Difference between revisions of "Part:BBa K2541400"
 
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__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_K2541400 short</partinfo>
 
<partinfo>BBa_K2541400 short</partinfo>
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<h5>
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<P style="text-indent:2em;">
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It is a superfolder GFP, a robustly folded version of GFP, which is BbsI restriction site free and can be used in Golden Gate assembly. BBa_K2451400 is an improved part based on superfolder GFP BBa_I746916 (https://parts.igem.org/Part:BBa_I746916).
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</p>
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</h5>
  
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It is a superfolder GFP, a robustly folded version of GFP, which is BbsI restriction site free and can be used in goldengate assembly.
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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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Green fluorescent protein (GFP) exhibits intrinsic fluorescence and is commonly used as a reporter gene in intact cells and organisms <sup>[1]</sup>. Many mutants of the protein with either modified spectral properties, increased fluorescence intensity, or improved folding properties have been reported <sup>[2]</sup>.
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</p>
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<P style="text-indent:2em;">
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GFP often misfolds when expressed as fusions with other proteins, while a robustly folded version of GFP, called superfolder GFP (sfGFP), was developed and described by Pédelacq et al at 2006<sup>[3]</sup> that folds well even when fused to poorly folded polypeptides. We decided to use sfGFP as our reporter protein due to its faster folded feature and higher fluorescence intensity. The superfolder GFP had been registered in iGEM BBa_I746916. There is another superfolder GFP designed by Overkamp W et al at 2013<sup>[4]</sup>, which is a codon optimized sfGFP. It was be used in ''Escherichia coli'' by Segall-Shapiro T H et al at 2018<sup>[5]</sup>.
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</p>
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<P style="text-indent:2em;">
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This year our team registered the superfolder GFP designed by Overkamp W et al with a BBa_K2541400 (called sfGFP_optimism). Compared with superfolder GFP (BBa_I746916), sfGFP_optimism (BBa_K2541400) is BbsI restriction site free, and the BbsI restriction endonuclease is an economical and efficient enzyme used in Golden Gate assembly, so sfGFP_optimism can be used in Golden Gate assembly to achieve efficient and rapid assembly of gene fragments.
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</p>
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</h5>
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[[File:Jilin_China-sfGFP-1.0.png|center|Jilin_China-sfGFP-1.0]]
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<center>
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Figure 1. Expression of three types of sfGFP(BBa_I746916, BBa_K2541401, BBa_K2541400), cultivated overnight.
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</center>
  
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<h1>'''Biology and Usage'''</h1>
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<h1>'''2. Characterization'''</h1>
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Green fluorescent protein (GFP) offers efficient ways of visualizing promoter activity and protein localization in vivo, and many different variants are currently available to study bacterial cell biology. It exhibits intrinsic fluorescence and is commonly used as a reporter gene in intact cells and organisms [1]. Many mutants of the protein with either modified spectral properties, increased fluorescence intensity, or improved folding properties have been reported [2].  
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<h5>
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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 [3]that folds well even when fused to poorly folded polypeptides. Furthermore, sfGFP might be particularly suitable for gene expression studies, since the emergence of fluorescence closely matches induction of transcription. The superfolder GFP had been registered in iGEM BBa_I746916. Its codon usage is a compromise for optimum expression in E. coli and B. subtilis. There is another superfolder GFP designed by Overkamp W et al at 2013[4], which is codon optimized for S. pneumoniae. It was be used in Escherichia coli by Segall-Shapiro T H et al at 2018[5].
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<P style="text-indent:2em;">
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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 rapid assembly of gene fragments. And sfGFP (BBa_K2541400) has x fold increased fluorescence intensity than superfolder GFP(BBa_I746916).
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We constructed sfGFP_optimism (BBa_K2541400) sequence and superfolder GFP (BBa_I746916) on the pSB1C3 vector. The BbsI recognition site free was confirmed by nucleic acid electrophoresis (Figure 2). The sfGFP_optimism can not be digested by BbsI. And the length of these sequences are correct.
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</p>
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</h5>
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[[File:sfGFP_optimism f1 new1.png|center|sfGFP_optimism f1 new1]]
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<center>
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Figure 2. L1: 1kb DNA marker; L2: BBa_I746916; L3: BBa_I746916+BbsI; L4: BBa_K2541401; L5: BBa_K2541401+BbsI; L6: BBa_K2541400; L7: BBa_K2541400+BbsI; L8: 1kb DNA marker.  
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</center>
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<h1>'''Characterization'''</h1>
 
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The improved sfGFP (K2541400) variant was standardised into BioBrick format and its fluorescence intensity was compared with superfolder GFP(BBa_I746916) .Its x fold increased fluorescence intensity is a very useful feature. And it is BbsI restriction site free, so it can be used in goldengate assembly to achieve efficient and rapid assembly of gene fragments.
 
  
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The new variant sfGFP (K2541400) was contributed to the Registry of Standard Biological Parts and it will be more widely used in the synthetic biology community.  
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<h5>
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<P style="text-indent:2em;">
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We got the emission and excitation spectra of two type sfGFP: sfGFP_optimism (BBa_K2541400) and superfolder GFP (BBa_I746916) (Figure 3).
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</p>
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</h5>
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<html>
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<center>
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<img src="https://static.igem.org/mediawiki/parts/5/50/SfGFP_op.svg" width="80%" />
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</center>
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<center>
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<img src="https://static.igem.org/mediawiki/parts/1/1e/SfGFP-1.svg" width="80%" />
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</center>
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</html>
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<center>
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Figure 3. Emission and Excitation Spectra of sfGFP_optimism(BBa_K2541400) and sfGFP(BBa_I746916).
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</center>
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<span class='h3bb'>Sequence and Features</span>
 
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<partinfo>BBa_K2541400 SequenceAndFeatures</partinfo>
 
  
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<h5>
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<P style="text-indent:2em;">
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For further characterization, we detected the expression intensity of these two types of sfGFP. According to the results (Figure 4), we found out that the fluorescence intensity of sfGFP_optimism (BBa_K2541400) is nearly 2.6 times higher than superfolder GFP (BBa_I746916).
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</p>
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</h5>
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<html><center><img src="https://static.igem.org/mediawiki/parts/8/83/Jilin_China-sfGFP-fluorescence-01.svg" width="80%" /></center></html>
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Figure 5. <b>The expression of three types of sfGFP in E.coli.</b> The grey line represents fluorescent expression of sfGFP_optimism (BBa_K2541400), the orange line represents fluorescent expression of sfGFP(BbsI free) (BBa_K2541401), the blue line represents fluorescent expression of superfolder GFP (BBa_I746916) and the yellow line represents fluorescent expression of negative control (BBa_J364007).
  
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<h1>'''3. Conclusion'''</h1>
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<h5>
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<P style="text-indent:2em;">
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We have made an improvement on the superfolder GFP (BBa_I746916). Our sfGFP_optimism (BBa_K2541400) is BbsI restriction site free, which can be used in Golden Gate assembly to achieve efficient and rapid assembly of gene fragments. And its fluorescence intensity is higher than superfolder GFP (BBa_I746916).
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</p>
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</h5>
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K2541400 SequenceAndFeatures</partinfo>
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
 
<partinfo>BBa_K2541400 parameters</partinfo>
 
<partinfo>BBa_K2541400 parameters</partinfo>
 
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Latest revision as of 19:00, 17 October 2018


sfGFP_optimism

It is a superfolder GFP, a robustly folded version of GFP, which is BbsI restriction site free and can be used in Golden Gate assembly. BBa_K2451400 is an improved part based on superfolder GFP BBa_I746916 (https://parts.igem.org/Part:BBa_I746916).

1. Usage and Biology

Green fluorescent protein (GFP) exhibits intrinsic fluorescence and is commonly used as a reporter gene in intact cells and organisms [1]. Many mutants of the protein with either modified spectral properties, increased fluorescence intensity, or improved folding properties have been reported [2].

GFP often misfolds when expressed as fusions with other proteins, while a robustly folded version of GFP, called superfolder GFP (sfGFP), was developed and described by Pédelacq et al at 2006[3] that folds well even when fused to poorly folded polypeptides. We decided to use sfGFP as our reporter protein due to its faster folded feature and higher fluorescence intensity. The superfolder GFP had been registered in iGEM BBa_I746916. There is another superfolder GFP designed by Overkamp W et al at 2013[4], which is a codon optimized sfGFP. It was be used in Escherichia coli by Segall-Shapiro T H et al at 2018[5].

This year our team registered the superfolder GFP designed by Overkamp W et al with a BBa_K2541400 (called sfGFP_optimism). Compared with superfolder GFP (BBa_I746916), sfGFP_optimism (BBa_K2541400) is BbsI restriction site free, and the BbsI restriction endonuclease is an economical and efficient enzyme used in Golden Gate assembly, so sfGFP_optimism can be used in Golden Gate assembly to achieve efficient and rapid assembly of gene fragments.

Jilin_China-sfGFP-1.0

Figure 1. Expression of three types of sfGFP(BBa_I746916, BBa_K2541401, BBa_K2541400), cultivated overnight.

2. Characterization

We constructed sfGFP_optimism (BBa_K2541400) sequence and superfolder GFP (BBa_I746916) on the pSB1C3 vector. The BbsI recognition site free was confirmed by nucleic acid electrophoresis (Figure 2). The sfGFP_optimism can not be digested by BbsI. And the length of these sequences are correct.

sfGFP_optimism f1 new1

Figure 2. L1: 1kb DNA marker; L2: BBa_I746916; L3: BBa_I746916+BbsI; L4: BBa_K2541401; L5: BBa_K2541401+BbsI; L6: BBa_K2541400; L7: BBa_K2541400+BbsI; L8: 1kb DNA marker.


We got the emission and excitation spectra of two type sfGFP: sfGFP_optimism (BBa_K2541400) and superfolder GFP (BBa_I746916) (Figure 3).

Figure 3. Emission and Excitation Spectra of sfGFP_optimism(BBa_K2541400) and sfGFP(BBa_I746916).


For further characterization, we detected the expression intensity of these two types of sfGFP. According to the results (Figure 4), we found out that the fluorescence intensity of sfGFP_optimism (BBa_K2541400) is nearly 2.6 times higher than superfolder GFP (BBa_I746916).

Figure 5. The expression of three types of sfGFP in E.coli. The grey line represents fluorescent expression of sfGFP_optimism (BBa_K2541400), the orange line represents fluorescent expression of sfGFP(BbsI free) (BBa_K2541401), the blue line represents fluorescent expression of superfolder GFP (BBa_I746916) and the yellow line represents fluorescent expression of negative control (BBa_J364007).

3. Conclusion

We have made an improvement on the superfolder GFP (BBa_I746916). Our sfGFP_optimism (BBa_K2541400) is BbsI restriction site free, which can be used in Golden Gate assembly to achieve efficient and rapid assembly of gene fragments. And its fluorescence intensity is higher than superfolder GFP (BBa_I746916).


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 421
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]