Team:Groningen/Promoters draft

From 2010.igem.org

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Promoters
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'''Promoters'''
An important question is which promoter we should use to control the chaplin expression. We assume that an ideal promoter would not be active until the biofilm has formed because the expression of hydrophobic proteins might influence the formation of it. Two promoters where found that are active in biofilms but not during normal growth.  
An important question is which promoter we should use to control the chaplin expression. We assume that an ideal promoter would not be active until the biofilm has formed because the expression of hydrophobic proteins might influence the formation of it. Two promoters where found that are active in biofilms but not during normal growth.  
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yqxM
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'''yqxM'''
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The yqxM-sipW-tasA operon is controlled by the yqxM promoter. It is needed for biofilm formation, since tasA is a key protein of the extracellular matrix in such. Since the caplins should worke in a similar way to tasA we think the yqxM promoter would be very suitable.
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srfA
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The yqxM-sipW-tasA operon is controlled by the yqxM promoter. It is needed for biofilm formation, since tasA is a key protein of the extracellular matrix in such. Since the caplins should work in a similar way to tasA we think the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K305006 yqxM]promoter would be very suitable.
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The srfA operon has been reported to be important for the swarming motility, natural competence and sporulation in Bacillus Subtilis. It is controlled by the ComXPA quorum sensing system and hence active in states of high cell densities. Therefore the srfA promoter would be suitable for chaplin expression. Two different lenghts of the srfA promoter where choosen due to uncertanties concerning the region between the response element ant the transcription start side of the srfAA protein. In the original promoter this region is unusually long, by shorthening it 190bp’s we hope to achieve a higher transcription efficiency. So we came up with two different promoters, the original one and the shorthened one.
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Quorum sensing and promoter interactions
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'''srfA'''
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<img src="http://2010.igem.org/wiki/images/e/ec/Team-Groningen-Pathwaymodel.png" style="float: right; width: 360px" alt="Schematic Overview" title="">
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References
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The srfA operon has been reported to be important for the swarming motility, natural competence and sporulation in ''Bacillus Subtilis''. It is controlled by the ComXPA quorum sensing system and hence active in states of high cell densities. Therefore the srfA promoter would be suitable for chaplin expression. Two different lengths of the srfA promoter where chosen due to uncertainties concerning the region between the response element ant the transcription start side of the srfAA protein. In the original promoter this region is unusually long, by shortening it 190bp’s we hope to achieve a higher transcription efficiency. So we came up with two different promoters, the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K305008 original] one and the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K305007 shortened] one.
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Stöver AG, Driks A.Regulation of synthesis of the Bacillus subtilis transition-phase, spore-associated antibacterial protein TasA. Journal of Bacteriology, September 1999, p. 5476-5481, Vol. 181, No. 17
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'''Quorum sensing and promoter interactions'''
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Nakano MM, Xia LA, Zuber P.Transcription initiation region of the srfA operon, which is controlled by the comP-comA signal transduction system in Bacillus subtilis. J Bacteriol. 1991 Sep;173(17):5487-93.
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<img src="http://2010.igem.org/wiki/images/e/ec/Team-Groningen-Pathwaymodel.png">
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A Novel Regulatory Protein Governing Biofilm Formation in Bacillus subtilis
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'''References'''
 +
 
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Stöver AG, Driks A.Regulation of synthesis of the ''Bacillus subtilis'' transition-phase, spore-associated antibacterial protein TasA. Journal of Bacteriology, September 1999, p. 5476-5481, Vol. 181, No. 17
 +
 
 +
Nakano MM, Xia LA, Zuber P.Transcription initiation region of the srfA operon, which is controlled by the comP-comA signal transduction system in ''Bacillus subtilis''. J Bacteriol. 1991 Sep;173(17):5487-93.
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A Novel Regulatory Protein Governing Biofilm Formation in ''Bacillus subtilis''''Italic text''
Frances Chu,1 Daniel B. Kearns, Anna McLoon, Yunrong Chai, Roberto Kolter and Richard Losicka Mol Microbiol. 2008 June; 68(5): 1117–1127.  
Frances Chu,1 Daniel B. Kearns, Anna McLoon, Yunrong Chai, Roberto Kolter and Richard Losicka Mol Microbiol. 2008 June; 68(5): 1117–1127.  
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Hayashi K, Ohsawa T, Kobayashi K, Ogasawara N, Ogura M.The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilis. J Bacteriol. 2005 Oct;187(19):6659-67.
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Hayashi K, Ohsawa T, Kobayashi K, Ogasawara N, Ogura M.The H2O2 stress-responsive regulator PerR positively regulates srfA expression in ''Bacillus subtilis''. J Bacteriol. 2005 Oct;187(19):6659-67.

Revision as of 13:55, 24 October 2010

Promoters

An important question is which promoter we should use to control the chaplin expression. We assume that an ideal promoter would not be active until the biofilm has formed because the expression of hydrophobic proteins might influence the formation of it. Two promoters where found that are active in biofilms but not during normal growth.

yqxM

The yqxM-sipW-tasA operon is controlled by the yqxM promoter. It is needed for biofilm formation, since tasA is a key protein of the extracellular matrix in such. Since the caplins should work in a similar way to tasA we think the yqxMpromoter would be very suitable.

srfA

The srfA operon has been reported to be important for the swarming motility, natural competence and sporulation in Bacillus Subtilis. It is controlled by the ComXPA quorum sensing system and hence active in states of high cell densities. Therefore the srfA promoter would be suitable for chaplin expression. Two different lengths of the srfA promoter where chosen due to uncertainties concerning the region between the response element ant the transcription start side of the srfAA protein. In the original promoter this region is unusually long, by shortening it 190bp’s we hope to achieve a higher transcription efficiency. So we came up with two different promoters, the original one and the shortened one.

Quorum sensing and promoter interactions

<img src="Team-Groningen-Pathwaymodel.png">

References

Stöver AG, Driks A.Regulation of synthesis of the Bacillus subtilis transition-phase, spore-associated antibacterial protein TasA. Journal of Bacteriology, September 1999, p. 5476-5481, Vol. 181, No. 17

Nakano MM, Xia LA, Zuber P.Transcription initiation region of the srfA operon, which is controlled by the comP-comA signal transduction system in Bacillus subtilis. J Bacteriol. 1991 Sep;173(17):5487-93.

A Novel Regulatory Protein Governing Biofilm Formation in Bacillus subtilis'Italic text Frances Chu,1 Daniel B. Kearns, Anna McLoon, Yunrong Chai, Roberto Kolter and Richard Losicka Mol Microbiol. 2008 June; 68(5): 1117–1127.

Hayashi K, Ohsawa T, Kobayashi K, Ogasawara N, Ogura M.The H2O2 stress-responsive regulator PerR positively regulates srfA expression in Bacillus subtilis. J Bacteriol. 2005 Oct;187(19):6659-67.