Difference between revisions of "Template:Virginia/Part Collection"

 
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<h1 id="description">Description</h1>
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<h1 id="parts-collection">Parts Collection</h1>
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<table style="width:100%">
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<table style="width:100%" class="va-parts">
 
     <tr>
 
     <tr>
 
         <th>Name</th>
 
         <th>Name</th>
 
         <th>Description</th>  
 
         <th>Description</th>  
 
         <th>Part</th>
 
         <th>Part</th>
 +
    </tr>
 +
<tr>
 +
        <td>spacerLXf</td>
 +
        <td>This is a 10 nucleotide spacer used to build K2535005. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won&#39;t be assembled in the wrong place. </td>
 +
        <td> K2535003</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>T7 promoter</td>
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         <td>spacerLXr </td>
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         <td>T7 promoter controlled sfGFP used in all 2nd plasmids as an expression indicator</td>
+
         <td>This is a 10 nucleotide spacer used to build K2535005. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won&#39;t be assembled in the wrong place. </td>
−
         <td>pT7_rbs_sfGFP_term I746909, (from iGEM07_Cambridge) </td>
+
         <td>K2535004</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
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         <td>Constitutive sfGFP</td>
+
         <td>spacerLRf </td>
−
         <td>A constitutively expressed sfGFP used as positive control in flow cytometry. </td>
+
         <td>This is a 10 nucleotide spacer used to build K2535009. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won&#39;t be assembled in the wrong place. </td>
−
         <td>K608002 + K1365020</td>
+
        <td>K2535007</td>
 +
    </tr>
 +
    <tr>
 +
        <td>spacerLRr </td>
 +
        <td>This is a 10 nucleotide spacer used to build K2535009. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won&#39;t be assembled in the wrong place.</td>
 +
        <td>K2535008 </td>
 +
    </tr>
 +
    <tr>
 +
        <td>spacerYf </td>
 +
        <td>This is a 10 nucleotide spacer used to build K2535013. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won&#39;t be assembled in the wrong place.</td>
 +
        <td> K2535011</td>
 +
    </tr>
 +
    <tr>
 +
        <td>spacerYr</td>
 +
        <td>This is a 10 nucleotide spacer used to build K2535013. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won&#39;t be assembled in the wrong place.</td>
 +
         <td>K2535012</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
 
         <td>LuxS</td>
 
         <td>LuxS</td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly. LuxS is a protein, not native to the Lsr Operon, that catalyzes the cleavage of metabolites to synthesize the autoinducer molecule AI-2 (Gonzalez et al 2006). The LuxS gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with. </td>
+
         <td>LuxS is a protein, not native to the Lsr Operon, that catalyzes the cleavage of metabolites to synthesize the autoinducer molecule AI-2 (Gonzalez et al 2006).</td>
−
         <td>spacer_pT7_rbs_LuxS_term_spacer</td>
+
        <td>K2535000</td>
 +
    </tr>
 +
    <tr>
 +
        <td>LuxS-Block</td>
 +
        <td>spacer_pT7_rbs_LuxS_term_spacer. LuxS is a protein, not native to the Lsr Operon, that catalyzes the cleavage of metabolites to synthesize the autoinducer molecule AI-2 (Gonzalez et al 2006). The LuxS gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with. </td>
 +
         <td> K2535005 </td>
 +
    </tr>
 +
    <tr>
 +
        <td>LuxS-sfGFP</td>
 +
        <td> pT7_rbs_sfGFP_term_LuxS-Block. This is a composite part of LuxS-Block and I746909. This part can be regulated using T7 to track LuxS expression based on the sfGFP reporter. Both LuxS and sfGFP are controlled by a T7 promoter.</td>
 +
        <td> K2535006</td>
 +
    </tr>
 +
    <tr>
 +
        <td>LsrK-Block</td>
 +
        <td>spacer_ pT7_rbs_LsrK_term_spacer. LsrK is a kinase that is native to the Lsr Operon. It converts intracellular AI-2 to phosphorylated AI-2 (AI-2P), which derepresses the Lsr Operon (Xavier et al 2004). The LsrK gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with.  </td>
 +
        <td>K2535009</td>
 +
    </tr>
 +
    <tr>
 +
        <td>LsrK-sfGFP</td>
 +
        <td>pT7_rbs_sfGFP_term_LsrK-Block. This is a composite part of LsrK-Block and I746909. This part can be regulated using T7 to track LsrK expression based on the sfGFP reporter. Both LsrK and sfGFP are controlled by a T7 promoter.</td>
 +
        <td>K2535010</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>LuxS 2nd plasmid</td>
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         <td>YdgG </td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly.This is a composite part of LuxS and I746909. </td>
+
         <td> YdgG is a membrane transport protein, not native to the Lsr Operon, which exports AI-2 out of the cell (Herzberg et al 2006).</td>
−
         <td>pT7_rbs_sfGFP_term_LuxS</td>
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         <td> K2535002</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>LsrK</td>
+
         <td>YdgG-Block</td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly. LsrK is a kinase that is native to the Lsr Operon. It converts intracellular AI-2 to phosphorylated AI-2 (AI-2P),  which derepresses the Lsr Operon (Xavier et al 2004). The LsrK gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with.  
+
         <td>spacer_ pT7_rbs_YdgG_term_spacer. YdgG is a membrane transport protein, not native to the Lsr Operon, which exports AI-2 out of the cell (Herzberg et al 2006). The YdgG gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with. </td>
−
        </td>
+
         <td>K2535013</td>
−
         <td>spacer_ pT7_rbs_LsrK_term_spacer</td>
+
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>LsrK 2nd plasmid</td>
+
         <td>YdgG-sfGFP</td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly.This is a composite part of LsrK and I746909. </td>
+
         <td>pT7_rbs_sfGFP_term_YdgG-Block. This is a composite part of YdgG-Block and I746909. This part can be regulated using T7 to track YdgG expression based on the sfGFP reporter. Both YdgG and sfGFP are controlled by a T7 promoter. </td>
−
         <td>pT7_rbs_sfGFP_term_LsrK</td>
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         <td>K2535014</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>YdgG</td>
+
         <td>LsrK-LuxS-sfGFP</td>
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         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly. YdgG is a membrane transport protein, not native to the Lsr Operon, which exports AI-2 out of the cell (Herzberg et al 2006). The YdgG gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with. </td>
+
         <td>pt7_rbs_sfGFP_term_LsrK-Block_LuxS-Block. This is a composite part of LsrK and LuxS put together with I746909 (sfGFP regulated by a T7 promoter). This part allows the upregulation of LuxS and LsrK so that intracellular AI-2 production and AI-2 phosphorylation are increased concurrently. </td>
−
         <td> spacer_ pT7_rbs_YdgG_term_spacer</td>
+
         <td> K2535015</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>YdgG 2nd plasmid</td>
+
         <td>LsrK-YdgG-sfGFP</td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly.This is a composite part of YdgG and I746909. </td>
+
         <td>This is a composite part of LsrK and YdgG put together with I746909 (sfGFP regulated by a T7 promoter).  This part allows the upregulation of LsrK and YdgG so that AI-2 is phosphorylated to AI-2P and AI-2 out of the cell are increased concurrently. </td>
−
         <td> pT7_rbs_sfGFP_term_YdgG</td>
+
         <td>K2535016 </td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>LsrK-LuxS 2nd plasmid</td>
+
         <td>LuxS-YdgG-sfGFP</td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly.This is a composite part of LsrK and LuxS put together with I746909. This part allows the upregulation of LuxS and LsrK so that intracellular AI-2 production and phosphorylation are increased concurrently.  
+
         <td>pt7_rbs_sfGFP_term_LuxS-Block_YdgG-Block. This is a composite part of LuxS and YdgG put together with I746909 (sfGFP regulated by a T7 promoter). This part allows the upregulation of LuxS and YdgG so that intracellular AI-2 production and export out of the cell are increased concurrently.</td>
−
        </td>
+
         <td>K2535020</td>
−
         <td>pt7_rbs_sfGFP_term_LsrK_LuxS</td>
+
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>LsrK-YdgG 2nd plasmid</td>
+
         <td>LsrK-LuxS-YdgG-sfGFP</td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly.This is a composite part of LsrK and YdgG put together with I746909.  This part allows the upregulation of LuxS and YdgG so that intracellular AI-2 production and export out of the cell are increased concurrently.  </td>
+
         <td>pt7_rbs_sfGFP_term_LsrK_LuxS_YdgG. This is a composite part of LsrK, LuxS, and YdgG put together with I746909 (sfGFP regulated by a T7 promoter).  This part allows the upregulation of LsrK, LuxS, and YdgG so that intracellular AI-2 production, AI-2 phosphorylation, and export out of the cell are all increased concurrently.  </td>
−
         <td>pt7_rbs_sfGFP_term_LsrK_YdgG</td>
+
         <td> K2535017 </td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>LsrK-LuxS-YdgG 2nd plasmid</td>
+
         <td>pLsr_rbs_LsrR_rbs </td>
−
         <td>Built in high copy pGGA cloning vector due to simplicity of using Golden Gate assembly.  </td>
+
         <td>This part is an AI-2 (autoinducer 2 from the Lsr Operon) dependent promoter that self regulates itself. pLsr is the specific promoter that is bidirectional. Dimers of the LsrR gene bind to and repress this promoter. However, AI-2P (phosphorylated AI-2) can bind to these dimers and cause them to dissociate, depressing the promoter.  Since the expression of this plasmid produces LsrR, which represses the promoter pLsr, this system is self regulating. </td>
−
         <td>pt7_rbs_sfGFP_term_LsrK_LuxS_YdgG</td>
+
         <td>K2535018</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
−
         <td>1st plasmid</td>
+
         <td>sQS: Synthetic Quorum Response Plasmid Insert</td>
−
         <td>This plasmid contains an AI-2 regulated promoter, pLsr, which is bidirectional. Dimers of LsrR bind to and repress this promoter. However, AI-2P can bind to these dimers and cause them to dissociate, depressing the promoter.  Since the expression of this plasmid produces LsrR, which represses the promoter pLsr, this system is self regulating. </td>
+
         <td>term_pLsr_rbs_LsrR_rbs_T7_term. Built in low copy pACYC cloning vector and optimized for use in a low copy vector to prevent leakiness of AI-2 regulated promoter. This plasmid contains an AI-2 regulated promoter, pLsr, which is bidirectional. Dimers of LsrR bind to and repress this promoter. However, AI-2P can bind to these dimers and cause them to dissociate, depressing the promoter.  Since the expression of this plasmid produces LsrR, which represses the promoter pLsr, this system is self regulating. sQS plasmid is used to regulate quorum enhancement plasmids. T7 is therefore only expressed in the presence of AI-2P. This plasmid can be used to regulate T7 expression based on AI-2 level in a media. </td>
−
         <td> pLsr_rbs_LsrR_rbs_T7_term </td>
+
         <td>K2535019</td>
 
     </tr>
 
     </tr>
 
</table>
 
</table>
 +
 +
<h1 id="references">References</h1>
 +
<p>Gonzalez J, Neshavan N (2006). Messing with Bacterial Quorum Sensing. Microbiology and Molecular Biology
 +
Reviews 70, 859-875.    </p>
 +
<p>Herzberg M, Kaye I, Peti W, Wood T (2006) YdgG (TqsA) Controls Biofilm Formation in Escherichia
 +
coli K-12 through Autoinducer 2 Transport. J Bacteriol. 2006 Jan; 188(2): 587–598.        </p>
 +
<p>Xavier K, Bassler B (2004). Regulation of Uptake and Processing of the Quorum-Sensing Autoinducer AI-2 in
 +
Escherichia coli. J Bacteriol 187, 238-245.      </p>

Latest revision as of 20:12, 17 October 2018

Parts Collection

Name Description Part
spacerLXf This is a 10 nucleotide spacer used to build K2535005. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won't be assembled in the wrong place. K2535003
spacerLXr This is a 10 nucleotide spacer used to build K2535005. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won't be assembled in the wrong place. K2535004
spacerLRf This is a 10 nucleotide spacer used to build K2535009. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won't be assembled in the wrong place. K2535007
spacerLRr This is a 10 nucleotide spacer used to build K2535009. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won't be assembled in the wrong place. K2535008
spacerYf This is a 10 nucleotide spacer used to build K2535013. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won't be assembled in the wrong place. K2535011
spacerYr This is a 10 nucleotide spacer used to build K2535013. When using Gibson and Golden gate assembly, the spacer at the beginning of the sequence helps create a unique sequence so that if multiple parts have the same beginning sequence, they won't be assembled in the wrong place. K2535012
LuxS LuxS is a protein, not native to the Lsr Operon, that catalyzes the cleavage of metabolites to synthesize the autoinducer molecule AI-2 (Gonzalez et al 2006). K2535000
LuxS-Block spacer_pT7_rbs_LuxS_term_spacer. LuxS is a protein, not native to the Lsr Operon, that catalyzes the cleavage of metabolites to synthesize the autoinducer molecule AI-2 (Gonzalez et al 2006). The LuxS gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with. K2535005
LuxS-sfGFP pT7_rbs_sfGFP_term_LuxS-Block. This is a composite part of LuxS-Block and I746909. This part can be regulated using T7 to track LuxS expression based on the sfGFP reporter. Both LuxS and sfGFP are controlled by a T7 promoter. K2535006
LsrK-Block spacer_ pT7_rbs_LsrK_term_spacer. LsrK is a kinase that is native to the Lsr Operon. It converts intracellular AI-2 to phosphorylated AI-2 (AI-2P), which derepresses the Lsr Operon (Xavier et al 2004). The LsrK gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with. K2535009
LsrK-sfGFP pT7_rbs_sfGFP_term_LsrK-Block. This is a composite part of LsrK-Block and I746909. This part can be regulated using T7 to track LsrK expression based on the sfGFP reporter. Both LsrK and sfGFP are controlled by a T7 promoter. K2535010
YdgG YdgG is a membrane transport protein, not native to the Lsr Operon, which exports AI-2 out of the cell (Herzberg et al 2006). K2535002
YdgG-Block spacer_ pT7_rbs_YdgG_term_spacer. YdgG is a membrane transport protein, not native to the Lsr Operon, which exports AI-2 out of the cell (Herzberg et al 2006). The YdgG gene is regulated by a T7 driven promoter in order to cooperate with the AI-2 sensitive plasmid that this part is used in conjunction with. K2535013
YdgG-sfGFP pT7_rbs_sfGFP_term_YdgG-Block. This is a composite part of YdgG-Block and I746909. This part can be regulated using T7 to track YdgG expression based on the sfGFP reporter. Both YdgG and sfGFP are controlled by a T7 promoter. K2535014
LsrK-LuxS-sfGFP pt7_rbs_sfGFP_term_LsrK-Block_LuxS-Block. This is a composite part of LsrK and LuxS put together with I746909 (sfGFP regulated by a T7 promoter). This part allows the upregulation of LuxS and LsrK so that intracellular AI-2 production and AI-2 phosphorylation are increased concurrently. K2535015
LsrK-YdgG-sfGFP This is a composite part of LsrK and YdgG put together with I746909 (sfGFP regulated by a T7 promoter). This part allows the upregulation of LsrK and YdgG so that AI-2 is phosphorylated to AI-2P and AI-2 out of the cell are increased concurrently. K2535016
LuxS-YdgG-sfGFP pt7_rbs_sfGFP_term_LuxS-Block_YdgG-Block. This is a composite part of LuxS and YdgG put together with I746909 (sfGFP regulated by a T7 promoter). This part allows the upregulation of LuxS and YdgG so that intracellular AI-2 production and export out of the cell are increased concurrently. K2535020
LsrK-LuxS-YdgG-sfGFP pt7_rbs_sfGFP_term_LsrK_LuxS_YdgG. This is a composite part of LsrK, LuxS, and YdgG put together with I746909 (sfGFP regulated by a T7 promoter). This part allows the upregulation of LsrK, LuxS, and YdgG so that intracellular AI-2 production, AI-2 phosphorylation, and export out of the cell are all increased concurrently. K2535017
pLsr_rbs_LsrR_rbs This part is an AI-2 (autoinducer 2 from the Lsr Operon) dependent promoter that self regulates itself. pLsr is the specific promoter that is bidirectional. Dimers of the LsrR gene bind to and repress this promoter. However, AI-2P (phosphorylated AI-2) can bind to these dimers and cause them to dissociate, depressing the promoter. Since the expression of this plasmid produces LsrR, which represses the promoter pLsr, this system is self regulating. K2535018
sQS: Synthetic Quorum Response Plasmid Insert term_pLsr_rbs_LsrR_rbs_T7_term. Built in low copy pACYC cloning vector and optimized for use in a low copy vector to prevent leakiness of AI-2 regulated promoter. This plasmid contains an AI-2 regulated promoter, pLsr, which is bidirectional. Dimers of LsrR bind to and repress this promoter. However, AI-2P can bind to these dimers and cause them to dissociate, depressing the promoter. Since the expression of this plasmid produces LsrR, which represses the promoter pLsr, this system is self regulating. sQS plasmid is used to regulate quorum enhancement plasmids. T7 is therefore only expressed in the presence of AI-2P. This plasmid can be used to regulate T7 expression based on AI-2 level in a media. K2535019

References

Gonzalez J, Neshavan N (2006). Messing with Bacterial Quorum Sensing. Microbiology and Molecular Biology Reviews 70, 859-875.

Herzberg M, Kaye I, Peti W, Wood T (2006) YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport. J Bacteriol. 2006 Jan; 188(2): 587–598.

Xavier K, Bassler B (2004). Regulation of Uptake and Processing of the Quorum-Sensing Autoinducer AI-2 in Escherichia coli. J Bacteriol 187, 238-245.