Team:TUDelft/Temperature analysis

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>> work in progress
 
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=Analysis=
 
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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.
 
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==RNA switch==
 
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A way to respond to environmental changes is through [http://en.wikipedia.org/wiki/Transcriptional_regulation transcriptional 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.
 
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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. 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.
 
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==RNA thermometer==
 
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There are different RNA switches having different factors that 'switch the system on'. For example, RNA switches that are switched on by small ligands are called riboswitches and those that are switched on by short trans-RNA stretches are called trans-acting RNA switches. The ones we are interested in are the RNA thermometers. These RNA switches respond to a change in temperature. When the temperature rises above 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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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 the 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).
 
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==RNA thermometer families==
 
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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 [http://en.wikipedia.org/wiki/RNA_structure secondary structure]. Two of these families: Rose and PrfA, as specified by the [http://rfam.sanger.ac.uk/ Rfam database], 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 <sup id="cite_ref-1"> [[Team:TUDelft/Temperature_analysis#cite_note-1 |[1]]] </sup>.
 
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==Conserved secondary structure==
 
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==What is needed to have a functioning RNA thermometer==
 
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It appears that not much is needed to have a functioning RNA thermometer. It is shown that no accessory factors, such as ligands or proteins, are needed for the temperature sensing (ref Chowdhurry). When looking at the ROSE structure it is also shown that the extra hairpins, all but the temperature sensitive one, are not needed for the temperature sensing (ref Chowdhurry2). The working of the RNA thermometer and its switching temperature seem to depend mainly on the stability of the temperature sensitive hairpin.
 
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This would mean that there should be a similarity between stabilities of the temperature sensitive hairpins of the known ROSE RNA thermometers.
 
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==References==
==References==

Revision as of 17:30, 26 October 2008


References

  1. ^ Waldminghaus T, Heidrich N, Branti S, Narberhaus F (2007). "FourU: a novel type of RNA thermometer in Salmonella". Molecular Microbiology, Volume 65, Issue 2, 413-424. PMID:17630972
  2. ^ Chowdhurry S, Maris C, Allain F H T, Narberhaus F (2006). "Molecular basis for temperature sensing by an RNA thermometer". The EMBO Journal, 2006, 25, 2487–2497. PMID:16710302
  3. ^ Chowdhury S, Ragaz C, Kreuger E, and Narberhaus F (2003). "Temperature-controlled Structural Alterations of an RNA Thermometer". J. Biol. Chem.,November 28, 2003, Vol. 278, Issue 48, 47915-47921. PMID:12963744
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