Difference between revisions of "Team:Nankai/Parts"

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<div class="col-md-8 blog-posts">
 
<div class="col-md-8 blog-posts">
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<h4>What is γ-PGA?</h4>
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<h4>Parts Abstract</h4>
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<p>Poly-γ-glutamic acid (γ-PGA) is an important, naturally occurring polyamide consisting of D/L-glutamate monomers. Unlike typical peptide linkages, the amide linkages in γ-PGA are formed between the α-amino group and the γ-carboxyl group. γ-PGA exhibits many favorable features such as biodegradable, water soluble, edible and non-toxic to humans and the environment. Therefore, it has been widely used in fields of foods, medicines, cosmetics and agriculture and many unique applications, such as a sustained release material and drug carrier, curable biological adhesive, biodegradable fibres, and highly water absorbable hydrogels.</p>
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<table width="544" border="1">
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<h4>How can we produce it?</h4>
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  <tr>
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<p>Strains capable for producing γ-PGA are divided into two categories based on their requirement for glutamate acid: glutamate-dependent strains and glutamate-independent strains. Glutamate-independent strains are preferable for industrial production because of their low cost and simplified fermentation process. However, compared with glutamate-dependent strains, their lower γ-PGA productivity limits their industrial application.Therefore, the construction of a glutamate-independent strain with high γ-PGA yield is important for industrial applications.</p>
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    <th width="78" bgcolor="#999999" scope="col">Number</th>
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<h4>Who can produce it?</h4>
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    <th width="45" bgcolor="#999999" scope="col">Name</th>
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<p>Bacillusamyloliquefaciens LL3, isolated from fermented food, is a glutamate-independent strain, which can produce 3-4 g/L γ-PGA with sucrose as its carbon source and ammonium sulfate as its nitrogen source. The B. amyloliquefaciens LL3 strain was deposited in the China Center for Type Culture Collection (CCTCC) with accession number CCTCC M 208109 and its whole genome has been sequenced in 2011. In this study, we aimed to improve the γ-PGA production based on the B. amyloliquefaciens NK-1 strain (a derivative of LL3 strain with its endogenous plasmid and upp gene deleted).</p>
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    <th width="77" bgcolor="#999999" scope="col">Type</th>
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<h4>What did we do?</h4>
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    <th width="178" bgcolor="#999999" scope="col">Description</th>
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<p>In order to improve γ-PGA production, we employed two strategies to fine-tune the synthetic pathways and balance the metabolism in the glutamate-independent B. amyloliquefaciens NK-1 strain. Firstly, we constructed a metabolic toggle switch in the NK-1 strain to inhibit the expression of ODHC (2-oxoglutarate dehydrogenase complex) by adding IPTG in the stationary stage and distribute the metabolic flux more frequently to be used for γ-PGA precursor-glutamate synthesis. As scientists had found that the activity of ODHC was rather low when glutamate was highly produced in a Corynebacterium glutamicum strain. Second, to balance the increase of endogenous glutamate production, we optimized the expression level of pgsBCA genes (responsible for γ-PGA synthesis) by replacing its native promoter to seven different strength of promoters. Through these two strategies, we aimed to obtain a γ-PGA production improved mutant strain.<a href="https://2015.igem.org/Team:Nankai/Experiments">Click for more detail.</a></p>
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    <th width="71" bgcolor="#999999" scope="col">Creator</th>
 +
    <th width="55" bgcolor="#999999" scope="col">Length</th>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628001">BBa_K1628001</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Pbca</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Promoter</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq"> an original promoter of coding sequence pgsBCA</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Tianyi Huang</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">364</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628002">BBa_K1628002</a></td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">SPxyl </span></td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">Promoter</span></td>
 +
    <td bgcolor="#FFFFFF">&nbsp;</td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">Tianyi Huang</span></td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">217</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628003">BBa_K1628003</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">BJ27UP</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Promoter</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">a synthetic promoter</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Xinhao Song</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">100</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628004">BBa_K1628004</a></td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">C2up</span></td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">Promoter</span></td>
 +
    <td bgcolor="#FFFFFF">&nbsp;</td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">Xinhao Song</span></td>
 +
    <td bgcolor="#FFFFFF"><span class="zaq">108</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628005">BBa_K1628005</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">A2cup</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Promoter</span></td>
 +
    <td bgcolor="#CCCCCC">&nbsp;</td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Yibing Wei</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">107</span></td>
 +
  </tr>
 +
  <tr bgcolor="#FFFFFF">
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628006">BBa_K1628006</a></td>
 +
    <td><span class="zaq">P43</span></td>
 +
    <td><span class="zaq">Promoter</span></td>
 +
    <td>&nbsp;</td>
 +
    <td><span class="zaq">Yibing Wei</span></td>
 +
    <td><span class="zaq">445</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628007">BBa_K1628007</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">PamyA</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Promoter</span></td>
 +
    <td bgcolor="#CCCCCC">&nbsp;</td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Zhaoran Zhang</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">613</span></td>
 +
  </tr>
 +
  <tr bgcolor="#FFFFFF">
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628101">BBa_K1628101</a></td>
 +
    <td><span class="zaq">pgsB</span></td>
 +
    <td><span class="zaq">Coding</span></td>
 +
    <td>&nbsp;</td>
 +
    <td><span class="zaq">Tianyi Huang</span></td>
 +
    <td><span class="zaq">1182</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628102">BBa_K1628102</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">pgsCA</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Coding</span></td>
 +
    <td bgcolor="#CCCCCC">&nbsp;</td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Xinhao Song</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">1631</span></td>
 +
  </tr>
 +
  <tr bgcolor="#FFFFFF">
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628201">BBa_K1628201</a></td>
 +
    <td><span class="zaq">PlacI/lacI</span></td>
 +
    <td><span class="zaq">Translational Unit </span></td>
 +
    <td>&nbsp;</td>
 +
    <td><span class="zaq">Yibing Wei</span></td>
 +
    <td><span class="zaq">1386</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628202">BBa_K1628202</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Pgrac</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Promoter </span></td>
 +
    <td bgcolor="#CCCCCC">&nbsp;</td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Tianyi Huang</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">120</span></td>
 +
  </tr>
 +
  <tr bgcolor="#FFFFFF">
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628203">BBa_K1628203</a></td>
 +
    <td><span class="zaq">xylR</span></td>
 +
    <td><span class="zaq">Coding </span></td>
 +
    <td>&nbsp;</td>
 +
    <td><span class="zaq">Zhaoran Zhang</span></td>
 +
    <td><span class="zaq">1167</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628301">BBa_K1628301</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">P1-GFP</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Device</span></td>
 +
    <td bgcolor="#CCCCCC">&nbsp;</td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Tianyi Huang</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">?</span></td>
 +
  </tr>
 +
  <tr bgcolor="#FFFFFF">
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628302">BBa_K1628202</a></td>
 +
    <td><span class="zaq">P2-GFP</span></td>
 +
    <td><span class="zaq">Device</span></td>
 +
    <td>&nbsp;</td>
 +
    <td><span class="zaq">Xinhao Song</span></td>
 +
    <td><span class="zaq">?</span></td>
 +
  </tr>
 +
  <tr>
 +
    <td bgcolor="#CCCCCC"><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1628303">BBa_K1628303</a></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">P3-GFP </span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Device</span></td>
 +
    <td bgcolor="#CCCCCC">&nbsp;</td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">Yibing Wei</span></td>
 +
    <td bgcolor="#CCCCCC"><span class="zaq">?</span></td>
 +
  </tr>
 +
</table>
 +
<p>&nbsp;</p>
 +
<p>&nbsp;</p>
 
 
 
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<div class="sidebar-widget">
 
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<img src="https://static.igem.org/mediawiki/2015/f/f2/Nankai_projectpic3.JPG">
 
<img src="https://static.igem.org/mediawiki/2015/f/f2/Nankai_projectpic3.JPG">
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                                                 <p>Preparing for LB medium.</p>
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                                                 <p>Part-picture-1</p>
 
<img src="https://static.igem.org/mediawiki/2015/6/6e/Nankai_projectpic1.JPG">
 
<img src="https://static.igem.org/mediawiki/2015/6/6e/Nankai_projectpic1.JPG">
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                                                 <p>Cultured LL3.</p>
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                                                 <p>Part-picture-2</p>
 
<img src="https://static.igem.org/mediawiki/2015/2/2d/Nankai_projectpic2.jpg">
 
<img src="https://static.igem.org/mediawiki/2015/2/2d/Nankai_projectpic2.jpg">
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                                                <p>In the progress of fermentation.</p>
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                      <p>Part-picture-3</p>
  
 
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Revision as of 09:40, 11 September 2015

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Team Parts

Parts Abstract

Number Name Type Description Creator Length
BBa_K1628001 Pbca Promoter an original promoter of coding sequence pgsBCA Tianyi Huang 364
BBa_K1628002 SPxyl Promoter   Tianyi Huang 217
BBa_K1628003 BJ27UP Promoter a synthetic promoter Xinhao Song 100
BBa_K1628004 C2up Promoter   Xinhao Song 108
BBa_K1628005 A2cup Promoter   Yibing Wei 107
BBa_K1628006 P43 Promoter   Yibing Wei 445
BBa_K1628007 PamyA Promoter   Zhaoran Zhang 613
BBa_K1628101 pgsB Coding   Tianyi Huang 1182
BBa_K1628102 pgsCA Coding   Xinhao Song 1631
BBa_K1628201 PlacI/lacI Translational Unit   Yibing Wei 1386
BBa_K1628202 Pgrac Promoter   Tianyi Huang 120
BBa_K1628203 xylR Coding   Zhaoran Zhang 1167
BBa_K1628301 P1-GFP Device   Tianyi Huang ?
BBa_K1628202 P2-GFP Device   Xinhao Song ?
BBa_K1628303 P3-GFP Device   Yibing Wei ?

 

 

Team Parts
Basic Parts
Composite Parts
Part Collection

    Part-picture-1

    Part-picture-2

    Part-picture-3

    References

    1. Ashiuchi, M., Misono, H., 2002. Biochemistry and molecular genetics of poly-γ-glutamate synthesis. Appl. Biochem. Biotechnol. 59, 9–14.
    2. Kunioka, M., 1997. Biosynthesis and chemical reactions of poly(amino acid)s from microorganisms. Appl. Microbiol. Biotechnol. 47, 469–475.
    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.
    4. Li, C., 2002. Poly(L-glutamic acid)--anticancer drug conjugates. Adv. Drug Deliver. Rev. 54, 695–713.
    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.
    6. Richard, A., Margaritis, A., 2001. Poly (glutamic acid) for biomedical applications. Crit. Rev. Biotechnol. 21, 219–232.
    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.
    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.
    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.
    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.
    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.

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