Difference between revisions of "Part:BBa K1033916"

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===Functional Parameters===
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==Functional Parameters: Austin_UTexas==
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<partinfo>BBa_K1033916 parameters</partinfo>
 
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<h3><center>Burden Imposed by this Part:</center></h3>
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<center><img src = "https://static.igem.org/mediawiki/parts/f/fa/T--Austin_Utexas--no_burden_icon.png" style = "width:160px;height:120px"></center>
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<figcaption><center><b>Burden Value: 1.9 ± 2.5% </b></center></figcaption>
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<p> Burden is the percent reduction in the growth rate of <i>E. coli</i> cells transformed with a plasmid containing this BioBrick (± values are 95% confidence limits). This BioBrick did not exhibit a burden that was significantly greater than zero (i.e., it appears to have little to no impact on growth). Therefore, users can depend on this part to remain stable for many bacterial cell divisions and in large culture volumes. Refer to any one of the
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<a href="https://parts.igem.org/Part:BBa_K3174002">BBa_K3174002</a> - <a href="https://parts.igem.org/Part:BBa_K3174007">BBa_K3174007</a> pages for more information on the methods, an explanation of the sources of burden,  and other conclusions from a large-scale measurement project conducted by the <a href="http://2019.igem.org/Team:Austin_UTexas">2019 Austin_UTexas team</a>.</p>
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<p>This functional parameter was added by the <a href="https://2020.igem.org/Team:Austin_UTexas/Contribution">2020 Austin_UTexas team.</a></p>
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Revision as of 20:39, 27 August 2020

amajLime, yellow-green chromoprotein

This chromoprotein from the coral Anemonia majano, amajLime (also known as amajCFP or amFP486), naturally exhibits strong color when expressed. The protein has an absorption maximum at 458 nm giving it a yellow-green color visible to the naked eye. Compared to many other chromoproteins, such as amilCP (BBa_K592009), amilGFP (BBa_K592010), spisPink (BBa_K1033932), asPink (BBa_K1033933) and aeBlue (BBa_K864401), the color development is slower. The color is readily observed in both LB or on agar plates after 24-48 hours of incubation. The protein amajLime has significant sequence homologies with proteins in the GFP family.

Usage and Biology

This part is useful as a reporter.

Source

Anemonia majano. The protein was first extracted and characterized by Matz et. al. under the name amFP486 (UniProtKB/Swiss-Prot: Q9U6Y6.1 GI:56749103). This version is codon optimized for E coli by Genscript.


Characterization

Team: UAlberta 2019


Fig.1 Extracted amajLime under white light (top) and UV light (bottom)


Summary of Contribution:

Team UAlberta repeated much of the same measurements conducted by Hong Kong-CUHK iGEM 2017 in order to provide corroboration of previously submitted data for the amajLime Chromoprotein. However, our extracted amajLime was contained in Tris-buffered Saline (50 mmol Tris-Cl, 150 mmol NaCl) and we conducted a quantum yield measurement according to established methods in [4].

Fig.2 Emission and Excitation spectra of amajLime in Tris-buffered Saline (50 mmol Tris-Cl pH 9.1, 150 mmol NaCl)


Table 1. Measurement Parameters for Fluorescence and Absorbance
Measurement Parameter
Plate Reader Cytation5
Plate Type NUNC 96-Well Optical-bottom Microplate
Wavelength Step Size (nm) 2
Absorbance Scan: Excitation Wavelength Measurement Range (nm) [400-700]
Fluorescence Scan: Emission Wavelength Measurement Range (nm) [472/9-700]
Fixed Excitation Wavelength (nm) 452/9
Gain (G) 50
Number of Flashes 10
Optics: Read from Bottom
Read Height (mm) 7


Table 2. Values Used to Determine Quantum Yield
Measurement in TBS pH 9.1 (50 mmol Tris-Cl, 150 mmol NaCl)
Measured Parameter amajLime Sample Fluorescein Standard
Absorbance at 452 nm 0.076 0.047
Integrated Fluorescence Area 185417 88037
Quantum Yield 0.50
Relative Quantum Yield 0.65



Discussion

Our results are consistent with the data previously obtained by Hong Kong-CUHK iGEM 2017, however, our absorbance data does display offset error at longer wavelengths. Our determined relative quantum yield for amajLime of 0.65 with a standard quantum yield of 0.5 is also consistent with the previously published value of 0.71 for wild type amajLime [4].



Group: Hong Kong-CUHK iGEM 2017
Author: Yuet Ching Lin
Summary: Although amajLime is described as chromoprotein in the main page, we characterized its spectral properties and found the max excitation and emission wavelength at 445 nm and 485 nm respectively
Documentation:
Fluorescent properties of amajLime:

.

Fig.1 Emission and Excitation spectra in blue and green respectively.



Group: Hong Kong-CUHK iGEM 2017
Author: Yuet Ching Lin
Summary: We measured the fluorescent signal of amajLime in buffers with different pH.
Documentation:
Charaterization of amajLime pH stabillity:

We transformed part BBa_K1033916 with constituitive promoter: J23100 in C41 and grew in 2XYT for 24 hours.. After purifying the amajLime by Ion Exchange Chromatography and Hydrophobic Interaction Chromatography, we measured the fluoresece (ex ,em ) of purified amajLime, which is diluted to 10µg/100µl (total 200µl) in triplicates, into different buffers (ranges from pH2 to pH12; Volume of amajLime:buffer = 1:4.3). To facilitate reproducibility of the experiment, we correlated the relative fluorescent intensity to an absolute fluorophore concentration by referring it to a standard curve of the corresponding fluorophores(Fluorescein) using the interlab study protocol. The result shows that the stability drops dramatically in pH condition below 6 and relatively stable in pH 6-10.

Fig.2 Vary pH attributed to different fluorescent intensity of amajLime.
Measurement Type Fluorescence
Microplate name COSTAR 96
Scan mode orbital averaging
Scan diameter [nm] 3
Excitation 470-15
Emission 515-20
Dichronic filter auto 491.2
Gain 500
Focal height [nm] 9

Table 1 Plate reader setting of fluorescent measurement

References

[http://www.nature.com/nbt/journal/v17/n10/full/nbt1099_969.html] Matz, Mikhail V., et al. "Fluorescent proteins from nonbioluminescent Anthozoa species." Nature biotechnology 17.10 (1999): 969-973.

[http://www.pnas.org/content/102/36/12712.short] Henderson, J. Nathan, and S. James Remington. "Crystal structures and mutational analysis of amFP486, a cyan fluorescent protein from Anemonia majano." Proceedings of the National Academy of Sciences of the United States of America 102.36 (2005): 12712-12717.

[http://www.ncbi.nlm.nih.gov/pubmed/18648549] Alieva, N. O., et al. 2008. Diversity and evolution of coral fluorescent proteins. PLoS One 3:e2680.

[1] P. J. Cranfill et al., “Quantitative assessment of fluorescent proteins,” Nat. Methods, vol. 13, no. 7, pp. 557–562, Jun. 2016.

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]



Functional Parameters: Austin_UTexas

BBa_K1033916 parameters

Burden Imposed by this Part:

Burden Value: 1.9 ± 2.5%

Burden is the percent reduction in the growth rate of E. coli cells transformed with a plasmid containing this BioBrick (± values are 95% confidence limits). This BioBrick did not exhibit a burden that was significantly greater than zero (i.e., it appears to have little to no impact on growth). Therefore, users can depend on this part to remain stable for many bacterial cell divisions and in large culture volumes. Refer to any one of the BBa_K3174002 - BBa_K3174007 pages for more information on the methods, an explanation of the sources of burden, and other conclusions from a large-scale measurement project conducted by the 2019 Austin_UTexas team.

This functional parameter was added by the 2020 Austin_UTexas team.