Team:Heidelberg/Parts

From 2013.igem.org

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<h2 id="Natural Parts">Natural Parts</h2>
<h2 id="Natural Parts">Natural Parts</h2>
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<a class="fancybox fancyGraphical" href="https://static.igem.org/mediawiki/2013/2/27/Slider_kuvette.png" style="float:left; margin-right: 10px;" title="Indigoidine synthetase activated by the different PPTases that we submitted.">
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    <figcaption style="width:200px;"> Indigoidine synthetase activated by the different PPTases that we submitted</figcaption>
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We offer several natural parts to the library. Firstly, three modules from the Tyrocidine cluster from <em>B. parabrevis</em> that are specific for three different amino acids: <a href="http://parts.igem.org/Part:BBa_K1152000">BBa_K1152000</a> (tycA) for Phenylalanine, <a href="http://parts.igem.org/Part:BBa_K1152001">BBa_K1152001</a> (tycB1) for Proline and <a href="http://parts.igem.org/Part:BBa_K1152003">BBa_K1152003</a> (tycC6) for Leucine. Secondly, we have submitted the Indigiodine synthetase indC from <em>P. luminescens</em> (cds: <a href="http://parts.igem.org/Part:BBa_K1152008">BBa_K1152008</a>, integratable device: <a href="http://parts.igem.org/Part:BBa_K1152013">BBa_K1152013</a>). And thirdly, we offer a collection of PPTases which are required enzymes in order to activate NRPSs and turn them from the apo- into the hoho-form: <a href="http://parts.igem.org/Part:BBa_K1152009">BBa_K1152009</a>, <a href="http://parts.igem.org/Part:BBa_K1152010">BBa_K1152010</a>, <a href="http://parts.igem.org/Part:BBa_K1152011">BBa_K1152011</a>, <a href="http://parts.igem.org/Part:BBa_K1152012">BBa_K1152012</a>.
We offer several natural parts to the library. Firstly, three modules from the Tyrocidine cluster from <em>B. parabrevis</em> that are specific for three different amino acids: <a href="http://parts.igem.org/Part:BBa_K1152000">BBa_K1152000</a> (tycA) for Phenylalanine, <a href="http://parts.igem.org/Part:BBa_K1152001">BBa_K1152001</a> (tycB1) for Proline and <a href="http://parts.igem.org/Part:BBa_K1152003">BBa_K1152003</a> (tycC6) for Leucine. Secondly, we have submitted the Indigiodine synthetase indC from <em>P. luminescens</em> (cds: <a href="http://parts.igem.org/Part:BBa_K1152008">BBa_K1152008</a>, integratable device: <a href="http://parts.igem.org/Part:BBa_K1152013">BBa_K1152013</a>). And thirdly, we offer a collection of PPTases which are required enzymes in order to activate NRPSs and turn them from the apo- into the hoho-form: <a href="http://parts.igem.org/Part:BBa_K1152009">BBa_K1152009</a>, <a href="http://parts.igem.org/Part:BBa_K1152010">BBa_K1152010</a>, <a href="http://parts.igem.org/Part:BBa_K1152011">BBa_K1152011</a>, <a href="http://parts.igem.org/Part:BBa_K1152012">BBa_K1152012</a>.

Revision as of 19:51, 26 October 2013

Our Parts. Fascinating stuff out of the world of non-ribosomal peptides.

Natural Parts

Indigoidine synthetase activated by the different PPTases that we submitted

We offer several natural parts to the library. Firstly, three modules from the Tyrocidine cluster from B. parabrevis that are specific for three different amino acids: BBa_K1152000 (tycA) for Phenylalanine, BBa_K1152001 (tycB1) for Proline and BBa_K1152003 (tycC6) for Leucine. Secondly, we have submitted the Indigiodine synthetase indC from P. luminescens (cds: BBa_K1152008, integratable device: BBa_K1152013). And thirdly, we offer a collection of PPTases which are required enzymes in order to activate NRPSs and turn them from the apo- into the hoho-form: BBa_K1152009, BBa_K1152010, BBa_K1152011, BBa_K1152012.

We propose BBa_K1152013 as Best new BioBrick Part, Natural, because it encodes the original NRPS module from Photorhabdus luminescens capable of synthesizing Indigoidine, which offers the opportunity to combining it with modules from other NRPSs to yield fusion peptides with a blue pigment tag. Accompanying this BioBrick, we propose two standards (RFC 99 & RFC 100) and established protocols which allow for BioBrick assembly or Gibson assembly and through this to a high-throughput creation of synthesized, tagged peptides. Besides this, Indigoidine is belived to have antimicrobial and anti-cancerous effects.

We used Indigoidine in the subprojects that were dealing with the tagging of NPRs and, in the course of this, characterized its functionality thoroughly. Hence more information on Indigoidine is available on the Peptide-Tagging page and the Tag-Optimization page.

Engineered Parts

We propose BBa_K1152009 as Most Improved Registry Part, because:
  • it encodes for sfp, a 4'-Phosphopanthetheinyl-transferase (PPTase) crucial for the activation of T domains
  • it improved the parts BBa_K802006 and BBa_K302010, which do also encode for sfp from Bacillus subtilis but were deviating in three amino acids from the sequence published on NCBI
  • it is the first BioBrick in the registry that is explicitly encoding sfp, and it is annotated and characterized

    We propose BBa_K1152015, BBa_K1152016, BBa_K1152017, BBa_K1152018, BBa_K1152019, BBa_K1152020 as Best Part Collection, because:
  • they represent a valuable ensemble of various T domains with different properties
  • they were designed semi-rationally based on multiple sequence alignments
  • they exhibit distinct synthesis rates for Indigoidine depending on the T domains of this part collection

    Engineered Devices

    Our favorite part is BBa_K1152007: Helper construct for NRP-Indigoidine-tagging.
  • Highly efficient (i.e. 0 % false-positive rate) cloning due to negative selection with ccdB.
  • Compatibility with custom non-ribosomal peptide (NRP) synthesis.
  • Optimized fusion of the NRP to Indigoidine that serves as a tag that eases detection of positive clones that synthesize the desired construct. We propose BBa_K1152007 as Best new BioBrick Part or Device, Engineered, as mentioned above.

    • List of all submitted parts:

    Thanks to

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