Team:TUDelft/Temperature analysis

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==Analysis==
==Analysis==
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===Introduction===
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Cells are constantly subjected to changing environmental conditions and one example of such a changing environmental condition is temperature. A mechanism found in different organisms, that makes the cell respond to thermal changes, is the RNA thermometer. For the input of our system we are going to use this mechanism to let the cell produce a color or a smell at a certain temperature.
===RNA switch===
===RNA switch===
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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.
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A way to respond to environmental changes is through transcription regulation. This, most well known regulation system, acts at the DNA level in which proteins or protein complexes regulate the transcription of certain genes by binding to the DNA (figure x).
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This kind of regulation is also performed at the translational level. This is done by so called RNA switches; 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 the initiation of translation.
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Recently a number of regulatory systems that work at the RNA level has been discovered. These systems, which are called RNA switches, regulate the translation instead of the transcription. They all work in a similar way. In a certain state the RNA is folded in such a way that the Shine Dalgarno region (ribosome binding site) is occluded, preventing the ribosome to bind to the RNA and thereby preventing the initiation of the translation.
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figure 1: basic principle of an RNA switch
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In this case you could say that the switch is in the off-state, which means that the translation of the gene encoded by the RNA stretch is switched off.
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An external factor can cause a state transition from the off to the on state. This happens through a conformational change of the RNA caused by the external factor. After the conformational change the Shine Dalgarno is exposed, enabling the ribosome to bind to the RNA and thereby enabling the translation of the protein encoded by the RNA.
===RNA thermometer===
===RNA thermometer===
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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.
+
The different RNA switches have different factors that 'switches the system on'. For example, RNA switches that are switched on by small ligands are called riboswitches (figure x) and those that are switched on by short trans RNA (...) are called trans-acting RNA switches (figure x). The ones we are interested in are the RNA thermometers (figure x). These RNA switches respond to a change in temperature. When the temperature passes a certain threshold, the hairpin region around the Shine Dalgarno will melt and become exposed. This way a rise in temperature can cause the initiation of translation.
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figure 2: RNA thermometer
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RNA thermometers reside at the 5' end of an mRNA of a protein. This 5' non-coding mRNA region forms a structure that blocks the translation by occluding the Shine-Dalgarno region at a certain temperature, e.g. 30 degrees Celcius. When the temperature rises above a certain threshold temperature, e.g. 37 degrees, a conformational change of the structure (melting of part of the hairpin surrounding the Shine-Dalgarno region) will cause the Shine-Dalgarno to become exposed, enabling the ribosome to bind to the mRNA and initiate the translation of the the protein encoded by the mRNA (figure x).
===RNA thermometer families===
===RNA thermometer families===
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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).
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When we look at known RNA thermometers (the research area is relatively young and it is expected that more are to be found) they can be split up into different families based on their secondary structure (explain...). Two of these families: Rose and PrfA, as specified by the Rfam database (http://rfam.sanger.ac.uk/), are found in procaryotes and thus of interest to us. A third family is found in literature and is proposed to be called the FourU family.
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figure 3: RNA thermometer families
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===Specific RNA thermometers===
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In the literature we found three papers that described a RNA thermometer of which the functionality as a temperature sensitive regulator is proven experimentally.
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The first RNA thermometer is part of the ROSE family and is retrieved from the organism Bradyrhizobium japonicum. ...
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The second RNA thermometer is part of the FourU family...
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The third RNA thermometer is retrieved from the Listeria monocytogenes and belongs to the PrfA family. The switching temperature is at 37 degrees Celsius.
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==Links==
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==References==
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==Notes==
==links==
==links==

Revision as of 15:26, 25 August 2008

>> work in progress

Contents

Analysis

Introduction

Cells are constantly subjected to changing environmental conditions and one example of such a changing environmental condition is temperature. A mechanism found in different organisms, that makes the cell respond to thermal changes, is the RNA thermometer. For the input of our system we are going to use this mechanism to let the cell produce a color or a smell at a certain temperature.

RNA switch

A way to respond to environmental changes is through transcription regulation. This, most well known regulation system, acts at the DNA level in which proteins or protein complexes regulate the transcription of certain genes by binding to the DNA (figure x).

Recently a number of regulatory systems that work at the RNA level has been discovered. These systems, which are called RNA switches, regulate the translation instead of the transcription. They all work in a similar way. In a certain state the RNA is folded in such a way that the Shine Dalgarno region (ribosome binding site) is occluded, preventing the ribosome to bind to the RNA and thereby preventing the initiation of the translation.

In this case you could say that the switch is in the off-state, which means that the translation of the gene encoded by the RNA stretch is switched off.

An external factor can cause a state transition from the off to the on state. This happens through a conformational change of the RNA caused by the external factor. After the conformational change the Shine Dalgarno is exposed, enabling the ribosome to bind to the RNA and thereby enabling the translation of the protein encoded by the RNA.

RNA thermometer

The different RNA switches have different factors that 'switches the system on'. For example, RNA switches that are switched on by small ligands are called riboswitches (figure x) and those that are switched on by short trans RNA (...) are called trans-acting RNA switches (figure x). The ones we are interested in are the RNA thermometers (figure x). These RNA switches respond to a change in temperature. When the temperature passes a certain threshold, the hairpin region around the Shine Dalgarno will melt and become exposed. This way a rise in temperature can cause the initiation of translation.

RNA thermometers reside at the 5' end of an mRNA of a protein. This 5' non-coding mRNA region forms a structure that blocks the translation by occluding the Shine-Dalgarno region at a certain temperature, e.g. 30 degrees Celcius. When the temperature rises above a certain threshold temperature, e.g. 37 degrees, a conformational change of the structure (melting of part of the hairpin surrounding the Shine-Dalgarno region) will cause the Shine-Dalgarno to become exposed, enabling the ribosome to bind to the mRNA and initiate the translation of the the protein encoded by the mRNA (figure x).

RNA thermometer families

When we look at known RNA thermometers (the research area is relatively young and it is expected that more are to be found) they can be split up into different families based on their secondary structure (explain...). Two of these families: Rose and PrfA, as specified by the Rfam database (http://rfam.sanger.ac.uk/), are found in procaryotes and thus of interest to us. A third family is found in literature and is proposed to be called the FourU family.

Links

References

Notes

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

references

notes

Retrieved from "http://2008.igem.org/Team:TUDelft/Temperature_analysis"