR which regulates the gene transcription (first step on the way from DNA to proteins).
+
-
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.
+

Latest revision as of 23:14, 17 October 2014

Biological Tools

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. This way, the sensor cells will also act as a producer cell and trasnfer the signal to the following cells.

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


Figure 4 Simplified Quorum Sensing System

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.


Figure 5 Specific sites for the binding of integrases