Difference between revisions of "Team:Nankai/Basic Part"

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<h4>Basic Parts</h4>
 
<h4>Basic Parts</h4>
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<p style="position: relative; top:0px; left: 20px; width:400px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>Basic part example 1 </b></br>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628001">BBa_K1628001</a> (P<sub>bca</sub>)<br/>
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  <a href="http://partsregistry.org/Part:BBa_K1031221">BBa_K1031221</a>, <a href="http://partsregistry.org/Part:BBa_K1031222">BBa_K1031222</a>, <a href="http://partsregistry.org/Part:BBa_K1031223">BBa_K1031223</a> and <a href="http://partsregistry.org/Part:BBa_K1031224">BBa_K1031224</a> are the DmpR biosensors using different RBS preceding sfGFP. </br>
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Promoter P<sub>bca</sub> is the original promoter of <em>pgsBCA</em> operon. According to our promoter strength assay (showed in Figure 1), the strength of P<sub>bca</sub> is very weak.</p>
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  <a href="http://partsregistry.org/Part:BBa_K1031211">BBa_K1031211</a> is the DmpR transcriptional factor under a constitutive promoter.description  description  description  description  description  description  description  description  description  description  description  description  description  <br/>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628002">BBa_K1628002</a> (P<sub>xyl</sub>)<br/>
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</p>
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  Promoter P<sub>xyl</sub> is a promoter of xylose operon regulate by repressor XylR. Promoter P<sub>xyl</sub> together with promoter P<sub>lacI</sub>, repressor LacI (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628201">BBa_K1628201</a>), promoter P<sub>grac</sub> (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628202">BBa_K1628202</a>) and repressor XylR (<a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628203">BBa_K1628203</a>) formed a metabolic toggle switch. We used this device to regulate the expression of <em>odhAB</em> genes in <em>B. amyloliquefaciens</em> NK-1 (showed in Figure 2). Without IPTG, the promoter P<sub>grac</sub> is inhibited by suppressor LacI and the supreessor XylR will not synthesized, thus the promoter P<sub>xyl</sub> is active and <em>odhAB</em> genes are expressed. When IPTG is added, the<em> xylR</em> gene is expressed and the suppressor XylR is synthesized thereafter inhibited the expression of <em>odhAB</em> genes.</p>
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<p>&nbsp;</p>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628003">BBa_K1628003</a><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628002"></a> (BJ27UP <sub></sub>)<br/>
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<p style="position: relative; top:0px; left: 20px; width:400px; font-size:18px;font-family:calibri,Arial, Helvetica, sans-serif; text-align:justify; line-height:30px;"><b>Basic part example 2 </b></br>
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  Promoter BJ27UP is an artificially synthesized promoter. According to our promoter strength assay in <em>B. amyloliquefaciens</em> NK-1 (showed in Figure 1), the strength of BJ27UP is stronger than Pbcabut is still too weak compared with other promoters. </p>
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   <a href="http://partsregistry.org/Part:BBa_K1031221">BBa_K1031221</a>, <a href="http://partsregistry.org/Part:BBa_K1031222">BBa_K1031222</a>, <a href="http://partsregistry.org/Part:BBa_K1031223">BBa_K1031223</a> and <a href="http://partsregistry.org/Part:BBa_K1031224">BBa_K1031224</a> are the DmpR biosensors using different RBS preceding sfGFP. </br>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628004">BBa_K1628004</a><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628002"></a> (C2up<sub></sub>)<br/>
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   <a href="http://partsregistry.org/Part:BBa_K1031211">BBa_K1031211</a> is the DmpR transcriptional factor under a constitutive promoter.description  description  description  description  description  description  description  description  description  description  description  description  description <br/>
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   Promoter C2up is an artificially synthesized promoter. According to our promoter strength assay in <em>B. amyloliquefaciens</em> NK-1 (showed in Figure 1), C2up is the strongest promoters we used in our project.</p>
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</p>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628005">BBa_K1628005</a><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628002"></a> (A2up<sub></sub>)<br/>
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<p><span class="sidebar-widget"><img src="https://static.igem.org/mediawiki/2015/f/f2/Nankai_projectpic3.JPG" alt="Basic part picture" /></span></p>
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  Promoter A2cup is an artificially synthesized promoter. According to our promoter strength assay in <em>B. amyloliquefaciens</em> NK-1 (showed in Figure 1), A2up is a very strong promoter in <em>B. amyloliquefaciens</em> NK-1.</p>
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<p>&nbsp;</p>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628006">BBa_K1628006</a><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628002"></a> (P43)<br/>
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   Promoter P43 is a strong promoter in <em>Bacillus subtilis</em> 168. According to our promoter strength assay in (showed in Figure 1), P43 is a weak promoter in <em>B. amyloliquefaciens</em> NK-1.</p>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628007">BBa_K1628007</a><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628002"></a> (P<sub>amyA</sub>)<br/>
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  Promoter P<sub>amyA</sub> is a strong promoter in <em>Bacillus amyloliquefaciens</em> LL3. According to our promoter strength assay in (showed in Figure 1), P<sub>amyA</sub>is the second strongest promoter in our project.</p>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628101">BBa_K1628101</a> (<em>pgsB</em>)<br/>
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  <em>pgsB</em> is a gene responsible for γ-PGA synthesis in <em>pgsBCA</em> operon. Protein PgsBCA is a membrane protein and subunit PgsB’s main function is gathering substrate glutamic acid for γ-PGA synthesis (showed in Figure 3). </p>
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<p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628102">BBa_K1628102</a> (<em>pgsAC</em>)<br/>
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  <em>pgsC</em> and <em>pgsA</em> are two genes in <em>pgsBCA</em> operon. Protein PgsBCA is a membrane protein responsible for the synthesis of γ-PGA. Subunit <em>PgsC</em> is responsible for glutamic acid’s polymerization and subunit <em>PgsA</em> is responsible for the secretion of γ-PGA (showed in Figure 3)</p>
 
<p>&nbsp;</p>
 
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<img src="https://static.igem.org/mediawiki/2015/b/be/Partsfigure_new4.jpeg" width="561">
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                                                <p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;"> Figure 1. Promoter strength assay in <em>Bacillus amyloliquefaciens</em> NK-1.              </p>
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              <p><img src="https://static.igem.org/mediawiki/2015/2/25/Parts_figure3.jpeg" width="714" height="435"></p>
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              <p style="position: relative; top: 0px; left: 20px; width: 700px; font-size: 18px; font-family: calibri,Arial, Helvetica, sans-serif; text-align: justify; line-height: 30px;">Figure 3. The synthetic pathway of γ-PGA</p>
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              <p>&nbsp;</p>
 
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<h6><a href="https://2015.igem.org/Team:Nankai/Parts">Team Parts</a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Basic_Part">Basic Parts</a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Basic_Part">Basic Parts</a></h6>
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<h6><a href="https://2015.igem.org/Team:Nankai/Composite_Part">Composite Parts</a></h6>
 
<h6><a href="https://2015.igem.org/Team:Nankai/Composite_Part">Composite Parts</a></h6>
 
<h6><a href="https://2015.igem.org/Team:Nankai/Part_Collection">Part Collection</a></h6>
 
<h6><a href="https://2015.igem.org/Team:Nankai/Part_Collection">Part Collection</a></h6>
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<h6>References</h6>
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<h6>&nbsp;</h6>
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<p>1. Ashiuchi, M., Misono, H., 2002. Biochemistry and molecular genetics of poly-γ-glutamate synthesis. Appl. Biochem. Biotechnol. 59, 9–14.</br>
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2. Kunioka, M., 1997. Biosynthesis and chemical reactions of poly(amino acid)s from
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microorganisms. Appl. Microbiol. Biotechnol. 47, 469–475.</br>
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3. Shih, I.L., Van, Y.T., 2001. The production of poly(γ-glutamic acid) from microorganism and its various applications. Bioresour. Technol. 79, 207–225.</br>
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4. Li, C., 2002. Poly(L-glutamic acid)--anticancer drug conjugates. Adv. Drug Deliver. Rev. 54, 695–713.</br>
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5. Liang, H.F., Chen, C.T., Chen, S.C., Kulkarni, A.R., Chiu, Y.L., Chen, M.C., Sung, H.W., 2006. Paclitaxel-loaded poly(γ-glutamic acid)-poly(lactide) nanoparticles as a targeted drug delivery system for the treatment of liver cancer. Biomaterials. 27, 2051–2059.</br>
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6. Richard, A., Margaritis, A., 2001. Poly (glutamic acid) for biomedical applications. Crit. Rev. Biotechnol. 21, 219–232.</br>
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7. Park, Y.J., Liang, J., Yang, Z., Yang, V.C., 2001. Controlled release of clot-dissolving tissue-type plasmmogen activator from a poly(L-glutamic acid) semi-interpenetrating polymer network hydrogel. J. Control. Release. 74, 243–247.</br>
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8. Cao, M.F., Geng, W.T., Liu, L., Song, C.J., Xie, H., Guo, W.B., Jin, Y.H., Wang, S.F., 2011. Glutamic acid independent production of poly-γ-glutamic acid by Bacillus amyloliquefaciens LL3 and cloning of pgsBCA genes. Bioresour. Technol. 102, 4251–4257.</br>
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9. Geng, W.T., Cao, M.F., Song, C.J., Xie, H., Liu, L., Yang, C., Feng, J., Zhang, W., Jin, Y.H., Du, Y., Wang, S.F., 2011. Complete genome sequence of Bacillus amyloliquefaciens LL3, which exhibits glutamic acid-independent production of poly-γ-glutamic acid. J. Bacteriol. 193, 3393–3394.</br>
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10. Feng, J., Gao, W.X., Gu, Y.Y., Zhang, W., Cao, M.F., Song, C.J., Zhang, P., Sun, M., Yang, C.,  Wang, S.F., 2014a. Functions of poly-gamma-glutamic acid (γ-PGA) degradation genes in γ-PGA synthesis and cell morphology maintenance. Appl. Microbiol. Biotechnol. 98, 6397–6407.</br>
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11. Uy, D., Delaunay S., Germain, P., Engasser, J.M., Goergen, J.L. 2003. Instability of glutamate production by Corynebacterium glutamicum 2262 in continuous culture using the temperature-triggered process. J. Biotech. 104, 173-184.</p>
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Revision as of 13:34, 15 September 2015

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Your place: Home > Parts

Team Parts

Basic Parts

BBa_K1628001 (Pbca)
Promoter Pbca is the original promoter of pgsBCA operon. According to our promoter strength assay (showed in Figure 1), the strength of Pbca is very weak.

BBa_K1628002 (Pxyl)
Promoter Pxyl is a promoter of xylose operon regulate by repressor XylR. Promoter Pxyl together with promoter PlacI, repressor LacI (BBa_K1628201), promoter Pgrac (BBa_K1628202) and repressor XylR (BBa_K1628203) formed a metabolic toggle switch. We used this device to regulate the expression of odhAB genes in B. amyloliquefaciens NK-1 (showed in Figure 2). Without IPTG, the promoter Pgrac is inhibited by suppressor LacI and the supreessor XylR will not synthesized, thus the promoter Pxyl is active and odhAB genes are expressed. When IPTG is added, the xylR gene is expressed and the suppressor XylR is synthesized thereafter inhibited the expression of odhAB genes.

BBa_K1628003 (BJ27UP )
Promoter BJ27UP is an artificially synthesized promoter. According to our promoter strength assay in B. amyloliquefaciens NK-1 (showed in Figure 1), the strength of BJ27UP is stronger than Pbcabut is still too weak compared with other promoters.

BBa_K1628004 (C2up)
Promoter C2up is an artificially synthesized promoter. According to our promoter strength assay in B. amyloliquefaciens NK-1 (showed in Figure 1), C2up is the strongest promoters we used in our project.

BBa_K1628005 (A2up)
Promoter A2cup is an artificially synthesized promoter. According to our promoter strength assay in B. amyloliquefaciens NK-1 (showed in Figure 1), A2up is a very strong promoter in B. amyloliquefaciens NK-1.

BBa_K1628006 (P43)
Promoter P43 is a strong promoter in Bacillus subtilis 168. According to our promoter strength assay in (showed in Figure 1), P43 is a weak promoter in B. amyloliquefaciens NK-1.

BBa_K1628007 (PamyA)
Promoter PamyA is a strong promoter in Bacillus amyloliquefaciens LL3. According to our promoter strength assay in (showed in Figure 1), PamyAis the second strongest promoter in our project.

BBa_K1628101 (pgsB)
pgsB is a gene responsible for γ-PGA synthesis in pgsBCA operon. Protein PgsBCA is a membrane protein and subunit PgsB’s main function is gathering substrate glutamic acid for γ-PGA synthesis (showed in Figure 3).

BBa_K1628102 (pgsAC)
pgsC and pgsA are two genes in pgsBCA operon. Protein PgsBCA is a membrane protein responsible for the synthesis of γ-PGA. Subunit PgsC is responsible for glutamic acid’s polymerization and subunit PgsA is responsible for the secretion of γ-PGA (showed in Figure 3)

 

 

Figure 1. Promoter strength assay in Bacillus amyloliquefaciens NK-1.

Figure 3. The synthetic pathway of γ-PGA

 

 

 

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