Difference between revisions of "Part:BBa K2541407"
 
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__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K2541407 short</partinfo>
 
<partinfo>BBa_K2541407 short</partinfo>
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<h5>
 +
<P style="text-indent:2em;">
 +
A RNA-based thermosensor that can be used for temperature sensitive translational regulation which is based on the change of RNA sencondary structure. The cold-repressible RNA-based thermosensors can repress translation of downstream genes at low temperatures. The composite part is a measurement device, consisting of Anderson promoter (BBa_J23106), cold-repressible RNA-based thermosensor-4 (BBa_K2541204), sfGFP_optimism (BBa_K2541400) and double terminator (BBa_B0010 and BBa_B0012).
 +
</p>
 +
</h5>
  
−
A RNA thermosensor that can be used for temperature sensitive post-transcriptional regulation which is based on the change of RNA sencondary structure. The cold-repressible RNA thermosensors can repress translation of downstream genes at low temperatures. The composite part is composed of promoter BBa_J23106, cold-repressible RNA thermosensor-4 BBa_K2541204, reporetr protein sfGFP BBa_K2541400 and terminator BBa_B0015.
+
<h1>'''1. Usage and Biology'''</h1>
 +
<h5>
 +
<P style="text-indent:2em;">
 +
RNA-based temperature sensing is common in bacteria that live in fluctuating environments. Most naturally occurring RNA-based thermosensors have long sequences and complicated sencondary structure and function by sequestering the Shine–Dalgarno (SD) sequence in a stem-loop structure at low temperatures.  
 +
</p>
 +
<P style="text-indent:2em;">
 +
Here, we designed short, cold-repressible RNA thermosensors, which will form a stem-loop upstream of the SD sequence. These thermosensor sequences contain a double-strand RNA cleavage site for RNase III, an enzyme native to ''Escherichia coli'' and many other organisms. At low temperatures, the mRNA stem-loop is stable to expose the RNase III cleavage site and the transcript will be degraded. At elevated temperatures, the stem-loop will unfold and translation will occur unhindered. These short, modular cold-repressible RNA thermosensors can be exploited as convenient on/off switches of gene expression.
 +
</p>
 +
<P style="text-indent:2em;">
 +
Green fluorescent protein (GFP) is commonly used as a reporter gene in intact cells and organisms. This year we select sfGFP (BBa_K2541400), a robustly folded version of GFP, called superfolder GFP as a reporter protein. Compared to superfolder GFP (BBa_I746916), sfGFP_optimism (BBa_K2541400) is BbsI restriction site free, so it can be used in GoldenGate assembly to achieve efficient and rapid assembly of gene fragments. And sfGFP_optimism (BBa_K2541400) has stronger fluorescence intensity than superfolder GFP (BBa_I746916).
 +
</p>
 +
</h5>
 +
<html><center>
 +
  <div class="stem-loop cold-repressive">
 +
   
 +
  <input id="checked_4" type="checkbox" class="switch" />
  
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<h1>'''Usage and Biology'''</h1>
+
  <svg class="svg_animate" xmlns="http://www.w3.org/2000/svg" width="50%" viewBox="0 0 599.75 278.7">
−
== Cold-repressible RNA thermosensor-4 ==
+
    <defs>
−
RNA-based temperature sensing is common in bacteria that live in fluctuating environments. Most naturally-occurring RNA thermosensors have long sequences and complicated sencondary structure. Here, we designed short, cold-repressible RNA thermosensors, which will form a stem-loop upstream Shine–Dalgarno (SD) sequence. These thermosensors contain a double-strand RNA cleavage site for RNase III, an enzyme native to Escherichia coli and many other organisms, in the 5' untranslated region of the target gene. At low temperatures, the mRNA stem-loop is stable to expose the RNase III cleavage site and the transcript will be degraded. At elevated temperatures, the stem-loop will unfold and translation will occur unhindered. These short, modular cold-repressible RNA thermosensors can be applied to the construction of complex genetic circuits, facilitating rational reprogramming of cellular processes for synthetic biology applications.
+
    <style>
  
−
== sfGFP ==
+
.switch::before{
−
Green fluorescent protein (GFP) exhibits intrinsic fluorescence and is commonly used as a reporter gene in intact cells and organisms. Many mutants of the protein with either modified spectral properties, increased fluorescence intensity, or improved folding properties have been reported.  
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−
GFP often misfold when expressed as fusions with other proteins, while a robustly folded version of GFP, called superfolder GFP, was developed and described by Pédelacq et al at 2006 that folds well even when fused to poorly folded polypeptides. There is another superfolder GFP designed by Overkamp W et al at 2013, which is codon optimized for S. pneumoniae. It was be used in Escherichia coli by Segall-Shapiro T H et al at 2018.
+
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    stroke-width: 11px;
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−
This year our team registered the superfolder GFP designed by Overkamp W et al with a BBa_K2541400 (called sfGFP). Compared to superfolder GFP(BBa_I746916), sfGFP (BBa_K2541400) is BbsI restriction site free, so it can be used in GoldenGate assembly to achieve efficient and
+
      .cold-repressive .a {
−
rapid assembly of gene fragments. And sfGFP (BBa_K2541400) has stronger fluorescence intensity than superfolder GFP(BBa_I746916).
+
    stroke: #036;
 +
      }
  
−
== Conclusion ==
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−
The composite part can be used as a measurement device for different cold-repressible RNA thermosensors. Wu use GoldenGate assembly to change differrnt thermosensors to measure their melting temperature.
+
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 +
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−
<!-- -->
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      .cold-repressive .b {
−
<h1>'''Characterization'''</h1>
+
    stroke: #060;
−
The thermosensor is constructed on the pSB1C3 vector by GoldenGate assembly. As shown below, the measurement device is composed of Anderson promotor (BBa_J23106), thermosensor (BBa_K2541204) and  sfGFP (BBa_K2541400) and terminator (BBa_B0015). We measured the sfGFP expression to get the state of the cold-repressible RNA thermosensor at different temperatures.
+
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 +
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−
As shown in the figure, the thermosensor is "off" at [  ]. Our data show that efficient RNA thermosensors can be built from a single small RNA stem-loop structure masking the ribosome binding site, thus providing useful RNA-based toolkit for the regulation of gene expression.
+
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K2541407 SequenceAndFeatures</partinfo>
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    <text id="ribosome_text" class="h" transform="translate(429.01 165.45)">RNAse III</text>
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  <p>Figure 1. Mechanism of cold-repressible RNA-based thermosensors.</p>
 +
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 +
</html>
 +
 +
<h1>'''2. Design'''</h1>
 +
<h5>
 +
<P style="text-indent:2em;">
 +
The RNase III recognition site is distal box (db) sequence ad its cleavage site is proximal box (pb) sequence. We keep the db and pb sequence conserved which is necessary for RNase III to cleave. And we change their adjacent base pairs to increase or decrease the stem length to design cold-repressible RNA-based thermosensors with different melting temperatures, intensity and sensitivity. Moreover, changing adjacent base pairs may also influence RNase III catalytic efficiency.
 +
</p>
 +
<P style="text-indent:2em;">
 +
Adding stem length can optimize cold-repressible RNA-based thermosensors to higher temperature, while decreasing stem length has the opposite effect. The stem length is 12 base parings in K2541201. After designing, the theromsensor sequence is predicted by computational methods mFOLD to get its Tm, minimum free energy and secondary structure (figure 2). The Tm is 26.7°C and minimum free energy is -5.7kcal/mol.
 +
</p>
 +
</h5>
 +
[[File:K2541201 f2 new.png|center|K2541201 f2 new]]
 +
Figure 2. Design of K2541201. The RNA secondary structure, Tm and minimum free energy are predicted by mFOLD.
 +
 +
<h1>'''3.Characterization'''</h1>
 +
<h3>3.1 Measurement device</h3>
 +
<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 promoter (BBa_J23106), thermosensor (BBa_K2541201), sfGFP_optimism (BBa_K2541400) and double terminator (BBa_B0010 and BBa_B0012). We select a constitutive Anderson promoter J23106 as an appropriate promoter by pre-experiment. The sfGFP_optimism has faster folding speed and higher fluorescence intensity. The double terminator can reduce leakage (Figure 3). We characterized RNA-based thermosensors in ''E.coli'' DH5a.
 +
</p>
 +
</h5>
 +
[[File:measurement device 123.png|center|caption]]
 +
<html><center>
 +
Figure 3. The measurement device.
 +
  </script></center>
 +
</html>
 +
----
 +
 +
<h3>3.2 Measurement results</h3>
 +
<h5>
 +
<P style="text-indent:2em;">
 +
In figure 4, there are ten different cold-repressible 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 K2541201 reduces with decreased temperature.
 +
</p>
 +
</h5>
 +
[[File:K2541201 f4.png|center|K2541201 f4]]
 +
Figure 4. Characteristics of K2541201. Each set of five bars represents the activity level of a different thermosensor. The bar colors purple, green, yellow, orange and red represent the temperatures 15, 25, 29, 35 and 37°C, respectively. The height of the bars corresponds to the normalized fluorescence.
 +
 +
<h1>'''4. Collection of cold-repressible RNA-based thermosensors '''</h1>
 +
[[File:RIII figure6 新.png|center|RIII figure6 新]]
 +
Figure 5. Experimental measurements of the collection of cold-repressible RNA-based thermosensors show a variety of responses. (A) Rows represent activity levels of different thermosensors. (B) Each set of five bars represents the activity level of a different thermosensor. The bar colors purple, green, yellow, orange and red represent the temperatures 15, 25, 29, 35 and 37°C, respectively. The height of the bars corresponds to the normalized fluorescence.
 +
 +
 +
<h1>'''5. 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 a single small RNA stem-loop structure, thus providing useful SynRT toolkit for the regulation of gene expression.
 +
</p>
 +
</h5>
 +
 +
 +
<span class='h3bb'>Sequence and Features</span>
 +
<partinfo>BBa_K2541407 SequenceAndFeatures</partinfo>
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K2541407 parameters</partinfo>
 
<partinfo>BBa_K2541407 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 09:10, 16 October 2018


Cold-repressible RNA thermosensor measurement device

A RNA-based thermosensor that can be used for temperature sensitive translational regulation which is based on the change of RNA sencondary structure. The cold-repressible RNA-based thermosensors can repress translation of downstream genes at low temperatures. The composite part is a measurement device, consisting of Anderson promoter (BBa_J23106), cold-repressible RNA-based thermosensor-4 (BBa_K2541204), sfGFP_optimism (BBa_K2541400) and double terminator (BBa_B0010 and BBa_B0012).

1. Usage and Biology

RNA-based temperature sensing is common in bacteria that live in fluctuating environments. Most naturally occurring RNA-based thermosensors have long sequences and complicated sencondary structure and function by sequestering the Shine–Dalgarno (SD) sequence in a stem-loop structure at low temperatures.

Here, we designed short, cold-repressible RNA thermosensors, which will form a stem-loop upstream of the SD sequence. These thermosensor sequences contain a double-strand RNA cleavage site for RNase III, an enzyme native to Escherichia coli and many other organisms. At low temperatures, the mRNA stem-loop is stable to expose the RNase III cleavage site and the transcript will be degraded. At elevated temperatures, the stem-loop will unfold and translation will occur unhindered. These short, modular cold-repressible RNA thermosensors can be exploited as convenient on/off switches of gene expression.

Green fluorescent protein (GFP) is commonly used as a reporter gene in intact cells and organisms. This year we select sfGFP (BBa_K2541400), a robustly folded version of GFP, called superfolder GFP as a reporter protein. Compared to superfolder GFP (BBa_I746916), sfGFP_optimism (BBa_K2541400) is BbsI restriction site free, so it can be used in GoldenGate assembly to achieve efficient and rapid assembly of gene fragments. And sfGFP_optimism (BBa_K2541400) has stronger fluorescence intensity than superfolder GFP (BBa_I746916).

Stroke Version_1 RC anti-RC RNAse III

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

2. Design

The RNase III recognition site is distal box (db) sequence ad its cleavage site is proximal box (pb) sequence. We keep the db and pb sequence conserved which is necessary for RNase III to cleave. And we change their adjacent base pairs to increase or decrease the stem length to design cold-repressible RNA-based thermosensors with different melting temperatures, intensity and sensitivity. Moreover, changing adjacent base pairs may also influence RNase III catalytic efficiency.

Adding stem length can optimize cold-repressible RNA-based thermosensors to higher temperature, while decreasing stem length has the opposite effect. The stem length is 12 base parings in K2541201. After designing, the theromsensor sequence is predicted by computational methods mFOLD to get its Tm, minimum free energy and secondary structure (figure 2). The Tm is 26.7°C and minimum free energy is -5.7kcal/mol.

K2541201 f2 new

Figure 2. Design of K2541201. The RNA secondary structure, Tm and minimum free energy are predicted by mFOLD.

3.Characterization

3.1 Measurement device

The thermosensor sequence is constructed on the pSB1C3 vector by GoldenGate assembly. The measurement device is composed of Anderson promoter (BBa_J23106), thermosensor (BBa_K2541201), sfGFP_optimism (BBa_K2541400) and double terminator (BBa_B0010 and BBa_B0012). We select a constitutive Anderson promoter J23106 as an appropriate promoter by pre-experiment. The sfGFP_optimism has faster folding speed and higher fluorescence intensity. The double terminator can reduce leakage (Figure 3). We characterized RNA-based thermosensors in E.coli DH5a.

caption

Figure 3. The measurement device.

3.2 Measurement results

In figure 4, there are ten different cold-repressible 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 K2541201 reduces with decreased temperature.

K2541201 f4

Figure 4. Characteristics of K2541201. Each set of five bars represents the activity level of a different thermosensor. The bar colors purple, green, yellow, orange and red represent the temperatures 15, 25, 29, 35 and 37°C, respectively. The height of the bars corresponds to the normalized fluorescence.

4. Collection of cold-repressible RNA-based thermosensors

RIII figure6 新

Figure 5. Experimental measurements of the collection of cold-repressible RNA-based thermosensors show a variety of responses. (A) Rows represent activity levels of different thermosensors. (B) Each set of five bars represents the activity level of a different thermosensor. The bar colors purple, green, yellow, orange and red represent the temperatures 15, 25, 29, 35 and 37°C, respectively. The height of the bars corresponds to the normalized fluorescence.


5. Conclusion

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


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 7
    Illegal NheI site found at 30
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 539
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]