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Team:TUDelft/Temperature analysis
From 2008.igem.org
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Contents |
Analysis
RNA switch
A cell must adapt to environmental changes in order to survive. A well known example of how a cell does this is the regulation of gene expression at the transcriptional level. For example a change in the environment can cause a transcription factor to bind to the DNA and thereby activating or repressing the transcription of a certain gene that is needed in order to adapt to that environmental change.
This kind of regulation is also performed at the translational level. This is done by so called RNA switch; an RNA structure that can be found at the 5' leading end of an mRNA (figure 1). These relatively short non-coding sequences, preceding the protein coding region, form a structure that occludes the Shine-Dalgarno region (ribosome binding site) under certain circumstances. This way the translation is blocked because the ribosome is not able to bind to the occluded Shine-Dalgarno region. A conformational change of this region, caused by an environmental condition, e.g. a ligand or a change in temperature, can cause the SD to become exposed. This way an environmental change can cause an initiation of translation.
figure 1: basic principle of an RNA switch
RNA thermometer
One type of RNA switch is the RNA thermometer (figure 2). This 5' end mRNA region forms a structure that blocks the translation by occluding the Shine-Dalgarno region at a certain temperature. When the temperature rises above a certain threshold temperature, a conformational change of the structure will cause the Shine-Dalgarno region to become exposed. The ribosome can then bind to the mRNA and initiate the translation of the the protein encoded by it.
figure 2: RNA thermometer
RNA thermometer families
When we look at the known RNA thermometers (the research area is relatively young and it is expected that lots more are to be found) they can be split up into four different families based on their secondary structure. Three of these (Rose, Hsp90, and PrfA) can be found in the Rfam database (http://rfam.sanger.ac.uk/), and a fourth is found in literature and proposed to be called the FourU family (reference).
figure 3: RNA thermometer families
Specific RNA thermometers
In the literature we found three papers that described a RNA thermometer of which the functionality as a temperature sensitive regulator is proven experimentally.
The first RNA thermometer is part of the ROSE family and is retrieved from the organism Bradyrhizobium japonicum. ...
The second RNA thermometer is part of the FourU family...
The third RNA thermometer is retrieved from the Listeria monocytogenes and belongs to the PrfA family. The switching temperature is at 37 degrees Celsius.
links
http://rfam.sanger.ac.uk/ http://rfam.sanger.ac.uk/family?entry=rose http://rfam.sanger.ac.uk/family?entry=prfa http://rfam.sanger.ac.uk/family?entry=hsp90_cre
