Difference between revisions of "Part:BBa K2541305"
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<partinfo>BBa_K2541305 short</partinfo>
 
<partinfo>BBa_K2541305 short</partinfo>
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<h5>
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<P style="text-indent:2em;">
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A RNA-based thermosensor that can be used for temperature sensitive post-transcriptional regulation which is based on the change of RNA advanced structure. The cold-inducible RNA-based thermosensors can initiate translation of downstream genes at low temperatures.
 +
</p>
 +
</h5>
  
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A RNA thermosensor that can be used for temperature sensitive post-transcriptional regulation which is based on the change of RNA advanced structure. The cold-inducible RNA thermosensors can initiate translation of downstream genes at low temperatures.
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<h1>'''1. Usage and Biology'''</h1>
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<h5>
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<P style="text-indent:2em;">
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There are multiple families of cold-inducible proteins in prokaryotes, the most widely studied of which are the Csp family of cold shock proteins in ''E.coli''. CspA represents cspA family, which has been quite extensively studied for the mechanism of its cold response. There is a temperature-sensing region in the 5’untranslated region (5'UTR) of CspA mRNA, which can regulate the accessibility of the translation initiation region by altering the advanced structure of RNA, thereby regulating the initiation of translation.
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</p>
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<P style="text-indent:2em;">
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At low temperatures (<20℃), 5’UTR of cspA mRNA can form an advanced structure called pseudoknot, which is more efficiently translated because the conformation exposes the Shine–Dalgarno (SD) sequence, it is beneficial to recruit ribosomes and somewhat less susceptible to degradation. At normal temperatures, due to thermodynamic instability, pseudoknot unfolds. 5’UTR forms a secondary structure masking Shine–Dalgarno (SD) sequence to block translation initiation region, which impedes translation. We designed a series of cold-inducible RNA-based thermosensors with different melting temperatures, intensity and sensitivity based on the pseudoknot structure.
 +
</p>
 +
<P style="text-indent:2em;">
 +
Our team designed synthetic cold-inducible RNA-based thermosensors that are considerably simpler than naturally occurring cspA thermosensors and can be exploited as convenient on/off switches of gene expression.
 +
</p>
 +
</h5>
 +
<html><center>
 +
<div class="stem-loop cold-induced">
  
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<h1>'''Usage and Biology'''</h1>
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There are multiple families of cold-inducible proteins in prokaryotes, the most widely studied of which are the Csp family of cold shock proteins in E. coli. CspA family is represented by cspA, which has been quite extensively investigated. There is a temperature-sensing region in the 5'UTR of CspA mRNA, which can regulate the accessibility of the translation initiation region by altering the advanced structure of RNA, thereby regulating the initiation of translation. At low temperatures (<20℃), 5’UTR of cspA mRNA can form an advanced structure called pseudoknot, which is more efficiently translated because the conformation exposes the Shine–Dalgarno (SD) sequence, it is beneficial to recruit ribosomes and somewhat less susceptible to degradation. At normal temperatures, due to thermodynamic instability, pseudoknot unfolds. 5’UTR forms a secondary structure masking Shine–Dalgarno (SD) sequence to block translation initiation region, which impedes translation. In our design, we deleted the conserved region called the cold box upstream of the 5'UTR of cspA mRNA, so that the expression of CspA is not regulated by its own negative feedback. The pseudoknot in the cspA mRNA contains four sets of base pairings, and its stability is temperature-regulated. We increase base pairing or increase GC content, which may increase the temperature threshold for pseudoknot unfolding; we reduce base pairing or reduce GC content, which may cause the temperature threshold for pseudoknot unfolding to drop. Our team designed synthetic cold-inducible RNA thermosensors that are considerably simpler than naturally occurring cspA thermosensors and can be exploited as convenient on/off switches of gene expression.
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<!-- -->
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<h1>'''Characterization'''</h1>
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The thermosensor is constructed on the pSB1C3 vector by GoldenGate assembly. As shown below, the measurement device is composed of Anderson promotor (BBa_J23100), thermosensor (BBa_K2541305) and sfGFP(BBa_K2541400). We measured the sfGFP expression to get the actual melting temperature of the cold-inducible RNA thermosensor.
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As shown in the figure, the thermosensor melting temperature range is [   ]. Our data show that efficient RNA thermosensors can be built from RNA advanced structure masking the ribosome binding site, thus providing useful RNA-based toolkit for the regulation of gene expression.
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  <p>Figure 1. Mechanism of cold-inducible RNA-based thermosensors.</p>
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 +
</html>
 +
 
 +
<h1>'''2. Design'''</h1>
 +
<h5>
 +
<P style="text-indent:2em;">
 +
In our design, we deleted the conserved region called the cold box upstream of the 5'UTR of cspA mRNA, so that the expression of CspA is not regulated by its own negative feedback. The pseudoknot in the cspA mRNA contains four sets of base pairings, and its stability is temperature-regulated. Several structural parameters come into consideration to optimize cold-inducible RNA-based thermosensors: base pairing, base pair position and GC content in pseudoknot region. Increasing base pairing can raise the melting temperature of pseudoknot, thus enlarging the temperature range of open conformation. Increasing GC content can also raise the melting temperature of pseudoknot. We also change base pair at different position. What’s more, we delete the cold box which is at the upstream of cspA 5’UTR. In K2541305, we 具体做了啥。
 +
</p>
 +
</h5>
 +
[[File:K2541305 f2.png|center|K2541305 f2]]
 +
<center>Figure 2. Design of synthetic cold-inducible RNA-based thermosensor.</center>
 +
 
 +
<h1>'''3.Characterization'''</h1>
 +
<h5>
 +
<P style="text-indent:2em;">
 +
The thermosensor sequence is constructed on the pSB1C3 vector by GoldenGate assembly. The measurement device is composed of Anderson promotor (BBa_J23100), thermosensor (BBa_K2541305), sfGFP_optimism (BBa_K2541400) and double terminator (BBa_B0010 and BBa_B0012). We select a constitutive Anderson promoter J23100 as an appropriate promoter by pre-experiment. The sfGFP_optimism has faster folding speed and higher fluorescence intensity. The double terminator can reduce leakge (Figure 3). We characterized RNA-based thermosensors in ''E.coli'' DH5a.
 +
</p>
 +
</h5>
 +
[[File:measurement device figure3.png|center|caption]]
 +
<center>Figure 3. The measurement device.</center>
 +
----
 +
 
 +
 
 +
<h5>
 +
<P style="text-indent:2em;">
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In figure 4, there are eight different cold-inducible RNA-based thermosensors. pos.control is positive control. The final normalized fluorescence was calculated as follows: normalized fluorescence = [(Fluorescence/Abs<sub>600</sub>)<sub>TS</sub> - (Fluorescence/Abs<sub>600</sub>)<sub>neg</sub>] / [(Fluorescence/Abs<sub>600</sub>)<sub>pos</sub> - (Fluorescence/Abs<sub>600</sub>)<sub>neg</sub>] ( TS = thermosensor, pos = positive control, and neg = BBa_J364007 ). As shown in figure 4, the fluorescence intensity of K2541305 increases with decreased temperature.
 +
</p>
 +
</h5>
 +
[[File:K2541305 f4.png|center|K2541305 f4]]
 +
Figure 4. Characteristics of synthetic cold-inducible RNA-based thermosensors. Each set of three bars represents the activity level of a different thermosensor. The bar colors purple, yellow and red represent the temperatures 15, 20 and 25°C, respectively. The height of the bars corresponds to the normalized fluorescence.
 +
----
 +
 
 +
 
 +
[[File:cspA figure6.png|center|cspA figure6]]
 +
Figure 5. Experimental measurements of the collection of cold-inducible RNA-based thermosensors show a variety of responses. (A) Rows represent activity levels of different thermosensors. (B) Each set of three bars represents the activity level of a different thermosensor. The bar colors purple, yellow and red represent the temperatures 15, 20 and 25°C, respectively. The height of the bars corresponds to the normalized fluorescence.
 +
 
 +
<h1>'''4. Conclusion'''</h1>
 +
<h5>
 +
<P style="text-indent:2em;">
 +
Our data show that efficient RNA-based thermosensors with different melting temperatures, intensity and sensitivity can be built from RNA advanced structure, thus providing useful SynRT toolkit for the regulation of gene expression.
 +
</p>
 +
</h5>
  
  

Revision as of 16:10, 14 October 2018


Cold-inducible RNA-based thermosensor-5

A RNA-based thermosensor that can be used for temperature sensitive post-transcriptional regulation which is based on the change of RNA advanced structure. The cold-inducible RNA-based thermosensors can initiate translation of downstream genes at low temperatures.

1. Usage and Biology

There are multiple families of cold-inducible proteins in prokaryotes, the most widely studied of which are the Csp family of cold shock proteins in E.coli. CspA represents cspA family, which has been quite extensively studied for the mechanism of its cold response. There is a temperature-sensing region in the 5’untranslated region (5'UTR) of CspA mRNA, which can regulate the accessibility of the translation initiation region by altering the advanced structure of RNA, thereby regulating the initiation of translation.

At low temperatures (<20℃), 5’UTR of cspA mRNA can form an advanced structure called pseudoknot, which is more efficiently translated because the conformation exposes the Shine–Dalgarno (SD) sequence, it is beneficial to recruit ribosomes and somewhat less susceptible to degradation. At normal temperatures, due to thermodynamic instability, pseudoknot unfolds. 5’UTR forms a secondary structure masking Shine–Dalgarno (SD) sequence to block translation initiation region, which impedes translation. We designed a series of cold-inducible RNA-based thermosensors with different melting temperatures, intensity and sensitivity based on the pseudoknot structure.

Our team designed synthetic cold-inducible RNA-based thermosensors that are considerably simpler than naturally occurring cspA thermosensors and can be exploited as convenient on/off switches of gene expression.

Figure 1. Mechanism of cold-inducible RNA-based thermosensors.

2. Design

In our design, we deleted the conserved region called the cold box upstream of the 5'UTR of cspA mRNA, so that the expression of CspA is not regulated by its own negative feedback. The pseudoknot in the cspA mRNA contains four sets of base pairings, and its stability is temperature-regulated. Several structural parameters come into consideration to optimize cold-inducible RNA-based thermosensors: base pairing, base pair position and GC content in pseudoknot region. Increasing base pairing can raise the melting temperature of pseudoknot, thus enlarging the temperature range of open conformation. Increasing GC content can also raise the melting temperature of pseudoknot. We also change base pair at different position. What’s more, we delete the cold box which is at the upstream of cspA 5’UTR. In K2541305, we 具体做了啥。

K2541305 f2
Figure 2. Design of synthetic cold-inducible RNA-based thermosensor.

3.Characterization

The thermosensor sequence is constructed on the pSB1C3 vector by GoldenGate assembly. The measurement device is composed of Anderson promotor (BBa_J23100), thermosensor (BBa_K2541305), sfGFP_optimism (BBa_K2541400) and double terminator (BBa_B0010 and BBa_B0012). We select a constitutive Anderson promoter J23100 as an appropriate promoter by pre-experiment. The sfGFP_optimism has faster folding speed and higher fluorescence intensity. The double terminator can reduce leakge (Figure 3). We characterized RNA-based thermosensors in E.coli DH5a.

caption
Figure 3. The measurement device.


In figure 4, there are eight different cold-inducible RNA-based thermosensors. pos.control is positive control. The final normalized fluorescence was calculated as follows: normalized fluorescence = [(Fluorescence/Abs600)TS - (Fluorescence/Abs600)neg] / [(Fluorescence/Abs600)pos - (Fluorescence/Abs600)neg] ( TS = thermosensor, pos = positive control, and neg = BBa_J364007 ). As shown in figure 4, the fluorescence intensity of K2541305 increases with decreased temperature.

K2541305 f4

Figure 4. Characteristics of synthetic cold-inducible RNA-based thermosensors. Each set of three bars represents the activity level of a different thermosensor. The bar colors purple, yellow and red represent the temperatures 15, 20 and 25°C, respectively. The height of the bars corresponds to the normalized fluorescence.


cspA figure6

Figure 5. Experimental measurements of the collection of cold-inducible RNA-based thermosensors show a variety of responses. (A) Rows represent activity levels of different thermosensors. (B) Each set of three bars represents the activity level of a different thermosensor. The bar colors purple, yellow and red represent the temperatures 15, 20 and 25°C, respectively. The height of the bars corresponds to the normalized fluorescence.

4. Conclusion

Our data show that efficient RNA-based thermosensors with different melting temperatures, intensity and sensitivity can be built from RNA advanced structure, thus providing useful SynRT toolkit for the regulation of gene expression.


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
    COMPATIBLE WITH RFC[1000]