Difference between revisions of "Part:BBa K4583014"

(2. Characterization using GFP in 2-plasmids bacteria)
 
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==Late Stationary Phase Promoter==
 
==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.
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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 part <html><a href="https://parts.igem.org/Part:BBa_K4583000"> BBa_K4583000(PYU3)</a></html> is the promoter of the gene <em>orf-0464</em>. Its most notable feature is that it will be expressed in the late stationary phase. Moreover, it is a self-inducible promoter, which means that no additional inducers need 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>Late stationary phase promoter</strong>
 
* <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 PYU3===
+
There are 3 parts that have similar features characcterized by our team: <html> <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>
 +
 
 +
==Characterization==
 
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.
 
* 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.
 
* 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.
 
For plasmid construction methods and other experimental procedures, see the Design page.
====1. Protocols====
+
===Protocols===
 
Our experimental conditions for characterizing this part were as follows:
 
Our experimental conditions for characterizing this part were as follows:
 
* <em>E. coli</em> MG1655
 
* <em>E. coli</em> MG1655
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* Plasmid Backbone: PACYC
 
* Plasmid Backbone: PACYC
 
* Equipment: Multi-Detection Microplate Reader (Synergy HT, Biotek, U.S.) and Molecular Devices SpectraMax i3x.
 
* 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).
+
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-min). 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====
+
===Characterization using GFP in 2-plasmids bacteria===
In this section we used the PACYC plasmid with <html><a href="https://parts.igem.org/Part:BBa_K4583000"> BBa_K4583000(PYU3)</a></html> 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
+
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>
 
<html>
 
<figure>
 
<figure>
 
   <img src="https://static.igem.wiki/teams/4583/wiki/pacycpyu3.png"width="410" height="240">
 
   <img src="https://static.igem.wiki/teams/4583/wiki/pacycpyu3.png"width="410" height="240">
   <figcaption><b>Fig. 2 </b>. Genetic Circuit when characterizing PYU3 using GFP </figcaption>
+
   <figcaption><b>Fig. 1 </b>. Genetic Circuit when characterizing PYU3 using GFP </figcaption>
 
</figure>
 
</figure>
 
</html>
 
</html>
  
Only one combination showed significant differences in expression time and expression intensity (L31-PesaRp-PYU16).
+
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>
 
<html>
 
<figure>
 
<figure>
 
   <img src="https://static.igem.wiki/teams/4583/wiki/pesar-pyu3.png"width="700" height="390">
 
   <img src="https://static.igem.wiki/teams/4583/wiki/pesar-pyu3.png"width="700" height="390">
   <figcaption><b>Fig. 3 </b>. Characterization results of PYU3 in the 2-plasmid bacteria</figcaption>
+
   <figcaption><b>Fig. 2 </b>. Characterization results of PYU3 in the 2-plasmid bacteria</figcaption>
 
</figure>
 
</figure>
 
</html>
 
</html>
  
====3. Characterization using BFP in 3-plasmids bacteria====
+
===Characterization using BFP in 3-plasmids bacteria===
In this section, we used the PACYC plasmid with PYU7 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_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.
+
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>
 
<html>
 
<figure>
 
<figure>
   <img src="https://static.igem.wiki/teams/4583/wiki/pyu3bfp.png"width="410" height="240">
+
   <img src="https://static.igem.wiki/teams/4583/wiki/pacycpyu3bfp.png"width="410" height="240">
   <figcaption><b>Fig. 4 </b>. Genetic Circuit when characterizing PYU3 using BFP </figcaption>
+
   <figcaption><b>Fig. 3 </b>. Genetic Circuit when characterizing PYU3 using BFP </figcaption>
 
</figure>
 
</figure>
 
</html>
 
</html>
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).
+
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.
+
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>
 
<html>
 
<figure>
 
<figure>
   <img src="https://static.igem.wiki/teams/4583/wiki/pyu33plasmid.png"width="600" height="400">
+
   <img src="https://static.igem.wiki/teams/4583/wiki/pyu33plasmid.png"width="700" height="450">
   <figcaption><b>Fig. 5 </b>. Characterization results of PYU3 in the 3-plasmids bacteria</figcaption>
+
   <figcaption><b>Fig. 4 </b>. Characterization results of PYU3 in the 3-plasmids bacteria</figcaption>
 
</figure>
 
</figure>
 
</html>
 
</html>
 +
  
 
==Auto-lysis system==
 
==Auto-lysis system==
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K4583014 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4583014 SequenceAndFeatures</partinfo>
 
+
==Reference==
 
+
[1] Talukder, A A et al. “RpoS-dependent regulation of genes expressed at late stationary phase in Escherichia coli.” FEBS letters vol. 386,2-3 (1996): 177-80. doi:10.1016/0014-5793(96)00426-7
<!-- Uncomment this to enable Functional Parameter display
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===Functional Parameters===
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<partinfo>BBa_K4583014 parameters</partinfo>
+
<!-- -->
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Latest revision as of 18:58, 11 October 2023


PYU3-RBS(B0034)-SRRz

PYU3-RBS(B0034)-SRRz

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 part BBa_K4583000(PYU3) is the promoter of the gene orf-0464. Its most notable feature is that it will be expressed in the late stationary phase. Moreover, it is a self-inducible promoter, which means that no additional inducers need 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

There are 3 parts that have similar features characcterized by our team: BBa_K4583001(PYU7) , BBa_K4583003(PYU16), and BBa_K4583004(PYU92)

Characterization

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-min). 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 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

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 SRRz gene to the plasmid backbone we constructed by Gibson's method to obtain PACYC-PYU3-SRRz,PACYC-PYU7-SRRz,PACYC-PYU16-SRRz,PACYC-PYU92-SRRz plasmid(Fig. 3).

Fig. 6 . Plasmid construction
Fig. 7 . Lysis effect of SRRz gene
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.

Due to time and effort constraints, we did not succeed in constructing all plasmids. The strain that we successfully construct are as follows:

\
No. Strains Backbone Promoter RBS Lysis gene
1 L19 PACYC PYU3 B0031 SRRz
2 L19 PACYC PYU3 B0032 SRRz
3 L19 PACYC PYU16 B0031 SRRz
4 L19 PACYC PYU16 B0034 SRRz
5 L31 PACYC PYU92 B0031 SRRz
6 L31 PACYC PYU92 B0032 SRRz
7 L31 PACYC PYU92 B0034 SRRz

We then proceeded to characterise these strains by placing them in Multi-Detection Microplate Reader (Synergy HT, Biotek, U.S.) to determine the OD600. We found that only two combinations were able to reduce their OD600 values.

Analysis of our results

Although we have only been able to prove the effectiveness of two systems (PesaS-B0034-PYU16-B0034-SRRz and PesaS-B0034-PYU92-B0034-SRRz ), we have learned a lot from them. During culturing a large amount of cellular debris is produced using the lysis system. This can interfere with the detection of OD600. This is probably why most systems "don't work": the debris blocks the light path and the OD600 does not reflect the number of viable bacteria.We propose several possible solutions.

  • Enumeration by live cell counting other than OD600.
  • Counting by spread plate method.
  • Allow the solution to stand for a period of time (15-30 min) and then collect the supernatant to measure OD600. The data obtained will be different from the true value but may reflect the lysis situation.

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]

Reference

[1] Talukder, A A et al. “RpoS-dependent regulation of genes expressed at late stationary phase in Escherichia coli.” FEBS letters vol. 386,2-3 (1996): 177-80. doi:10.1016/0014-5793(96)00426-7