Difference between revisions of "Part:BBa K4583058"
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* <strong>Self-inducible promoter without additional inducers</strong>
 
* <strong>Self-inducible promoter without additional inducers</strong>
 
* <strong>Biosafety</strong>
 
* <strong>Biosafety</strong>
−
===Characterization of Late Stationary Phase Promoter PYU7 ===
+
===Characterization of Late Stationary Phase Promoter PYU16 ===
 
Our characterization of this part is divided into two main parts.
 
Our characterization of this part is divided into two main parts.
 
* First, this promoter was placed upstream of<em> GFP </em>gene, forming a genetic circuit as shown in Fig. 1. This plasmid was transformed into a bacterium containing another plasmid for characterization. Green and red fluorescence were measured at fixed intervals to compare the expression time and intensity of the two.
 
* First, this promoter was placed upstream of<em> GFP </em>gene, forming a genetic circuit as shown in Fig. 1. This plasmid was transformed into a bacterium containing another plasmid for characterization. Green and red fluorescence were measured at fixed intervals to compare the expression time and intensity of the two.
Line 65: Line 65:
 
   <img src="https://static.igem.wiki/teams/4583/wiki/pesas-pyu16.png"width="300" height="190">
 
   <img src="https://static.igem.wiki/teams/4583/wiki/pesas-pyu16.png"width="300" height="190">
 
   <figcaption><b>Fig. 4 </b>. Characterization results of PYU16 in the 3-plasmids bacteria</figcaption>
 
   <figcaption><b>Fig. 4 </b>. Characterization results of PYU16 in the 3-plasmids bacteria</figcaption>
 +
</figure>
 +
</html>
 +
==Usage==
 +
We designed a auto-lysis system based on this part. The auto-lysis system will express at the late stationary phase and peaks at about 40h.
 +
<html>
 +
<figure>
 +
  <img src="https://static.igem.wiki/teams/4583/wiki/e-lysis.png"width="540" height="210">
 +
  <figcaption><b>Fig. 1 </b>. Genetic circuit of  auto-lysis system based on phi X 174 <i>E</i> gene</figcaption>
 
</figure>
 
</figure>
 
</html>
 
</html>
  
 +
==Late Stationary Phase Promoter==
 +
When the bacteria enter the stationary phase, the physiological state of the bacteria changes significantly. During this phase, many genes will respond to make timely adjustments. This 4 parts <html><a href="https://parts.igem.org/Part:BBa_K4583000">BBa_K4583000 (PYU3)</a>, <a href="https://parts.igem.org/Part:BBa_K4583001">BBa_K4583001 (PYU7)</a>, <a href="https://parts.igem.org/Part:BBa_K4583003">BBa_K4583003 (PYU16)</a>, and <a href="https://parts.igem.org/Part:BBa_K4583004">BBa_K4583004 (PYU92)</a></html> are the promoters of <i>E. coil</i>. Their most notable feature is that they will express in the late stationary phase. Moreover, they are self-inducible promoters, which means that no additional inducers are needed to be added for expression. Exogenous inducers are expensive and need to be added artificially, whereas self-induced promoters are cost-effective and relatively stable. This part is also very safe because it comes from E. coli MG1655, a commonly engineered bacterium.
 +
* <strong>Late stationary phase promoter</strong>
 +
* <strong>Self-inducible promoter without additional inducers</strong>
 +
* <strong>Biosafety</strong>
 +
===Characterization of Late Stationary Phase Promoter PYU3 (an example)===
 +
<strong>You can found the results of other 3 promoters in their own page</strong>
 +
Our characterization of this part is divided into two main parts.
 +
* First, this promoter was placed upstream of<em> GFP </em>gene, forming a genetic circuit as shown in Fig. 1. This plasmid was transformed into a bacterium containing another plasmid for characterization. Green and red fluorescence were measured at fixed intervals to compare the expression time and intensity of the two.
 +
* Second, this promoter was placed upstream of the <em> BFP </em> gene, forming a genetic circuit as shown in Fig. 3. This plasmid was then transformed into bacteria containing two other plasmids. Green, red and blue fluorescence were measured at fixed time intervals to compare the difference in expression time and intensity between this part and the other two parts.
 +
For plasmid construction methods and other experimental procedures, see the Design page.
 +
====1. Protocols====
 +
Our experimental conditions for characterizing this part were as follows:
 +
* <em>E. coli</em> MG1655
 +
* 30<sup>o</sup>C, 48h,  under vigorous shaking
 +
* Plasmid Backbone: PACYC
 +
* Equipment: Multi-Detection Microplate Reader (Synergy HT, Biotek, U.S.) and Molecular Devices SpectraMax i3x.
 +
We used GFP (excitation at 485 nm and emission at 528 nm)and BFP (excitation at 400 nm and emission at 450 nm) to characterize this part. As our focus was mainly on the expression time, we processed the obtained fluorescence data by means of the following equation: x'=(x-min)/(max-x). This treatment makes all data fall between 0 and 1, which is easier to use for comparisons between different fluorescence data (since our focus is on expression time).
 +
 +
====2. Characterization using GFP in 2-plasmids bacteria====
 +
In this section we used the PACYC plasmid with PYU3 upstream of <em>GFP</em> gene(Fig. 1).  We transformed it into L19 and L31 with <html><a href="https://parts.igem.org/Part:BBa_K4583009"> BBa_K4583009(PesaRwt)</a>, <a href="https://parts.igem.org/Part:BBa_K4583010"> BBa_K4583010(PesaRc)</a>, <a href="https://parts.igem.org/Part:BBa_K4583011"> BBa_K4583011(PesaRp)</a></html> plasmids respectively (6 combinations in total) and characterized them using 24-well plates.  The characterization results are shown in Fig. 2
 +
 +
<html>
 +
<figure>
 +
  <img src="https://static.igem.wiki/teams/4583/wiki/pacycpyu3.png"width="410" height="240">
 +
  <figcaption><b>Fig. 1 </b>. Genetic Circuit when characterizing PYU3 using GFP </figcaption>
 +
</figure>
 +
</html>
 +
 +
As can be seen from the characterization results, with the exception of three combinations (L19-PesaRp-PYU3, L31-PesaRc-PYU3, and L31-PesaRp-PYU3) the expression time of this element is significantly different from that of the other element in terms of time and intensity.
 +
 +
In the case of the combination L19-PesaRwt-PYU3, for example, the expression of the other part peaked at about 12 h, whereas the expression of this part peaked at about 38 h. The expression of the other part peaked at about 12 h, whereas the expression of this part peaked at about 38 h.
 +
 +
<html>
 +
<figure>
 +
  <img src="https://static.igem.wiki/teams/4583/wiki/pyu3p.png"width="700" height="390">
 +
  <figcaption><b>Fig. 2 </b>. Characterization results of PYU3 in the 2-plasmid bacteria</figcaption>
 +
</figure>
 +
</html>
 +
 +
====3. Characterization using BFP in 3-plasmids bacteria====
 +
In this section, we used the PACYC plasmid with PYU3 upstream of the <em>BFP</em> gene (Fig. 3). Based on the results of the last Characterization, we transformed it into L19 and L31 with  <html><a href="https://parts.igem.org/Part:BBa_K4583009"> BBa_K4583009(PesaRwt)</a>, <a href="https://parts.igem.org/Part:BBa_K4583010"> BBa_K4583010(PesaRc)</a>, <a href="https://parts.igem.org/Part:BBa_K4583011"> BBa_K4583011(PesaRp)</a></html> and <html><a href="https://parts.igem.org/Part:BBa_K4583012"> BBa_K4583012(PesaS)</a> plasmid respectively (4 combinations in total) and characterized them using 24-well plates. The characterization results are shown in Fig. 4.
 +
<html>
 +
<figure>
 +
  <img src="https://static.igem.wiki/teams/4583/wiki/pacycpyu3bfp.png"width="410" height="240">
 +
  <figcaption><b>Fig. 3 </b>. Genetic Circuit when characterizing PYU3 using BFP </figcaption>
 +
</figure>
 +
</html>
 +
From the characterization results, we can see that there is a significant delay in the expression of this part from the other promoters. PYU3 is expressed at the stationary phase and peaks at the late stationary phase.
 +
We found roughly the same results for both characterizations, but with slightly different onset times. This may be related to the instrumentation used.For this characterization, we used a Molecular Devices SpectraMax i3x, which has a much higher precision. In addition, the difference between the 2-plasmids system and the 3-plasmids system may also account for the difference.
 +
<html>
 +
<figure>
 +
  <img src="https://static.igem.wiki/teams/4583/wiki/pyu33plasmid.png"width="700" height="450">
 +
  <figcaption><b>Fig. 4 </b>. Characterization results of PYU3 in the 3-plasmids bacteria</figcaption>
 +
</figure>
 +
</html>
 +
 +
==Auto-lysis system==
 +
We ligated the E gene to the plasmid backbone we constructed by Gibson's method to obtain PACYC-PYU3-E,PACYC-PYU3-E,PACYC-PYU3-E,PACYC-PYU3-E,PACYC-PYU92-E plasmid(Fig. 3).
 +
<html>
 +
<figure>
 +
  <img src="https://static.igem.wiki/teams/4583/wiki/e-lysis-2.png"width="540" height="210">
 +
  <figcaption><b>Fig. 2 </b>. Plasmid construction </figcaption>
 +
</figure>
 +
</html>
 +
In order to enhance its lysis effect in L19 and L31 strains, we decided to do so by increasing the RBS of the promoters of PYU3,PYU7,PYU16. We added RBS named B0031,B0032,B0033,B0034 with four different intensity gradients with RBS intensity of 0.01,0.07,0.3,1. A second experiment was performed.
 +
<html>
 +
<figure>
 +
  <img src="https://static.igem.wiki/teams/4583/wiki/e-lysis-2.png"width="540" height="210">
 +
  <figcaption><b>Fig. 3 </b>. Adding RBS on the down stream of promoter</figcaption>
 +
</figure>
 +
</html>
 +
We succeeded in building the system, but failed to successfully validate it. Our speculation is that PYU3, PYU7, PYU16 and PYU92 are not expressed strongly enough. Our next plan is to replace the stronger RBS.
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
 
===Usage and Biology===
 
===Usage and Biology===

Revision as of 19:12, 11 October 2023


PYU16-RBS(B0034)-E

PYU16-RBS(B0034)-E

Usage

We designed a auto-lysis system based on this part. The auto-lysis system will express at the late stationary phase and peaks at about 40h.

Fig. 1 . Genetic circuit of auto-lysis system based on phi X 174 E gene

Late Stationary Phase Promoter

When the bacteria enter the stationary phase, the physiological state of the bacteria changes significantly. During this phase, many genes will respond to make timely adjustments. This 4 parts BBa_K4583000 (PYU3), BBa_K4583001 (PYU7), BBa_K4583003 (PYU16), and BBa_K4583004 (PYU92) are the promoters of E. coil. Their most notable feature is that they will express in the late stationary phase. Moreover, they are self-inducible promoters, which means that no additional inducers are needed to be added for expression. Exogenous inducers are expensive and need to be added artificially, whereas self-induced promoters are cost-effective and relatively stable. This part is also very safe because it comes from E. coli MG1655, a commonly engineered bacterium.

  • Late stationary phase promoter
  • Self-inducible promoter without additional inducers
  • Biosafety

Characterization of Late Stationary Phase Promoter PYU16

Our characterization of this part is divided into two main parts.

  • First, this promoter was placed upstream of GFP gene, forming a genetic circuit as shown in Fig. 1. This plasmid was transformed into a bacterium containing another plasmid for characterization. Green and red fluorescence were measured at fixed intervals to compare the expression time and intensity of the two.
  • Second, this promoter was placed upstream of the BFP gene, forming a genetic circuit as shown in Fig. 3. This plasmid was then transformed into bacteria containing two other plasmids. Green, red and blue fluorescence were measured at fixed time intervals to compare the difference in expression time and intensity between this part and the other two parts.

For plasmid construction methods and other experimental procedures, see the Design page.

Protocols

Our experimental conditions for characterizing this part were as follows:

  • E. coli MG1655
  • 30oC, 48h, under vigorous shaking
  • Plasmid Backbone: PACYC
  • Equipment: Multi-Detection Microplate Reader (Synergy HT, Biotek, U.S.) and Molecular Devices SpectraMax i3x.

We used GFP (excitation at 485 nm and emission at 528 nm)and BFP (excitation at 400 nm and emission at 450 nm) to characterize this part. As our focus was mainly on the expression time, we processed the obtained fluorescence data by means of the following equation: x'=(x-min)/(max-x). This treatment makes all data fall between 0 and 1, which is easier to use for comparisons between different fluorescence data (since our focus is on expression time).

Characterization using GFP in 2-plasmids bacteria

In this section we used the PACYC plasmid with BBa_K4583003(PYU16) upstream of GFP gene(Fig. 1). We transformed it into L19 and L31 with BBa_K4583009(PesaRwt), BBa_K4583010(PesaRc), BBa_K4583011(PesaRp) plasmids respectively (6 combinations in total) and characterized them using 24-well plates. The characterization results are shown in Fig. 2

Fig. 1 . Genetic Circuit when characterizing PYU16 using GFP

Only one combination showed significant differences in expression time and expression intensity (L31-PesaRp-PYU16).

Fig. 2 . Characterization results of PYU16 in the 2-plasmid bacteria

Characterization using BFP in 3-plasmids bacteria

In this section, we used the PACYC plasmid with PYU7 upstream of the BFP gene (Fig. 3). Based on the results of the last Characterization, we transformed it into L19 and L31 with BBa_K4583011(PesaRp) and BBa_K4583012(PesaS) plasmid respectively (4 combinations in total) and characterized them using 24-well plates. The characterization results are shown in Fig. 4.

Fig. 3 . Genetic Circuit when characterizing PYU16 using BFP
From the characterization results, we can see that there is a significant delay in the expression of this part from the other promoters. PYU16 is expressed at the stationary phase and peaks at the late stationary phase (42h). We found roughly the same results for both characterizations, but with slightly different onset times. This may be related to the instrumentation used. For this characterization, we used a Molecular Devices SpectraMax i3x, which has a much higher precision. In addition, the difference between the 2-plasmids system and the 3-plasmids system may also account for the difference.
Fig. 4 . Characterization results of PYU16 in the 3-plasmids bacteria

Usage

We designed a auto-lysis system based on this part. The auto-lysis system will express at the late stationary phase and peaks at about 40h.

Fig. 1 . Genetic circuit of auto-lysis system based on phi X 174 E gene

Late Stationary Phase Promoter

When the bacteria enter the stationary phase, the physiological state of the bacteria changes significantly. During this phase, many genes will respond to make timely adjustments. This 4 parts BBa_K4583000 (PYU3), BBa_K4583001 (PYU7), BBa_K4583003 (PYU16), and BBa_K4583004 (PYU92) are the promoters of E. coil. Their most notable feature is that they will express in the late stationary phase. Moreover, they are self-inducible promoters, which means that no additional inducers are needed to be added for expression. Exogenous inducers are expensive and need to be added artificially, whereas self-induced promoters are cost-effective and relatively stable. This part is also very safe because it comes from E. coli MG1655, a commonly engineered bacterium.

  • Late stationary phase promoter
  • Self-inducible promoter without additional inducers
  • Biosafety

Characterization of Late Stationary Phase Promoter PYU3 (an example)

You can found the results of other 3 promoters in their own page Our characterization of this part is divided into two main parts.

  • First, this promoter was placed upstream of GFP gene, forming a genetic circuit as shown in Fig. 1. This plasmid was transformed into a bacterium containing another plasmid for characterization. Green and red fluorescence were measured at fixed intervals to compare the expression time and intensity of the two.
  • Second, this promoter was placed upstream of the BFP gene, forming a genetic circuit as shown in Fig. 3. This plasmid was then transformed into bacteria containing two other plasmids. Green, red and blue fluorescence were measured at fixed time intervals to compare the difference in expression time and intensity between this part and the other two parts.

For plasmid construction methods and other experimental procedures, see the Design page.

1. Protocols

Our experimental conditions for characterizing this part were as follows:

  • E. coli MG1655
  • 30oC, 48h, under vigorous shaking
  • Plasmid Backbone: PACYC
  • Equipment: Multi-Detection Microplate Reader (Synergy HT, Biotek, U.S.) and Molecular Devices SpectraMax i3x.

We used GFP (excitation at 485 nm and emission at 528 nm)and BFP (excitation at 400 nm and emission at 450 nm) to characterize this part. As our focus was mainly on the expression time, we processed the obtained fluorescence data by means of the following equation: x'=(x-min)/(max-x). This treatment makes all data fall between 0 and 1, which is easier to use for comparisons between different fluorescence data (since our focus is on expression time).

2. Characterization using GFP in 2-plasmids bacteria

In this section we used the PACYC plasmid with PYU3 upstream of GFP gene(Fig. 1). We transformed it into L19 and L31 with BBa_K4583009(PesaRwt), BBa_K4583010(PesaRc), BBa_K4583011(PesaRp) plasmids respectively (6 combinations in total) and characterized them using 24-well plates. The characterization results are shown in Fig. 2

Fig. 1 . Genetic Circuit when characterizing PYU3 using GFP

As can be seen from the characterization results, with the exception of three combinations (L19-PesaRp-PYU3, L31-PesaRc-PYU3, and L31-PesaRp-PYU3) the expression time of this element is significantly different from that of the other element in terms of time and intensity.

In the case of the combination L19-PesaRwt-PYU3, for example, the expression of the other part peaked at about 12 h, whereas the expression of this part peaked at about 38 h. The expression of the other part peaked at about 12 h, whereas the expression of this part peaked at about 38 h.

Fig. 2 . Characterization results of PYU3 in the 2-plasmid bacteria

3. Characterization using BFP in 3-plasmids bacteria

In this section, we used the PACYC plasmid with PYU3 upstream of the BFP gene (Fig. 3). Based on the results of the last Characterization, we transformed it into L19 and L31 with BBa_K4583009(PesaRwt), BBa_K4583010(PesaRc), BBa_K4583011(PesaRp) and BBa_K4583012(PesaS) plasmid respectively (4 combinations in total) and characterized them using 24-well plates. The characterization results are shown in Fig. 4.

Fig. 3 . Genetic Circuit when characterizing PYU3 using BFP
From the characterization results, we can see that there is a significant delay in the expression of this part from the other promoters. PYU3 is expressed at the stationary phase and peaks at the late stationary phase. We found roughly the same results for both characterizations, but with slightly different onset times. This may be related to the instrumentation used.For this characterization, we used a Molecular Devices SpectraMax i3x, which has a much higher precision. In addition, the difference between the 2-plasmids system and the 3-plasmids system may also account for the difference.
Fig. 4 . Characterization results of PYU3 in the 3-plasmids bacteria

Auto-lysis system

We ligated the E gene to the plasmid backbone we constructed by Gibson's method to obtain PACYC-PYU3-E,PACYC-PYU3-E,PACYC-PYU3-E,PACYC-PYU3-E,PACYC-PYU92-E plasmid(Fig. 3).

Fig. 2 . Plasmid construction
In order to enhance its lysis effect in L19 and L31 strains, we decided to do so by increasing the RBS of the promoters of PYU3,PYU7,PYU16. We added RBS named B0031,B0032,B0033,B0034 with four different intensity gradients with RBS intensity of 0.01,0.07,0.3,1. A second experiment was performed.
Fig. 3 . Adding RBS on the down stream of promoter
We succeeded in building the system, but failed to successfully validate it. Our speculation is that PYU3, PYU7, PYU16 and PYU92 are not expressed strongly enough. Our next plan is to replace the stronger RBS. 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]