Difference between revisions of "Team:Manchester-Graz/Parts"

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<h2> Part Documentation</h2>
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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<h4>Note</h4>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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<h4>Adding parts to the registry</h4>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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<h4>What information do I need to start putting my parts on the Registry?</h4>
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<p>The information needed to initially create a part on the Registry is:</p>
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<li>Part Name</li>
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<li>Part type</li>
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<h1>Parts</h1>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<thead><tr><th>Biobrick</th><th>Description</th></tr></thead>
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<li>Design considerations</li>
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<tr><th><a href="http://parts.igem.org/Part:BBa_K1670000"> BBa_K1670000</a></th>
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<th>This part encodes for the homoserine lactone-synthase of the CepR/I-system from <i>Bulkholderia cenocepacia</i> that produces octanoyl-homoserine lactone (C8-HSL). Upstream of the start codon a ribosome-binding site is already placed.</th></tr>
  
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<tr class="odd"><th><a href="http://parts.igem.org/Part:BBa_K1670002"> BBa_K1670002</a></th>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
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<th>BBa_K1670002 (CepR) is the regulatory counterpart of the CepR/I quorum sensing system of <i>Bulkholderia cenocepacia</i>. The protein forms inclusion bodies in the absence of C8-HSL and needs to bind C8-HSL to stay in a soluble form [1] When a threshold of C8-HSL is reached, the homoserine lactone binds CepR and induces a dimerization of the regulatory protein and allows binding to its corresponding DNA-binding site in an imperfect dyad manner[1] and works as an activator of the corresponding promoter. The gene is codon optimized for <i> E.coli</i> BL21 and contains a synthetic ribosome binding site.</th></tr>
  
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<tr><th><a href="http://parts.igem.org/Part:BBa_K1670003"> BBa_K1670003</a></th>
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<th>BBa_K1670003 (P<sub>aidA</sub>_mRFP) contains the CepR/I regulated aidA promoter. The CepR binding box is located 44 bp upstream of the predicted transcription start. The part also encodes for a mRFP fluorescent reporter, based on BBa_K1362461. Two silent mutations (T213A, T435A) were introduced to delete two HindIII recognition sites. mRFP can be exchanged using an XhoI restriction site directly upstream of the start codon and the biobrick suffix. </th></tr>
  
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<tr class="odd"><th><a href="http://parts.igem.org/Part:BBa_K1670004"> BBa_K1670004</a></th>
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<th>BBa_K1670004 (EsaI) encodes for the homoserine lactone – synthase of the EsaR/I system from <i> Erwinia stewartii </i> that produces 3-oxo-hexanoyl-homoserine lactone (3OC6-HSL). Upstream of the start codon a ribosome-binding site is already placed.</th></tr>
  
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<tr><th><a href="http://parts.igem.org/Part:BBa_K1670005"> BBa_K1670005</a></th>
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<th>BBa_K1670005 encodes for the regulatory protein EsaR of the EsaR/I quorum sensing system from <i> Erwinia stewartii </i>. Contrary to most other quorum sensing systems, EsaR works as a repressor rather than an activator. It binds at its corresponding binding box between the -10 and the -35 region of its corresponding promoter and inhibits transcription. Binding of 3OC6-HSL to EsaR induced an allosteric change in the structure that prevents its DNA-binding ability and thus induces expression. If the binding box is positioned shortly upstream of the promoter, EsaR also works as an activator of the respective promoter as long as it can bind to the DNA. We use a D91G variant of the gene that shows higher sensitivity towards 3OC6-HSL [2].</th></tr>
  
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<tr class="odd"><th><a href="http://parts.igem.org/Part:BBa_K1670001"> BBa_K1670001</a></th>
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<th>BBa_K1670001 contains the EsaR/I regulated esaRC promoter, an engineered variant of the native esaR-promoter from <i> Erwinia stewartii </i> that contains two EsaR-boxes at the -10 region and between the -10 and -35 region[3] that allow a tighter control of the expression of the genes under the control of P<sub>esaRC</sub>. The part already contains a codon optimized CFP based on BBa_E0020 with a synthetic ribosome-binding site as a fluorescent reporter.  CFP can be replaced using the NdeI restriction site in the start codon as well as the biobrick suffix.</th></tr>
  
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<tr><th><a href=" http://parts.igem.org/Part:BBa_K1670008"> BBa_K1670008</a></th>
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<th>Tyrosinase from <i>Marinomonas mediterranea</i> which converts L-Tyrosine to L-DOPA. The enzyme activity of tyrosinase is enhanced by copper supplementation via the chaperone BBa_K1670009.</th></tr>
  
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<h4>Inspiration</h4>
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<tr class="odd"><th><a href="http://parts.igem.org/Part:BBa_K1670009"> BBa_K1670009</a></th>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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<th> Tyrosinase chaperone of <i>M. mediterranea</i> responsible for copper delivery to the enzyme. Aids enzymatic conversion of L-Tyrosine to L-DOPA.</th></tr>
  
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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<tr><th><a href="http://parts.igem.org/Part:BBa_K1670006"> BBa_K1670006</a></th>
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<ul>
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<th> Coding sequence for an aromatic amino acid decarboxylase which catalyses enzymatic conversion of L-Tyrosine to Tyramine as well as L-DOPA to Dopamine and L-Phenylalanine to Phenylethylamine. </th></tr>
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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</ul>
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<tr class="odd"><th><a href="http://parts.igem.org/Part:BBa_K1670007"> BBa_K1670007</a></th>
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<th> Transaminase from <i>Chromobacterium violaceum</i> transfers an amine group from alanine to DOPAL producing pyruvate as well as dopamine. </th></tr>
  
  
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<h4>Part Table </h4>
 
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<groupparts>iGEM015 Example</groupparts>
 
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[1] Weingart, C., White, C., Liu, S., Chai, Y., Cho, H., Tsai, C., Wei, Y., Delay, N., Gronquist, M., Eberhard, A. and Winans, S. (2005) Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro. Molecular Microbiology. 7 (2), pp 452-467<br>
  
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[2] Shong, J. and Collins, C. (2013) Engineering the esaR promoter for tunable quorum sensing-dependent gene expression. American Chemical Society. 2 (10), pp. 568–575. <br>
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[3] Shong, J., Huang, Y-M., Bystroff, C. and Collins, C. (2013) Directed evolution of the quorum-sensing regulator EsaR for increased signal sensitivity. American Chemical Society. 8 (4), pp 789–795. <br>
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<a class="footerlinks" href="https://2015.igem.org/Team:Manchester-Graz" style="text-decoration:none;">Home</a><br>
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iGEM Subteam Graz<br>
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TU Graz, Institute of Molecular Biotechnology<br>
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Petersgasse 14<br>
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8010 Graz<br><br>
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iGEM Subteam Manchester <br>
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University of Manchester<br>
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Manchester Institute of Biotechnology<br>
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131 Princess Street<br>
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Manchester M17DN
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Latest revision as of 02:47, 20 November 2015

iGEM Manchester Header

iGEM Manchester - Parts

Parts

BiobrickDescription
BBa_K1670000 This part encodes for the homoserine lactone-synthase of the CepR/I-system from Bulkholderia cenocepacia that produces octanoyl-homoserine lactone (C8-HSL). Upstream of the start codon a ribosome-binding site is already placed.
BBa_K1670002 BBa_K1670002 (CepR) is the regulatory counterpart of the CepR/I quorum sensing system of Bulkholderia cenocepacia. The protein forms inclusion bodies in the absence of C8-HSL and needs to bind C8-HSL to stay in a soluble form [1] When a threshold of C8-HSL is reached, the homoserine lactone binds CepR and induces a dimerization of the regulatory protein and allows binding to its corresponding DNA-binding site in an imperfect dyad manner[1] and works as an activator of the corresponding promoter. The gene is codon optimized for E.coli BL21 and contains a synthetic ribosome binding site.
BBa_K1670003 BBa_K1670003 (PaidA_mRFP) contains the CepR/I regulated aidA promoter. The CepR binding box is located 44 bp upstream of the predicted transcription start. The part also encodes for a mRFP fluorescent reporter, based on BBa_K1362461. Two silent mutations (T213A, T435A) were introduced to delete two HindIII recognition sites. mRFP can be exchanged using an XhoI restriction site directly upstream of the start codon and the biobrick suffix.
BBa_K1670004 BBa_K1670004 (EsaI) encodes for the homoserine lactone – synthase of the EsaR/I system from Erwinia stewartii that produces 3-oxo-hexanoyl-homoserine lactone (3OC6-HSL). Upstream of the start codon a ribosome-binding site is already placed.
BBa_K1670005 BBa_K1670005 encodes for the regulatory protein EsaR of the EsaR/I quorum sensing system from Erwinia stewartii . Contrary to most other quorum sensing systems, EsaR works as a repressor rather than an activator. It binds at its corresponding binding box between the -10 and the -35 region of its corresponding promoter and inhibits transcription. Binding of 3OC6-HSL to EsaR induced an allosteric change in the structure that prevents its DNA-binding ability and thus induces expression. If the binding box is positioned shortly upstream of the promoter, EsaR also works as an activator of the respective promoter as long as it can bind to the DNA. We use a D91G variant of the gene that shows higher sensitivity towards 3OC6-HSL [2].
BBa_K1670001 BBa_K1670001 contains the EsaR/I regulated esaRC promoter, an engineered variant of the native esaR-promoter from Erwinia stewartii that contains two EsaR-boxes at the -10 region and between the -10 and -35 region[3] that allow a tighter control of the expression of the genes under the control of PesaRC. The part already contains a codon optimized CFP based on BBa_E0020 with a synthetic ribosome-binding site as a fluorescent reporter. CFP can be replaced using the NdeI restriction site in the start codon as well as the biobrick suffix.
BBa_K1670008 Tyrosinase from Marinomonas mediterranea which converts L-Tyrosine to L-DOPA. The enzyme activity of tyrosinase is enhanced by copper supplementation via the chaperone BBa_K1670009.
BBa_K1670009 Tyrosinase chaperone of M. mediterranea responsible for copper delivery to the enzyme. Aids enzymatic conversion of L-Tyrosine to L-DOPA.
BBa_K1670006 Coding sequence for an aromatic amino acid decarboxylase which catalyses enzymatic conversion of L-Tyrosine to Tyramine as well as L-DOPA to Dopamine and L-Phenylalanine to Phenylethylamine.
BBa_K1670007 Transaminase from Chromobacterium violaceum transfers an amine group from alanine to DOPAL producing pyruvate as well as dopamine.

[1] Weingart, C., White, C., Liu, S., Chai, Y., Cho, H., Tsai, C., Wei, Y., Delay, N., Gronquist, M., Eberhard, A. and Winans, S. (2005) Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro. Molecular Microbiology. 7 (2), pp 452-467
[2] Shong, J. and Collins, C. (2013) Engineering the esaR promoter for tunable quorum sensing-dependent gene expression. American Chemical Society. 2 (10), pp. 568–575.
[3] Shong, J., Huang, Y-M., Bystroff, C. and Collins, C. (2013) Directed evolution of the quorum-sensing regulator EsaR for increased signal sensitivity. American Chemical Society. 8 (4), pp 789–795.