Team:ETH Zurich/project/background/biotoolssimple


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Biological Tools

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.

Quorum sensing – Communication using signal molecules

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.