Difference between revisions of "Part:BBa K4169005"

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<partinfo>BBa_K4169005</partinfo>
 
<partinfo>BBa_K4169005</partinfo>
 
===RNA Thermometer===
 
===RNA Thermometer===
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<p>Under natural conditions, some Rnas with special structures can form stem loops autonomously. Complete with RNA Gloria (HZAU-China 2021) was used in this study.</p>
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<p>Under natural conditions, some RNA with special structures can form stem loops autonomously. Complete with RNA Thermometer(HZAU-China 2021:BBa_K3733011) was used in this study.</p>
  
 
===Usage and Biology===
 
===Usage and Biology===
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<p>The ScGS is a bifunctional sesquiterpene cyclase, with the presence of Mg<sup>2+</sup>, the N-terminal half of this protein catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate(PP<sub>i</sub>). Then the C-terminal domain, highly homologous with the former, catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone.1111</p>
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<p>The RNA thermometer has a special sequence capable of forming stem-loop structures at 27 ° C and below and opening at 37 ° C. At the same time, there is a specific binding site for RNase E on the sequence that can form the secondary structure. At the transcriptional level, if this sequence is present on mRNA, it is able to bind RNase E and thus degrade the entire RNA strand. Therefore, we introduce the thermometer into the suicide module to achieve temperature sensitive suicide.
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===Sequence and Features===
 
===Sequence and Features===
 
<partinfo>BBa_K4169005 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4169005 SequenceAndFeatures</partinfo>
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===Functional Parameters===
 
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<p>To obtain ScGS, pET-28a(+)-ScGS(with His-tag) was transferred into <i>E.coli</i> BL21(DE3), and the cells were inoculated in 25 mL cultures of LB medium with 10 μg/mL kanamycin. These cultures were grown at 37℃ with 250 rpm shaking until the OD<sub>600</sub> reached 0.5-0.8, then 0.3 mM isopropyl <i>β</i>-D-1-thiogalactopyranoside(IPTG) were added, following by an overnight cultivation at 16℃ with 250 rpm shaking to induce protein expression. The washed and harvested cells were resuspended with a Binding Buffer, and then the cells were lysed by ultrasonication. Purification was performed according to the protocol of Ni-NTA Sefinose<sup>TM</sup> Resin (Sangon Biotech, Shanghai, China). As it shows in the following figure(<b>Figure 1.</b>), the existence of ScGS in our chasis was proved by SDS-PAGE analysis.</p>
 
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<center><img src="https://static.igem.org/mediawiki/parts/3/35/T--HZAU-China--ScGS-1.png
 
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<center><b>Figure 1. </b>SDS-PAGE analysis of ScGS with His-tag expression </center>
 
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<p>In order to identify the synthesis of geosmin, engineered bacteria in TB medium containing 5% glycerol were first induced ScGS expression with 0.7mM IPTG when OD<sub>600</sub> reached about 0.7, following by an overnight culture at 18℃ and continuing cultivation for next 72h at 25℃. From this way we could smell a strong and unusual odor from the culture comparing to the control.</p>
 
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<p>For further demonstration, we prepared the sample via headspace liguid-phase microextraction(HS-LPME) and a gas chromatography-mass spectrometry(GC-MS) test was conducted. The results given by GC-MS fairly shows the existence of geosmin in our culture(<b>Figure 2.</b>), thus proves the feasibility of the part.</p>
 
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<center><img src="https://static.igem.org/mediawiki/parts/a/ae/T--HZAU-China-gcms.png" style="width:869px;height:433px"></center>
 
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<b>Figure 2. </b>Identification of geosmin by GC-MS. <b>A.</b> Total ion current chromatogram of geosmin standard(<b>Red Line</b>) and extracted product(<b>Blue line</b>). <b>B.</b> Mass spectrum of geosmin standard. <b>C.</b> Mass spectrum of the extracted product.
 
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<h3>References</h3>
 
<h3>References</h3>
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<p>Hoynes-O'Connor A, Hinman K, Kirchner L, Moon TS. De novo design of heat-repressible RNA thermosensors in E. coli. Nucleic Acids Res. 2015 Jul 13;43(12):6166-79.
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<p>Hoynes-O'Connor A, Hinman K, Kirchner L,et al. De novo design of heat-repressible RNA thermosensors in E. coli.[J] Nucleic Acids Research. 2015 Jul 13;43(12):6166-79.</p>
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Latest revision as of 14:04, 12 October 2022

BBa_K4169005

RNA Thermometer

Under natural conditions, some RNA with special structures can form stem loops autonomously. Complete with RNA Thermometer(HZAU-China 2021:BBa_K3733011) was used in this study.

Usage and Biology

The RNA thermometer has a special sequence capable of forming stem-loop structures at 27 ° C and below and opening at 37 ° C. At the same time, there is a specific binding site for RNase E on the sequence that can form the secondary structure. At the transcriptional level, if this sequence is present on mRNA, it is able to bind RNase E and thus degrade the entire RNA strand. Therefore, we introduce the thermometer into the suicide module to achieve temperature sensitive suicide.

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 SapI site found at 39


References

Hoynes-O'Connor A, Hinman K, Kirchner L,et al. De novo design of heat-repressible RNA thermosensors in E. coli.[J] Nucleic Acids Research. 2015 Jul 13;43(12):6166-79.