Difference between revisions of "Part:BBa K2012000"
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with c-di-GMP function</p>
 
with c-di-GMP function</p>
 
<img src="https://static.igem.org/mediawiki/parts/4/49/Illustration_of_riboswitch_mechanism.png" width="600px"/>
 
<img src="https://static.igem.org/mediawiki/parts/4/49/Illustration_of_riboswitch_mechanism.png" width="600px"/>
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<h1>Illustration of riboswitch mechanism</h1>
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            <b> Figure 1. Illustration of riboswitch mechanism.</b>
 
<p>As show in the illustration, transcript of riboswitches region would form a hairpin and terminate transcription under low concentration of c-di-GMP. </p>
 
<p>As show in the illustration, transcript of riboswitches region would form a hairpin and terminate transcription under low concentration of c-di-GMP. </p>
 
</br>
 
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</br>
 
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<img src="https://static.igem.org/mediawiki/parts/6/66/Schematic_of_riboswitches.png"  width="800px"/>
 
<img src="https://static.igem.org/mediawiki/parts/6/66/Schematic_of_riboswitches.png"  width="800px"/>
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<h1>Schematic of riboswitches</h1>
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<b>Figure 2. Schematic of riboswitches.</b>
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<p>(a)Comparison of Bc3, Bc4, Bc5 terminators. Red rectangle shows the GC rich region of three terminators, respectively. (b) Secondary structure comparisons of Bc3, Bc4 and Bc5 aptamers with Vc2 aptamer. Conserved motifs such as tetra-loop (blue motif in stem P2), tetra-loop receptor (green motif in stem P3) and G·C base pair (C base in stem P2 and G base in stem P3 were drawn in magenta) connecting P2 with P3 were all colored to facilitate comparison. c-di-GMP was drawn in cyan and its interacting bases drawn in red.(Zhou et al., 2016) (c) Multiply local sequence blast of riboswitches’ terminators. Blue rectangle shows U region of riboswitches.</p>
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<p>(a)Comparison of Bc3, Bc4, Bc5 terminators. Red rectangle shows the GC rich region of three terminators, respectively. (b) Secondary structure comparisons of Bc3, Bc4 and Bc5 aptamers with Vc2 aptamer. Conserved motifs such as tetra-loop (blue motif in stem P2), tetra-loop receptor (green motif in stem P3) and G·C base pair (C base in stem P2 and G base in stem P3 were drawn in magenta) connecting P2 with P3 were all colored to facilitate comparison. c-di-GMP was drawn in cyan and its interacting bases drawn in red. (c) Multiply local sequence blast of riboswitches’ terminators. Blue rectangle shows U region of riboswitches.</p>
  
 
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</br>
 
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<img src="https://static.igem.org/mediawiki/parts/5/50/Characterization2.png"  width="800px"/>
 
<img src="https://static.igem.org/mediawiki/parts/5/50/Characterization2.png"  width="800px"/>
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<h1>Characterization of Riboswitch</h1>
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<p><b>Figure 3. Characterization of Riboswitch.</b> PC: pET-28-pleD\J23106+sfGFP  64F: pET-28-pleD\ J23106+Bc3+sfGFP 65F: pET-28-pleD\ J23106+Bc5+sfGFP  644F: pET-28-pleD\ J23106+Bc4+Bc4+sfGFP  635F: pET-28-pleD\ J23106+Bc3-5+sfGFP  74F: pET-28-pleD\ J23117+Bc3+sfGFP
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<p>(PC:pET-28-pleD\J23106+sfGFP  64F: pET-28-pleD\ J23106+Bc3+sfGFP
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75F: pET-28-pleD\ J23117+Bc5sfGFP  735F: pET-28-pleD\ J23117+Bc3-5+sfGFP.
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65F: pET-28-pleD\ J23106+Bc5+sfGFP  644F: pET-28-pleD\ J23106+Bc4+Bc4+sfGFP  635F: pET-28-pleD\ J23106+Bc3-5+sfGFP  74F: pET-28-pleD\ J23117+Bc3+sfGFP
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75F: pET-28-pleD\ J23117+Bc5sfGFP  735F: pET-28-pleD\ J23117+Bc3-5+sfGFP
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</br>
 
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<img src="https://static.igem.org/mediawiki/parts/b/bb/Characterization3.png"  width="800px"/>
 
<img src="https://static.igem.org/mediawiki/parts/b/bb/Characterization3.png"  width="800px"/>
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<h1>Characterization of Riboswitch</h1>
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<p><b>Figure 4. Characterization of Riboswitch.</b> We use “read-through rate” (RTR) of the downstream gene to measure the terminator forming efficiency of a riboswitch. The read-through rate of each riboswitch in liquid medium was assessed by relative fluorescence intensity, which is the ratio of specific activity of a test strain to specific activity of the control strain (pET-28-pleD/J23117+sfGFP) with the same promoter of test circuits (such as J23117+Bc3-5+sfGFP).
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<p>We use “read-through rate” (RTR) of the downstream gene to measure the terminator forming efficiency of a riboswitch.  
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The read-through rate of each riboswitch in liquid medium was assessed by relative fluorescence intensity, which is the ratio of specific activity of a test strain to specific activity of the control strain (pET-28-pleD/J23117+sfGFP) with the same promoter of test circuits (such as J23117+Bc3-5+sfGFP).
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</p>
 
</p>
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</br>
 
</br>
 
</br>
 
</br>
 
</br>
 
</br>
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<h1>Reference:</h1>
 
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<p>Zhou, H., Zheng, C., Su, J., Chen, B., Fu, Y., Xie, Y., . . . He, J. (2016). Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep, 6, 20871. doi:10.1038/srep20871</p>
 
 
</br>
 
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Revision as of 13:12, 1 November 2016


c-di-GMP tandem riboswitche bc3-5

Three complete c-di-GMP riboswitches (Bc3, Bc4 and Bc5 RNA) with similar structures, which are arranged in tandem to constitute a triple-tandem (Bc3-5 RNA) riboswitch in the 5′-UTR of the cspABCDE mRNA in Bacillus thuringiensis subsp. chinensis CT-43. They are c-di-GMP riboswitches (termed c-di-GMP-I), c-di-GMP-I binds the second messenger c-di-GMP through hydrogen bonding or base stacking of the two guanosines of c-di-GMP with five specific bases in the aptamer, resulting in transcriptional changes of downstream genes correlating with c-di-GMP function

Figure 1. Illustration of riboswitch mechanism.

As show in the illustration, transcript of riboswitches region would form a hairpin and terminate transcription under low concentration of c-di-GMP.




Figure 2. Schematic of riboswitches.

(a)Comparison of Bc3, Bc4, Bc5 terminators. Red rectangle shows the GC rich region of three terminators, respectively. (b) Secondary structure comparisons of Bc3, Bc4 and Bc5 aptamers with Vc2 aptamer. Conserved motifs such as tetra-loop (blue motif in stem P2), tetra-loop receptor (green motif in stem P3) and G·C base pair (C base in stem P2 and G base in stem P3 were drawn in magenta) connecting P2 with P3 were all colored to facilitate comparison. c-di-GMP was drawn in cyan and its interacting bases drawn in red. (c) Multiply local sequence blast of riboswitches’ terminators. Blue rectangle shows U region of riboswitches.




Figure 3. Characterization of Riboswitch. PC: pET-28-pleD\J23106+sfGFP 64F: pET-28-pleD\ J23106+Bc3+sfGFP 65F: pET-28-pleD\ J23106+Bc5+sfGFP 644F: pET-28-pleD\ J23106+Bc4+Bc4+sfGFP 635F: pET-28-pleD\ J23106+Bc3-5+sfGFP 74F: pET-28-pleD\ J23117+Bc3+sfGFP 75F: pET-28-pleD\ J23117+Bc5sfGFP 735F: pET-28-pleD\ J23117+Bc3-5+sfGFP.




Figure 4. Characterization of Riboswitch. We use “read-through rate” (RTR) of the downstream gene to measure the terminator forming efficiency of a riboswitch. The read-through rate of each riboswitch in liquid medium was assessed by relative fluorescence intensity, which is the ratio of specific activity of a test strain to specific activity of the control strain (pET-28-pleD/J23117+sfGFP) with the same promoter of test circuits (such as J23117+Bc3-5+sfGFP).







Usage and Biology

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]