Difference between revisions of "Part:BBa K3183002"

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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K3183000 SequenceAndFeatures</partinfo>
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<partinfo>BBa_K3183002 SequenceAndFeatures</partinfo>
  
  
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===Use by Team Oxford 2019===
 
===Use by Team Oxford 2019===
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The ldhL promoter is a constitutive promoter that has been used in <i> Lactobacillus reuteri </i> in our composite part <partinfo>BBa_K3183100</partinfo>.
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The ldhL promoter is a constitutive promoter that has been used in <i> Lactobacillus reuteri </i> in our composite part <partinfo>BBa_K3183100</partinfo> and <partinfo>BBa_K3183101</partinfo>.
  
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===Characterisation===
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===Part characterization by Oxford iGEM 2019===
  
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The part was characterised in the composite part <partinfo>BBa_K3183101</partinfo>.
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====Measurement of promoter strength: <partinfo>BBa_K3183101</partinfo>====
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 +
<br><b>
 +
Summary
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</b><br>
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A major use of this part was to facilitate the quantification and comparison of promoter strengths <i>in vivo</i>. The principle of such an assay is to correlate the fluorescence intensity of our bacterial sample to the fluorescence intensity of a fluorescein solution of known concentration, thus allowing us to estimate the exact protein concentration under the control of the promoter reached in the cytoplasm.
 +
<br><b><br>
 +
Method:
 +
</b><br><br>
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The composite part was inserted into pTRKH3 vector <partinfo>BBa_K3183050</partinfo> by Gibson assembly and transformed into <i>E. coli</i> by heat-shock transformation. Successfully transformed colonies were picked and used in fluorometric assay using excitation at 500nm and detecting emission 520nm. The assay was used to compare the protein expression strength of the two promoters by measuring fluorescence intensity and OD600 over time. Then, to normalize the results, the blank corrected ratio of fluorescence intensity and absorbance at 600nm was used to compare the promoters.
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<br><b>
 +
Results:
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<br><br></b>
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[[File:T--Oxford--Results-ldh.png|thumb|left|430px|
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Figure 1: ldh promoter FI and OD600 time dependence - Blank corrected Fluorescence intensity and OD600 was plotted against time for ldh promoter. A large peak in OD600 can be observed, which could be an outlier due to measurement error. <i>Error bars represent Standard error of the mean. n = 3</i> ]]
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 +
[[File:T--Oxford--Results-erm-vs-ldh.png|thumb|right|430px|
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Figure 2: Promoter strength comparison - The blank corrected fluorescence intensity and OD600 ratio was plotted against time for both promoters. On the plot, the mean of ldh promoter seems to be larger than that of erm promoter. However, due to the broad standard deviation, no significant conclusion can be made. On the other hand, for erm promoter, it could be observed that the FI/OD600 decreases over time. One hypothesis is that due to the cell growth (increased OD600) and increased scattering, the fluorescence intensity decreases. <i>Error bars represent 1 standard deviation. n = 3</i>]]
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 +
<br><b>
 +
Discussion:
 +
<br></b>
 +
The results section shows that the blank corrected fluorescence intensity have very high standard deviations. This is likely because, instead of purifying the protein and exchanging the buffer, we performed our assays on living cells; this had a number of consequences on the accuracy of our results:
 +
<li>The MRS medium in which the cells were grown has very high background fluorescence, such that its intrinsic noise significantly overshadowed the signal and sometimes lead to unreasonable results. </li>
 +
<li>The optical density of the solution due to light scattering by bacteria led to a significant drop in signal intensity, which would have been extremely difficult to correct for at large ODs</li>
 +
<li>The vastly different chemical properties (e.g. ionic strength, the presence of quenchers etc.)of the cytosolic environment from regular buffer solutions likely result in very different spectroscopic properties of the fluorophores, such as quantum yield and maximal absorption/emission wavelengths, thus reducing the feasibility of comparison of our sample to the calibration curve based on fluorescein.</li>
 +
Therefore, we argue that the data we obtained cannot be used to quantitatively assess the strength of the promoters and has, at most, qualitative value. Therefore, we suggest that in the future more rigorous assays performed by purifying the enzyme and measuring its fluorescence after the buffer was exchanged to one similar to that of the fluorescein solution.
 +
<br>
  
 
===References===
 
===References===
 
1. Kim, S F et al. “Cloning and nucleotide sequence of the Lactobacillus casei lactate dehydrogenase gene.” Applied and environmental microbiology vol. 57,8 (1991): 2413-7.<br>
 
1. Kim, S F et al. “Cloning and nucleotide sequence of the Lactobacillus casei lactate dehydrogenase gene.” Applied and environmental microbiology vol. 57,8 (1991): 2413-7.<br>
 
2. Lizier, Michela, et al. “Comparison of Expression Vectors in Lactobacillus Reuteri Strains.” FEMS Microbiology Letters, vol. 308, no. 1, 2010, pp. 8–15., doi:10.1111/j.1574-6968.2010.01978.x.
 
2. Lizier, Michela, et al. “Comparison of Expression Vectors in Lactobacillus Reuteri Strains.” FEMS Microbiology Letters, vol. 308, no. 1, 2010, pp. 8–15., doi:10.1111/j.1574-6968.2010.01978.x.

Latest revision as of 14:43, 16 November 2022


Lactate Dehydrogenase Constitutive Promoter for Lactobacillus sp.

P-slp is a constitutive promoter which can be used in Lactobacillus reuteri 10023C, and may have uses in other Lactobacillus species.

This is a constitutive promoter from the lactate dehydrogenase (ldhL) promoter from Lactobacillus acidophilus1. It has been subsequently characterised in six strains of Lactobacillus reuteri and Lactococcus lactis spp. cremoris MG13632.


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 219


Use by Team Oxford 2019

The ldhL promoter is a constitutive promoter that has been used in Lactobacillus reuteri in our composite part BBa_K3183100 and BBa_K3183101.

Part characterization by Oxford iGEM 2019

Measurement of promoter strength: BBa_K3183101


Summary
A major use of this part was to facilitate the quantification and comparison of promoter strengths in vivo. The principle of such an assay is to correlate the fluorescence intensity of our bacterial sample to the fluorescence intensity of a fluorescein solution of known concentration, thus allowing us to estimate the exact protein concentration under the control of the promoter reached in the cytoplasm.

Method:

The composite part was inserted into pTRKH3 vector BBa_K3183050 by Gibson assembly and transformed into E. coli by heat-shock transformation. Successfully transformed colonies were picked and used in fluorometric assay using excitation at 500nm and detecting emission 520nm. The assay was used to compare the protein expression strength of the two promoters by measuring fluorescence intensity and OD600 over time. Then, to normalize the results, the blank corrected ratio of fluorescence intensity and absorbance at 600nm was used to compare the promoters.
Results:

Figure 1: ldh promoter FI and OD600 time dependence - Blank corrected Fluorescence intensity and OD600 was plotted against time for ldh promoter. A large peak in OD600 can be observed, which could be an outlier due to measurement error. Error bars represent Standard error of the mean. n = 3
Figure 2: Promoter strength comparison - The blank corrected fluorescence intensity and OD600 ratio was plotted against time for both promoters. On the plot, the mean of ldh promoter seems to be larger than that of erm promoter. However, due to the broad standard deviation, no significant conclusion can be made. On the other hand, for erm promoter, it could be observed that the FI/OD600 decreases over time. One hypothesis is that due to the cell growth (increased OD600) and increased scattering, the fluorescence intensity decreases. Error bars represent 1 standard deviation. n = 3


Discussion:
The results section shows that the blank corrected fluorescence intensity have very high standard deviations. This is likely because, instead of purifying the protein and exchanging the buffer, we performed our assays on living cells; this had a number of consequences on the accuracy of our results:

  • The MRS medium in which the cells were grown has very high background fluorescence, such that its intrinsic noise significantly overshadowed the signal and sometimes lead to unreasonable results.
  • The optical density of the solution due to light scattering by bacteria led to a significant drop in signal intensity, which would have been extremely difficult to correct for at large ODs
  • The vastly different chemical properties (e.g. ionic strength, the presence of quenchers etc.)of the cytosolic environment from regular buffer solutions likely result in very different spectroscopic properties of the fluorophores, such as quantum yield and maximal absorption/emission wavelengths, thus reducing the feasibility of comparison of our sample to the calibration curve based on fluorescein.

    • Therefore, we argue that the data we obtained cannot be used to quantitatively assess the strength of the promoters and has, at most, qualitative value. Therefore, we suggest that in the future more rigorous assays performed by purifying the enzyme and measuring its fluorescence after the buffer was exchanged to one similar to that of the fluorescein solution.

    References

    1. Kim, S F et al. “Cloning and nucleotide sequence of the Lactobacillus casei lactate dehydrogenase gene.” Applied and environmental microbiology vol. 57,8 (1991): 2413-7.
    2. Lizier, Michela, et al. “Comparison of Expression Vectors in Lactobacillus Reuteri Strains.” FEMS Microbiology Letters, vol. 308, no. 1, 2010, pp. 8–15., doi:10.1111/j.1574-6968.2010.01978.x.