Team:Heidelberg/Notebook/Sensing Group/Cloning

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Sensing - Cloning strategy

The core part of the sensing project was the construction of the LuxQ-Tar chimeric receptor, which enables the E. coli killer bacteria to chemotactically respond to a Autoinducer 2 (AI-2) gradient and detect prey cells. The quorum-sensing system was amplified from the V. harveyi genome while the Tar receptor is from E. coli. On one hand LuxS needed to be cloned and transformed into one cell type, in order to make them produce and secrete AI-2. On the other hand the periplasmic ligand binding domain of LuxQ was fused with the cytoplasmic domain of Tar and cloned on one plasmid together with LuxP which is necessary for AI-2 binding. Generally, restriction sites required for cloning were introduced via the PCR primer. In silico cloning was performed in SerialCloner, Vector maps were designed with PlasMapper [1]. The sequenecs of used primers can be found in the Materials & Methods section. [back]

pTrc99a for LuxS and LuxQ cloning

pDK48 for cloning of fusion

pBAD33 used in Swarm-Assays

LuxS

LuxS was amplified from the Vibrio harveyi genome using the following primers: LuxSa (forward) and LuxSb (reverse). Subsequently, the product was cloned into the plasmid pTr99alpha using the NcoI and BamHI restriction sites and then transformed into DH5alpha competent cells. [back]

LuxQ

LuxQ was amplfied with primers LuxQa (forward) and LuxQc (reverse) from the V. harveyi genome. The obtained fragment was then cloned into the plasmid pTrc99alpha using the NcoI and BamHI restriction sites. Subsequently, the product was used as a template for PCR amplification with respect to cloning of the chimeric receptors (see below). [back]

LuxP

LuxP was amplified with primers LuxPc (forward) and LuxPd (reverse) from the V. harveyi genome. The PCR product was then cloned into the vector pDK48 containing the LuxQ-Tar chimeric receptor sequence. This was done using the restriction sites SalI and NotI. The resulting expression plasmid was used for the transformation of our killer cells. [back]

Fusion receptor

A detailed description of the Tar receptor and LuxQ quorum-sensing receptor can be found in the project description. Since it is believed that the linker region (transmembrane domain TM2) is critical for signal transduction, two different receptor constructs were designed, referred to as Fusion-1 and Fusion-2. Fusion-1 contained the cytoplasmic domain of Tar (residues 225-564) and the transmembrane domain,TM2 up to the N-terminus of LuxQ (residues 1-298). Fusion-2 contained the cytoplasmic domain as well as the second transmembrane domain, TM2 of Tar (residues 200-564) followed by the periplasmic domain up to the N-terminal end of LuxQ (residues 1-280). [back]

Schematic structure of the Fusion receptor constructs

The receptor chimeras were generated in two sequential PCR reactions (Fusion PCR). In the first PCR the two single fragments containing parts of the coding sequence of LuxQ (LuxQ-1: primers LuxQa/LuxQ-Tar-1b, LuxQ-2: primers LuxQa/LuxQ-Tar-2b) and Tar (Tar-1: primers LuxQ-Tar-1a/DK9b, Tar-2: primers LuxQ-Tar-2a/DK9b) were amplified. The reverse primer for LuxQ and the forward primer for Tar had complementary ends allowing annealing during the second PCR reaction. In addition to the amplified sequences from the first reaction the forward primer for LuxQ and the reverse primer for Tar were added to the reaction mix after the gel purification in order to be able to obtain the chimeric receptor sequence. Following amplification the chimeric products F1 and F2 were cloned into the expression vector pDK48 via the restriction sites NcoI and NdeI. The presence of the correct sequence was checked by sequencing.

Cloning Strategy for LuxS

Cloning Strategy for Fusion chimeras

References

[1] Dong, X.; Stothard, P.; Forsythe, I. J. & Wishart, D. S., PlasMapper: a web server for drawing and auto-annotating plasmid maps, Nucleic Acids Res, Vol. 32, pp. W660-W664, 2004

[back]

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 ==Sensing - Cloning strategy==
-The core part of the sensing project is the construction of the LuxQ-Tar chimeric receptor, which enables the ''E. coli'' killer bacteria to chemotactically respond to a Autoinducer 2 (AI-2) gradient and detect prey cells. The quorum-sensing system will be amplified from the ''V. harveyi'' genome while the Tar receptor is from ''E. coli''. On one hand LuxS needs to be cloned and transformed into one cell type, in order to make them produce and secrete AI-2. On the other hand the periplasmic ligand binding domain of LuxQ will be fused with the cytoplasmic domain of Tar and cloned on one plasmid together with LuxP which is necessary for AI-2 binding. Generally, restriction sites required for cloning are introduced via the PCR primer.
+The core part of the sensing project was the construction of the LuxQ-Tar chimeric receptor, which enables the ''E. coli'' killer bacteria to chemotactically respond to a Autoinducer 2 (AI-2) gradient and detect prey cells. The quorum-sensing system was amplified from the ''V. harveyi'' genome while the Tar receptor is from ''E. coli''. On one hand LuxS needed to be cloned and transformed into one cell type, in order to make them produce and secrete AI-2. On the other hand the periplasmic ligand binding domain of LuxQ was fused with the cytoplasmic domain of Tar and cloned on one plasmid together with LuxP which is necessary for AI-2 binding. Generally, restriction sites required for cloning were introduced via the PCR primer.
-''In silico'' cloning was performed in [http://serialbasics.free.fr/Serial_Cloner.html SerialCloner], Vector maps were designed with PlasMapper [1].
+''In silico'' cloning was performed in [http://serialbasics.free.fr/Serial_Cloner.html SerialCloner], Vector maps were designed with PlasMapper [1]. The sequenecs of used primers can be found in the [[Team:Heidelberg/Notebook/material#Synthetic_oligonucleotides | Materials & Methods]] section.
+[[https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Cloning back]]
-[[Image:HD PTrc99a.png|left|thumb|250px|pTrc99a for LuxS and LuxQ cloning]][[Image:HD PDK48.png|left|thumb|250px|pDK48 for cloning of fusion]][[Image:HD PBAD33.png|left|thumb|250px|pBAD33 used in Swarm-Assays]]
+[[Image:HD PTrc99a.png|left|thumb|230px|pTrc99a for LuxS and LuxQ cloning]][[Image:HD PDK48.png|left|thumb|275px|pDK48 for cloning of fusion]][[Image:HD PBAD33.png|left|thumb|275px|pBAD33 used in Swarm-Assays]]
 <br style="clear: both;"/>
 === LuxS ===
-LuxS will be amplified from the ''V. harveyi'' genome with primers LuxSa and LuxSb. Subsequently the product will be cloned into the pTr99alpha plasmid at the NcoI and BamHI sites and then transformed into DH5alpha competent cells.
+LuxS was amplified from the ''Vibrio harveyi'' genome using the following primers: LuxSa (forward) and LuxSb (reverse). Subsequently, the product was cloned into the plasmid pTr99alpha using the NcoI and BamHI restriction sites and then transformed into DH5alpha competent cells.
+[[https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Cloning back]]
 === LuxQ ===
-LuxQ will be amplied with primers LuxQa and LuxQc from the ''V. harveyi'' genome. The fragment will then be cloned into pTrc99alpha plasmid at the NcoI and BamHI site. Subsequently the product will be used as template for constructing the Fusion receptors.
+LuxQ was amplfied with primers LuxQa (forward) and LuxQc (reverse) from the ''V. harveyi'' genome. The obtained fragment was then cloned into the plasmid pTrc99alpha using the NcoI and BamHI restriction sites. Subsequently, the product was used as a template for PCR amplification with respect to cloning of the chimeric receptors (see below).
+[[https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Cloning back]]
 === LuxP ===
-LuxP will be amplied with primers LuxPc and LuxPd from the ''V. harveyi'' genome. Then the product will be cloned into native pDK48 plasmid. After the construction of the LuxQ-Tar Fusion gene in pDK48 plasmid, LuxP will also be introduced in the pDK48 plasmid at SalI and NotI sites. The whole construct of pDK48 will be transformed into our killer cell.
+LuxP was amplified with primers LuxPc (forward) and LuxPd (reverse) from the ''V. harveyi'' genome. The PCR product was then cloned into the vector pDK48 containing the LuxQ-Tar chimeric receptor sequence. This was done using the restriction sites SalI and NotI. The resulting expression plasmid was used for the transformation of our killer cells.
+[[https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Cloning back]]
 === Fusion receptor ===
-A detailed description of the Tar receptor and LuxQ quorum-sensing receptor can be found in the [[Team:Heidelberg/Project/Sensing | project description]]. Since it is believed that the linker region (transmembrane domain TM2) is critically for signal transduction, two different receptor constructs are designed, referred to as Fusion-1 and Fusion-2. Fusion-1 contains the cytoplasmic domain of Tar and TM2 to the N-terminal part of LuxQ (TM2, periplasmic domain, TM1). Fusion-2 contains the cytoplasmic domain and TM2 of Tar and the periplasmic domain to the N-terminal end of LuxQ (periplasmic domain, TM1).
+A detailed description of the Tar receptor and LuxQ quorum-sensing receptor can be found in the [[Team:Heidelberg/Project/Sensing | project description]]. Since it is believed that the linker region (transmembrane domain TM2) is critical for signal transduction, two different receptor constructs were designed, referred to as Fusion-1 and Fusion-2. Fusion-1 contained the cytoplasmic domain of Tar (residues 225-564) and the transmembrane domain,TM2 up to the N-terminus of LuxQ (residues 1-298). Fusion-2 contained the cytoplasmic domain as well as the second transmembrane domain, TM2 of Tar (residues 200-564) followed by the periplasmic domain up to the N-terminal end of LuxQ (residues 1-280).
+[[https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Cloning back]]
-The receptor chimeras will be built in two sequential PCR reactions (Fusion PCR). In the first PCR the two single fragments containing parts of the coding sequence of LuxQ and Tar will be generated. The reverse primer for LuxQ and the forward primer for Tar part have complementary ends allowing annealing during the second PCR reaction. In addition to the amplified sequences from the first reaction the forward primer for LuxQ and the reverse primer for Tar will be added to the reaction mix after the gel purification in order to obtain the chimeric receptor sequence.
+[[Image:HD Fusion Schema.png|thumb|center|400px|Schematic structure of the Fusion receptor constructs]]
+The receptor chimeras were generated in two sequential PCR reactions (Fusion PCR). In the first PCR the two single fragments containing parts of the coding sequence of LuxQ (LuxQ-1: primers LuxQa/LuxQ-Tar-1b, LuxQ-2: primers LuxQa/LuxQ-Tar-2b) and Tar (Tar-1: primers LuxQ-Tar-1a/DK9b, Tar-2: primers LuxQ-Tar-2a/DK9b) were amplified. The reverse primer for LuxQ and the forward primer for Tar had complementary ends allowing annealing during the second PCR reaction. In addition to the amplified sequences from the first reaction the forward primer for LuxQ and the reverse primer for Tar were added to the reaction mix after the gel purification in order to be able to obtain the chimeric receptor sequence. Following amplification the chimeric products F1 and F2 were cloned into the expression vector pDK48 via the restriction sites NcoI and NdeI. The presence of the correct sequence was checked by sequencing.
+[[Image:HD SensingCloning1.png|thumb|center|500px|Cloning Strategy for LuxS]]
+[[Image:HD_SensingCloning2.png|thumb|center|500px|Cloning Strategy for Fusion chimeras]]
 === References ===
 [1] Dong, X.; Stothard, P.; Forsythe, I. J. & Wishart, D. S., '''PlasMapper: a web server for drawing and auto-annotating plasmid maps''', Nucleic Acids Res, Vol. 32, pp. W660-W664, 2004
+[[https://2008.igem.org/Team:Heidelberg/Notebook/Sensing_Group/Cloning back]]