Difference between revisions of "Part:BBa K1962014"
 
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The "acid shock RNA" asr promoter is a pH sensitive promoter native to E. coli that has been documented by other iGEM teams. Here, we present a composite part to allow further characterisation of promoter activity. The composite part consists of the asr promoter(<partinfo>BBa_K1231000</partinfo>) and a combined biobrick containing RBS / GFP  / terminators (<partinfo>BBa_E0840</partinfo>).  
 
The "acid shock RNA" asr promoter is a pH sensitive promoter native to E. coli that has been documented by other iGEM teams. Here, we present a composite part to allow further characterisation of promoter activity. The composite part consists of the asr promoter(<partinfo>BBa_K1231000</partinfo>) and a combined biobrick containing RBS / GFP  / terminators (<partinfo>BBa_E0840</partinfo>).  
  
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{|width='80%' style='border:1px solid gray'
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<partinfo>BBa_K892008 AddReview 5</partinfo>
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<I>Parts Collection 2016</I>
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This is part of a Part Collection of 18 BioBricks designed by Dundee iGEM 2016. This collection will be useful to teams working with toxins as we have submitted new toxins to the registry. Working with bacterial toxins is difficult due to the risk of toxicity to the chassis, so the corresponding immunity for our toxins were also submitted. We have also submitted these toxins lacking their cytotoxic domains replacing it with a multiple cloning site which will allow for different toxic domains to be fused at the C-terminus and thereby generating a synthetic toxin. In addition, there are three well-characterised promoters that can be used to initiate gene expression at various points in the digestive tract, to enable devices to function within a human or animal. Finally, a lysis cassette was constructed to lyse or burst cells, thus releasing the toxins and destroying the GM bacteria to prevent its release to the environment.
  
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This <partinfo>BBa_K1962013</partinfo> is for measuring gene expression in response to pH and is important for calibrating the synthetic system.
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s===Usage and Biologys===
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===Usage and Biology===
  
 
Enterobacteria can respond to low pH by de novo synthesis of specific proteins and altered levels of gene expression. The response to environmental stresses, such as pH, is often a complex mechanism and also depends on other environmental factors such as nutrition, the presence or absence of oxygen or starvation. The E. coli asr (acid shock RNA) gene encodes small RNA, of about 450 nucleotides in length. This gene is inducible by low external pH and contributes to the organism’s survival2. It has been suggested that asr genes may be regulated by the two component system PhoBR2.
 
Enterobacteria can respond to low pH by de novo synthesis of specific proteins and altered levels of gene expression. The response to environmental stresses, such as pH, is often a complex mechanism and also depends on other environmental factors such as nutrition, the presence or absence of oxygen or starvation. The E. coli asr (acid shock RNA) gene encodes small RNA, of about 450 nucleotides in length. This gene is inducible by low external pH and contributes to the organism’s survival2. It has been suggested that asr genes may be regulated by the two component system PhoBR2.
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In 2013 the Northwestern iGEM team submitted two pH sensitive promoter Pasr (BBa_K1231000) and PgadA (BBa_K1231001). In order to further characterise both of these promoters we cloned gfp (BBa_E0840) downstream of both promoters. We then used this construct to measure and compare the GFP expression levels in response to different pH conditions.
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In 2013 the Northwestern iGEM team submitted two pH sensitive promoter Pasr (<partinfo>BBa_K1231000</partinfo>) and PgadA (<partinfo>BBa_K1231001</partinfo>). In order to further characterise both of these promoters we cloned gfp (BBa_E0840) downstream of both promoters. We then used this construct to measure and compare the GFP expression levels in response to different pH conditions.
  
 
We wanted to test both our pH sensitive promoters, Pasr and PgadA by monitoring for the production of GFP by western blotting. The western blots showed levels of GFP protein production by the cells at a range of pH values. In Fig 1A the expression of GFP at pH 5 is much higher than the other pH readings. This would indicate that at this pH the largest amount of GFP was being produced under the induction of the gadA promoter. The promoter is slightly leaky as there is also expression of protein within cells at other pH values. In Fig 1B the GFP protein expression under the regulation of Pasr can be seen, the range of activity for this promoter is much wider indicating that this promoter is leakier than PgadA. The level of expression of GFP under the regulation of Pasr appears to be uniform with only a slight increase in GFP at pH5.
 
We wanted to test both our pH sensitive promoters, Pasr and PgadA by monitoring for the production of GFP by western blotting. The western blots showed levels of GFP protein production by the cells at a range of pH values. In Fig 1A the expression of GFP at pH 5 is much higher than the other pH readings. This would indicate that at this pH the largest amount of GFP was being produced under the induction of the gadA promoter. The promoter is slightly leaky as there is also expression of protein within cells at other pH values. In Fig 1B the GFP protein expression under the regulation of Pasr can be seen, the range of activity for this promoter is much wider indicating that this promoter is leakier than PgadA. The level of expression of GFP under the regulation of Pasr appears to be uniform with only a slight increase in GFP at pH5.
  
 +
We now wanted to be able to use a more quantitative approach to assign optimal promoter function conditions. To do this we used a 96 well plate reader to monitor GFP fluorescence and cell growth over the space of 20 hours. This experiment took obtained GFP fluorescence (excitation wavelength = 395nm and excitation wavelength = 509nm) and OD600nm values every 20 minutes yielding a large volume of data and more quantitative values for promoter function over 20 hours. To normalise flouresence measurements we used the following formula:
 +
 +
GFP / OD600nm = Fluorescence per unit absorbance
 +
 +
The data was then plotted to observe the trend over time as well as taking a snap shot at 16h. The data collected from the plate reader experiments showed a slight difference in optimal pH for the pH sensitive promoter asr, as can be seen in Fig 2B and 3B the maximal fluorescence observed from GFP fluorescence per unit of absorbance over time was at a pH range of 8. For PgadA we observed a coherent trend of optimal promoter function around pH5/pH6 as can be seen in Fig 2A and 3A.
  
 
https://static.igem.org/mediawiki/parts/7/70/GadA-asrresult1a.png
 
https://static.igem.org/mediawiki/parts/7/70/GadA-asrresult1a.png
  
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Fig 1. GFP production under the control of pH sensitive promoters PgadA and Pasr. Promoters with gfp cloned downstream of them were transformed into MG1655 E. coli cells, 5 ml of these cells were incubated for 16h at 37 &deg C. After 16h, 200 uL of the overnight cultures were introduced into 1.8 ml of MOPS pH adjusted LB for the respective pH values indicated above. After 20 min at ambient conditions a 1ml aliquot was pelleted. The pellets were re-suspended in 100 ul Laemmli buffer and 15uL samples were then separated by SDS PAGE (12% acrylamide) and transferred to PVDF membrane followed by probing with anti-GFP antibody. Fig 2A - Shows the GFP production under the control of the PgadA and Fig 2B shows the GFP production under the control of the Pasr promoter both in varying pH conditions.
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Fig 1. GFP production under the control of pH sensitive promoters PgadA and Pasr. Promoters with gfp cloned downstream of them were transformed into MG1655 E. coli cells, 5 ml of these cells were incubated for 16h at 37oC. After 16h, 200 uL of the overnight cultures were introduced into 1.8 ml of MOPS pH adjusted LB for the respective pH values indicated above. After 20 min at ambient conditions a 1ml aliquot was pelleted. The pellets were re-suspended in 100 ul Laemmli buffer and 15uL samples were then separated by SDS PAGE (12% acrylamide) and transferred to PVDF membrane followed by probing with anti-GFP antibody. Fig 1A - Shows the GFP production under the control of the PgadA and Fig 1B shows the GFP production under the control of the Pasr promoter both in varying pH conditions.
  
 
https://static.igem.org/mediawiki/parts/e/e1/GadA-asrpHgraph.png
 
https://static.igem.org/mediawiki/parts/e/e1/GadA-asrpHgraph.png
 +
 +
Figure 2: 96 well plate reader experiments. Full time frame showing trends in GFP per unit of absorbance over 20h. The two pH sensitive promoters cloned with downstream gfp were transformed into MG1655 E. coli cells, 5 ml of these cells were incubated for 16h at 37oC. After 16h, 200 ul of the overnight cultures were introduced into 1.8ml of MOPS pH adjusted LB for the respective pH values. 200 ul of each pH-cell buffered LB was transferred into each well. A negative control containing no cells and a negative control containing non-buffered fresh LB were also transferred in 200ul samples into the plate. Data represents the mean value of 3 repeat samples for each construct. Fig 2A - shows GFP fluorescence for PgadA-gfp and Fig 2B - shows GFP fluorescence for Pasr-gfp
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https://static.igem.org/mediawiki/parts/8/88/GadA-asrpHgraph2a.png
 
https://static.igem.org/mediawiki/parts/8/88/GadA-asrpHgraph2a.png
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 +
Figure 3: 96 well plate reader experiments. 16h time snap-shot out of the total 20h which can be seen in Fig 2. 16h was the average time of overnight cultures thus this would have been enough time for the cell growth to stabilize and adapt to the conditions. Fig 3A - shows GFP fluorescence for PgadA-gfp and Fig 3B - shows GFP fluorescence for Pasr-gfp
  
  

Latest revision as of 23:50, 29 October 2016


A pH Sensing Device Based on The Asr Promoter

The "acid shock RNA" asr promoter is a pH sensitive promoter native to E. coli that has been documented by other iGEM teams. Here, we present a composite part to allow further characterisation of promoter activity. The composite part consists of the asr promoter(BBa_K1231000) and a combined biobrick containing RBS / GFP / terminators (BBa_E0840).

•••••

Parts Collection 2016

This is part of a Part Collection of 18 BioBricks designed by Dundee iGEM 2016. This collection will be useful to teams working with toxins as we have submitted new toxins to the registry. Working with bacterial toxins is difficult due to the risk of toxicity to the chassis, so the corresponding immunity for our toxins were also submitted. We have also submitted these toxins lacking their cytotoxic domains replacing it with a multiple cloning site which will allow for different toxic domains to be fused at the C-terminus and thereby generating a synthetic toxin. In addition, there are three well-characterised promoters that can be used to initiate gene expression at various points in the digestive tract, to enable devices to function within a human or animal. Finally, a lysis cassette was constructed to lyse or burst cells, thus releasing the toxins and destroying the GM bacteria to prevent its release to the environment.

This BBa_K1962013 is for measuring gene expression in response to pH and is important for calibrating the synthetic system.



Usage and Biology

Enterobacteria can respond to low pH by de novo synthesis of specific proteins and altered levels of gene expression. The response to environmental stresses, such as pH, is often a complex mechanism and also depends on other environmental factors such as nutrition, the presence or absence of oxygen or starvation. The E. coli asr (acid shock RNA) gene encodes small RNA, of about 450 nucleotides in length. This gene is inducible by low external pH and contributes to the organism’s survival2. It has been suggested that asr genes may be regulated by the two component system PhoBR2.

In this two-component system the protons from the environment (H+) activate the sensory part (PhoR- in the periplasm) of the two-component system, which then transduces the signal to the activator protein- PhoB, which can bind promoter DNA of asr. The promoter region of asr was analysed and showed to contain a sequence similar to the pho-box; this is a consensus sequence able to bind to the PhoB protein2. These interactions of H+ from the external environment with this two-component system are thought to lead to asr transcription. Interestingly the PhoBR system also controls the pho regulon which is induced by phosphate starvation, the link between these two factors is not fully understood however, it has been suggested that the level of Asr expressed in minimal media is higher than in enriched media.


In 2013 the Northwestern iGEM team submitted two pH sensitive promoter Pasr (BBa_K1231000) and PgadA (BBa_K1231001). In order to further characterise both of these promoters we cloned gfp (BBa_E0840) downstream of both promoters. We then used this construct to measure and compare the GFP expression levels in response to different pH conditions.

We wanted to test both our pH sensitive promoters, Pasr and PgadA by monitoring for the production of GFP by western blotting. The western blots showed levels of GFP protein production by the cells at a range of pH values. In Fig 1A the expression of GFP at pH 5 is much higher than the other pH readings. This would indicate that at this pH the largest amount of GFP was being produced under the induction of the gadA promoter. The promoter is slightly leaky as there is also expression of protein within cells at other pH values. In Fig 1B the GFP protein expression under the regulation of Pasr can be seen, the range of activity for this promoter is much wider indicating that this promoter is leakier than PgadA. The level of expression of GFP under the regulation of Pasr appears to be uniform with only a slight increase in GFP at pH5.

We now wanted to be able to use a more quantitative approach to assign optimal promoter function conditions. To do this we used a 96 well plate reader to monitor GFP fluorescence and cell growth over the space of 20 hours. This experiment took obtained GFP fluorescence (excitation wavelength = 395nm and excitation wavelength = 509nm) and OD600nm values every 20 minutes yielding a large volume of data and more quantitative values for promoter function over 20 hours. To normalise flouresence measurements we used the following formula:

GFP / OD600nm = Fluorescence per unit absorbance

The data was then plotted to observe the trend over time as well as taking a snap shot at 16h. The data collected from the plate reader experiments showed a slight difference in optimal pH for the pH sensitive promoter asr, as can be seen in Fig 2B and 3B the maximal fluorescence observed from GFP fluorescence per unit of absorbance over time was at a pH range of 8. For PgadA we observed a coherent trend of optimal promoter function around pH5/pH6 as can be seen in Fig 2A and 3A.

GadA-asrresult1a.png

Fig 1. GFP production under the control of pH sensitive promoters PgadA and Pasr. Promoters with gfp cloned downstream of them were transformed into MG1655 E. coli cells, 5 ml of these cells were incubated for 16h at 37oC. After 16h, 200 uL of the overnight cultures were introduced into 1.8 ml of MOPS pH adjusted LB for the respective pH values indicated above. After 20 min at ambient conditions a 1ml aliquot was pelleted. The pellets were re-suspended in 100 ul Laemmli buffer and 15uL samples were then separated by SDS PAGE (12% acrylamide) and transferred to PVDF membrane followed by probing with anti-GFP antibody. Fig 1A - Shows the GFP production under the control of the PgadA and Fig 1B shows the GFP production under the control of the Pasr promoter both in varying pH conditions.

GadA-asrpHgraph.png

Figure 2: 96 well plate reader experiments. Full time frame showing trends in GFP per unit of absorbance over 20h. The two pH sensitive promoters cloned with downstream gfp were transformed into MG1655 E. coli cells, 5 ml of these cells were incubated for 16h at 37oC. After 16h, 200 ul of the overnight cultures were introduced into 1.8ml of MOPS pH adjusted LB for the respective pH values. 200 ul of each pH-cell buffered LB was transferred into each well. A negative control containing no cells and a negative control containing non-buffered fresh LB were also transferred in 200ul samples into the plate. Data represents the mean value of 3 repeat samples for each construct. Fig 2A - shows GFP fluorescence for PgadA-gfp and Fig 2B - shows GFP fluorescence for Pasr-gfp


GadA-asrpHgraph2a.png

Figure 3: 96 well plate reader experiments. 16h time snap-shot out of the total 20h which can be seen in Fig 2. 16h was the average time of overnight cultures thus this would have been enough time for the cell growth to stabilize and adapt to the conditions. Fig 3A - shows GFP fluorescence for PgadA-gfp and Fig 3B - shows GFP fluorescence for Pasr-gfp





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 BsaI.rc site found at 813