Difference between revisions of "Part:BBa K4907021"

Latest revision as of 05:23, 12 October 2023

hrpR

Biology

This part codes for HrpR protein. HrpR protein binds to HrpS protein coded by hrpS (BBa_K4907022) forming a complex and then triggering the transcription of pHrpL(BBa_K4907019). pHrpL is the promoter of HrpL, which is an extracytoplasmic sigma factor regulating the expression of type III secretion system (T3SS) from Pseudomonas syringae pv. tomato DC3000, a plant pathogenic gram-negative bacterium. Specifically, it employs the T3SS to cause disease in tomatoes and Arabidopsis and to induce the hypersensitive response in nonhost plants. Expression of HrpL is controlled by transcriptional activators HrpR and HrpS (1). The pHrpL will not be activated by HrpR or HrpS alone. But when both HrpR and HrpS exist, they can form a complex that activates the pHrpL and induces the expression of downstream genes. This functions like an AND logic gate (2).

Usage and design

To prove the hrp AND gate can work. We used BBa_I0500 to construct the regulation system and obtained the composite part BBa_K4907124 and BBa_K4907125, which were assembled on the expression vector pSB1C3. And we used the pHrpL and GFP(BBa_K4907036) to construct the reporting system and obtained the composite part BBa_K4907123. Those three composite parts together form the verification system of hrp AND gate (Fig. 1) and corresponding gene circuits were transformed into E. coli DH10β for characterization.

Fig. 1 Gene circuits of verification system for hrp AND gate.

If we use CspA Cold-responsive elements to express proteins at low temperatures, there will be a risk of gene leakage at a higher temperature than we expected because the response temperature has a broad range. To solve this problem, we plan to combine a logic AND gate with the CspA CRE. Based on it, we designed an AND gate to respond to low temperature, namely, hrp AND gate. In this system, the hrpR and hrpS genes are regulated by the CspA CRE (Fig. 2). Under low-temperature conditions, only when both proteins are expressed, can the expression of downstream genes be induced, reducing the leaky expression.

Fig. 2 Gene circuits of hrp system regulated by the CspA CRE.

Characterization

Agarose gel electrophoresis (AGE)

When constructing this circuit of composite part BBa_K4907128 which includes the gene of HrpR, colony PCR and gene sequencing were used to verify that the transformants were correct. Target bands (1460 bp) can be observed at the position between 1000 and 1500 bp (Fig. 3).

Fig. 3 DNA gel electrophoresis of the colony PCR products of BBa_K4907128_pSB1C3.

Dual-plasmid system transformation

We used dual-plasmid system transformation to prove the hrp AND gate. One control and three experimental groups were set up. For R+S group, Plasmid BBa_K4907123_pSB3K3 and plasmid BBa_K4907126_pSB1C3 were transformed into E. coli DH10β which can express HrpR and HrpS. For the remaining two experimental groups, each can only express one of HrpR (BBa_K4907021) and HrpS (BBa_K4907022). As for the control, Plasmid BBa_BBa_K4907123_pSB3K3 and plasmid BBa_BBa_I0500_pSB1C3 were transformed into E. coli DH10β. The positive transformants were selected by kanamycin and chloramphenicol.

Fluorescence measurement

Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of GFP is observed by measuring the GFP Fluorescence/OD600 using microplate reader (Fig. 4). The results of fluorescence showed that the pHrpL will be activated when HrpR and HrpS are both expressed, but it will not be activated by HrpR or HrpS (BBa_K4907022) alone.

Fig. 4 The results of GFP Fluorescence/OD₆₀₀ to verify that hrp AND Gate can work.

Reference

1. M. Jovanovic, E. Lawton, J. Schumacher, M. Buck, Interplay among Pseudomonas syringae HrpR, HrpS and HrpV proteins for regulation of the type III secretion system. Fems Microbiology Letters 356, 201-211 (2014).
2. B. Wang, R. I. Kitney, N. Joly, M. Buck, Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nature Communications 2, 508 (2011).

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]

@@ Line 4: / Line 4: @@
 ===Biology===
-This part codes for HrpR protein. HrpR protein binds to HrpS protein coded by <i>hrpS</i> (<partinfo>BBa_K4907022</partinfo>) forming a complex and then triggering the transcription of hrpL promoter(<partinfo>BBa_K4907019</partinfo>). P<sub><i>hrpL</i></sub> is the promoter of HrpL, which is an extracytoplasmic sigma factor regulating the expression of type III secretion system (T3SS) from <i>Pseudomonas syringae</i> pv. <i>tomato</i> DC3000, a plant pathogenic gram-negative bacterium. Specifically, it employs the T3SS to cause disease in tomato and Arabidopsis and to induce the hypersensitive response in nonhost plants. Expression of HrpL is controlled by transcriptional activators HrpR and HrpS (1). The <i>hrpL</i> promoter will not be activated by HrpR or HrpS alone. But when both HrpR and HrpS exist, they can form a complex that activates the hrpL promoter and induces expression of downstream gene. This functions like an AND logic gate (2).
+This part codes for HrpR protein. HrpR protein binds to HrpS protein coded by <i>hrpS</i> (<partinfo>BBa_K4907022</partinfo>) forming a complex and then triggering the transcription of pHrpL(<partinfo>BBa_K4907019</partinfo>). pHrpL is the promoter of HrpL, which is an extracytoplasmic sigma factor regulating the expression of type III secretion system (T3SS) from <i>Pseudomonas syringae</i> pv. <i>tomato</i> DC3000, a plant pathogenic gram-negative bacterium. Specifically, it employs the T3SS to cause disease in tomatoes and Arabidopsis and to induce the hypersensitive response in nonhost plants. Expression of HrpL is controlled by transcriptional activators HrpR and HrpS (1). The pHrpL will not be activated by HrpR or HrpS alone. But when both HrpR and HrpS exist, they can form a complex that activates the pHrpL and induces the expression of downstream genes. This functions like an AND logic gate (2).
 ===Usage and design===
-To prove the hrp AND gate can work. We used <partinfo>BBa_I0500</partinfo> to construct the regulation system and obtained the composite part <partinfo>BBa_K4907124</partinfo> and <partinfo>BBa_K4907125</partinfo>, which were assembled on the expression vector pSB1C3. And we used the hrpL promoter and GFP(<partinfo>BBa_K4907036</partinfo>) to construct the reporting system and obtained the composite part <partinfo>BBa_K4907123</partinfo>. Those three composite parts together form the verification system of <i>hrp</i> AND gate (Fig. 1) and corresponding gene circuits were transformed into <i>E. coli</i> DH10β for characterization.
+To prove the <i>hrp</i> AND gate can work. We used <partinfo>BBa_I0500</partinfo> to construct the regulation system and obtained the composite part <partinfo>BBa_K4907124</partinfo> and <partinfo>BBa_K4907125</partinfo>, which were assembled on the expression vector pSB1C3. And we used the pHrpL and GFP(<partinfo>BBa_K4907036</partinfo>) to construct the reporting system and obtained the composite part <partinfo>BBa_K4907123</partinfo>. Those three composite parts together form the verification system of <i>hrp</i> AND gate (Fig. 1) and corresponding gene circuits were transformed into <i>E. coli</i> DH10β for characterization.
 <center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/and-gate.png" width="700px"></html></center>
 <center><b>Fig. 1 Gene circuits of verification system for <i>hrp</i> AND gate. </b></center>
-<br/>If we use CspA Cold-responsive elements to express proteins at low temperature, there will be a risk of gene leakage at a higher temperature than we expected because the response temperature of it has a broad range. To solve this problem, we plan to combine a logic AND gate with the CspA CRE. Based on it, we designed an AND gate to respond to low temperature, namely, <i>hrp</i> AND gate. In this system, the <i>hrpR</i> and <i>hrpS</i> genes are regulated by the CspA CRE (Fig. 2). Under low-temperature conditions, only when both proteins are expressed, then can the expression of downstream genes be induced, reducing the leaky expression.
+<br/>If we use CspA Cold-responsive elements to express proteins at low temperatures, there will be a risk of gene leakage at a higher temperature than we expected because the response temperature has a broad range. To solve this problem, we plan to combine a logic AND gate with the CspA CRE. Based on it, we designed an AND gate to respond to low temperature, namely, <i>hrp</i> AND gate. In this system, the <i>hrpR</i> and <i>hrpS</i> genes are regulated by the CspA CRE (Fig. 2). Under low-temperature conditions, only when both proteins are expressed, can the expression of downstream genes be induced, reducing the leaky expression.
-<center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/cspa-and-gate-new.png" width="700px"></html></center>
+<center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/cspa-and-gate.png" width="700px"></html></center>
 <center><b>Fig. 2 Gene circuits of <i>hrp</i> system regulated by the CspA CRE.</b></center>
 ===Characterization===
-====Double transformation====
+====Agarose gel electrophoresis (AGE)====
-we cloned composite part <partinfo>BBa_K4907124</partinfo> which includes hrpR into the vector pSB1C3. We used double transformation to prove the <i>hrp</i> AND gate. One control and three experimental groups were set up. For R+S group, Plasmid BBa_K4907123_pSB3K3 and plasmid BBa_K4907126_pSB1C3 were transformed into <i>E. coli</i> DH10β which can express HrpR and HrpS. For the remaining two experimental groups, each can only express one of HrpR and HrpS (<partinfo>BBa_K4907022</partinfo>). As for the control, Plasmid BBa_K4907123_pSB3K3 and plasmid BBa_I0500_pSB1C3 were transformed into <i>E. coli</i> DH10β. The positive transformants were selected by kanamycin and chloramphenicol.
+When constructing this circuit of composite part <partinfo>BBa_K4907128</partinfo> which includes the gene of HrpR, colony PCR and gene sequencing were used to verify that the transformants were correct. Target bands (1460 bp) can be observed at the position between 1000 and 1500 bp (Fig. 3).
+<center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/bba-k4907128-hrpr.png" width="400px"></html></center>
+<center><b>Fig. 3 DNA gel electrophoresis of the colony PCR products of BBa_K4907128_pSB1C3.</b></center>
+====Dual-plasmid system transformation====
+We used dual-plasmid system transformation to prove the <i>hrp</i> AND gate. One control and three experimental groups were set up. For R+S group, Plasmid BBa_K4907123_pSB3K3 and plasmid BBa_K4907126_pSB1C3 were transformed into <i>E. coli</i> DH10β which can express HrpR and HrpS. For the remaining two experimental groups, each can only express one of HrpR (<partinfo>BBa_K4907021</partinfo>) and HrpS (<partinfo>BBa_K4907022</partinfo>). As for the control, Plasmid BBa_<partinfo>K4907123</partinfo>_pSB3K3 and plasmid BBa_<partinfo>I0500</partinfo>_pSB1C3 were transformed into <i>E. coli</i> DH10β. The positive transformants were selected by kanamycin and chloramphenicol.
 ====Fluorescence measurement====
-Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of GFP is observed by measuring the GFP Fluorescence/OD600 using microplate reader (Fig. 3).The results of fluorescence showed that the P<sub><i>hrpL</i></sub> will be activated when HrpR and HrpS are both expressed, but it will not be activated by HrpR or HrpS (BBa_K4907022) alone.
+Colonies harboring the correct plasmid were cultivated and induced. The expression behavior of GFP is observed by measuring the GFP Fluorescence/OD600 using microplate reader (Fig. 4). The results of fluorescence showed that the pHrpL will be activated when HrpR and HrpS are both expressed, but it will not be activated by HrpR or HrpS (BBa_K4907022) alone.
-<center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/hrp-system.png" width="400px"></html></center>
+<center><html><img src="https://static.igem.wiki/teams/4907/wiki/parts/haoxihuan/hrp-syetem-rfu.png" width="300px"></html></center>
-<center><b>Fig. 3 The results of immunofluorescence to verify that <i>hrp</i> AND Gate can work.</b></center>
+<center><b>Fig. 4 The results of GFP Fluorescence/OD<sub>600</sub> to verify that <i>hrp</i> AND Gate can work.</b></center>
 ===Reference===
-.	M. Jovanovic, E. Lawton, J. Schumacher, M. Buck, Interplay among Pseudomonas syringae HrpR, HrpS and HrpV proteins for regulation of the type III secretion system. <i>Fems Microbiology Letters</i> <b>356</b>, 201-211 (2014).
+.	M. Jovanovic, E. Lawton, J. Schumacher, M. Buck, Interplay among <i>Pseudomonas syringae</i> HrpR, HrpS and HrpV proteins for regulation of the type III secretion system. <i>Fems Microbiology Letters</i> <b>356</b>, 201-211 (2014).
 <br/>2.	B. Wang, R. I. Kitney, N. Joly, M. Buck, Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. <i>Nature Communications</i><b> 2</b>, 508 (2011).