Difference between revisions of "Part:BBa K581004"
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<partinfo>BBa_K581004 short</partinfo>
 
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'''PtsG''' is a glucose permease which is subordinate to phosphotransferase system and serves as a transporter. Here,we studied this mRNA perform the conjugate part of the small RNA regulator '''sgrS(wt)'''[https://parts.igem.org/wiki/index.php?title=Part:BBa_K581005].
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ptsG mRNA is regulated by SgrS by short, imperfect base-pairing interactions, and its expression is thus repressed.
  
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                  [[Image:Mechanism.png]]
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===Usage and Biology===
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                ''' Fig.1''' Sequence alignment of wildtype ptsG/SgrS pair and its mutant complementary pairs.
  
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<span class='h3bb'>Sequence and Features</span>
 
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<partinfo>BBa_K581004 SequenceAndFeatures</partinfo>
 
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===Functional Parameters===
 
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<partinfo>BBa_K581004 parameters</partinfo>
 
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Teppei Morita et.al’ s work suggests that two mutations (C85G and C87G) in ptsG mRNA could completely impair the ability of SgrS to downregulate its expression, while compensatory mutations of SgrS (G178C and G176C) restore the gene silencing ability. These results indicate that it is the base pairing of the two RNAs rather than particular nucleotides that is important for SgrS action. They have also illustrated that sequence outside this region, even though complementary, is rather dispensable for the efficient silencing (Kawamoto et al., 2006). This makes mutant ptsG/SgrS pairs orthogonal to genetic context of the host cell. Therefore we choose this couple of conjugate mRNA/sRNA as the foundation of our comparator device design.
  
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<p><b>This BioBrick has been sequence verified.</b>
 
  
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<h2>Background</h2>
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Furthermore, as a proof-of-concept experiment, we constructed synthetic gene circuits, in which the 5’ untranslated region of ptsG mRNA was translationally fused to the coding sequence of the reporter gfp. The fluorescence intensity of GFP could reflect the repression effect that SgrS exerts on ptsG.
  
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<p>ptsG2 is the C87G mutant of ptsG(wt) and the conjugate part of SgrS2 in our comparator device.</p>
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ptsG(wt)-gfp in this part will be constitutively expressed in E.coli after transformation processing.
  
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<p>PtsG is a glucose permease which is subordinate to phosphotransferase system and serves as a transporter. Here,we studied this mRNA perform the conjugate part of the small RNA regulator sgrS(wt).
 
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ptsG mRNA is regulated by SgrS by short, imperfect base-pairing interactions, and its expression is thus repressed(see Fig.1).
 
  
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<img src="http://fmn.rrfmn.com/fmn058/20111006/0600/original_Y0mV_61420000b3931211.jpg" width="600px" align="center"/></a></h3>
 
  
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    ''Fig.1 The complementary pair of ptsG2 mRNA and corresponding SgrS2.''
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<!-- Add more about the biology of this part here
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===Usage and Biology===
  
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Teppei Morita et.al’ s work suggests that two mutations (C85G and C87G) in ptsG mRNA could completely impair the ability of SgrS to downregulate its expression, while compensatory mutations of SgrS (G178C and G176C) restore the gene silencing ability. These results indicate that it is the base pairing of the two RNAs rather than particular nucleotides that is important for SgrS action. They have also illustrated that sequence outside this region, even though complementary, is rather dispensable for the efficient silencing (Kawamoto et al., 2006). This makes mutant ptsG/SgrS pairs orthogonal to genetic context of the host cell. Therefore we choose this couple of conjugate mRNA/sRNA as the foundation of our comparator device design.</p>
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K581004 SequenceAndFeatures</partinfo>
  
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And as a proof-of-concept experiment, we constructed synthetic gene circuits, in which the 5’ untranslated region of ptsG mRNA was translationally fused to the coding sequence of the reporter gfp (Levine et al., 2007), as shown in Fig 2.
 
  
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    ''Fig.2 The modular experimental subunits of the comparator. (A) Salicylate leads to the transcription of ptsG-gfp mRNA, which is the target of constitutively expressed SgrS. This is how we implement both reporting and repressing outputs as a result of the activation of Psal. When there is more salicylate in the media, the GFP fluorescence intensity is expected to be stronger. (B) Salicylate leads to the transcription of SgrS, while the ptsG-gfp mRNA is downstream a constitutive promoter. In this scenario, as the concentration of salicylate increases, the repression effect SgrS exerts on ptsG would in turn be stronger, so the GFP fluorescence intensity is supposed to be weaker.''
 
  
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===Functional Parameters===
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<partinfo>BBa_K581004 parameters</partinfo>
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<h2>Experimental Data</h2>
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<h3>Methods<a href="http://2011.igem.org/Team:Peking_S/lab/protocol"><img src="https://static.igem.org/mediawiki/igem.org/d/d9/PkusSubtitleshort.png" width="240px" align="right"/></a></h3>
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<h2>References</h2>
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<p>[1] Geissmann, T.A., and Touati, D. (2004). Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator.  <i>The EMBO journal </i> <b>23:</b> 396-405</p>
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<p>[2] Kawamoto, H., Koide, Y., Morita, T., and Aiba, H. (2006). Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq. <i>Molecular microbiology</i><b> 61:</b> 1013-1022</p>
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<p>[3] Levine, E., Zhang, Z., Kuhlman, T., and Hwa, T. (2007). Quantitative characteristics of gene regulation by small RNA.  <i> PLoS biology </i><b>5: </b>e229
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Revision as of 22:42, 5 October 2011

ptsG2-GFP (ptsG2 5'UTR fused with gfp)


PtsG is a glucose permease which is subordinate to phosphotransferase system and serves as a transporter. Here,we studied this mRNA perform the conjugate part of the small RNA regulator sgrS(wt)[1]. ptsG mRNA is regulated by SgrS by short, imperfect base-pairing interactions, and its expression is thus repressed. 

                  Mechanism.png
                 Fig.1 Sequence alignment of wildtype ptsG/SgrS pair and its mutant complementary pairs.


Teppei Morita et.al’ s work suggests that two mutations (C85G and C87G) in ptsG mRNA could completely impair the ability of SgrS to downregulate its expression, while compensatory mutations of SgrS (G178C and G176C) restore the gene silencing ability. These results indicate that it is the base pairing of the two RNAs rather than particular nucleotides that is important for SgrS action. They have also illustrated that sequence outside this region, even though complementary, is rather dispensable for the efficient silencing (Kawamoto et al., 2006). This makes mutant ptsG/SgrS pairs orthogonal to genetic context of the host cell. Therefore we choose this couple of conjugate mRNA/sRNA as the foundation of our comparator device design.


Furthermore, as a proof-of-concept experiment, we constructed synthetic gene circuits, in which the 5’ untranslated region of ptsG mRNA was translationally fused to the coding sequence of the reporter gfp. The fluorescence intensity of GFP could reflect the repression effect that SgrS exerts on ptsG.

ptsG(wt)-gfp in this part will be constitutively expressed in E.coli after transformation processing.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 747