Difference between revisions of "Team:Groningen/Parts"

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{{Groningen/PartyParrot}}
 
{{Groningen/PartyParrot}}
 
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            <h1>Parts</h1>
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                <ul class="side-sticky">
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                    <li><a class="aBG" href="#overview">Parts overview</a></li>
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                    <li><a class="aBG" href="#basic">Basic parts</a></li>
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                    <li><a class="aBG" href="#composite">Composite parts - Groningen Collection</a></li>
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                 <div class="section-header">
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                     <h2 class="headline">Parts overview</h2>
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                        <li><a class="aBG" href="#overview">Parts overview</a></li>
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                        <li><a class="aBG" href="#basic">Basic parts</a></li>
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                        <li><a class="aBG" href="#composite">Composite parts - Groningen Collection</a></li>
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                    </ul>
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                 </div>
 
                 </div>
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                 <p>Achieving the highest alpha amylase activity is the main engineering goal of the team this year. We
−
            <div class="main_right">
+
                    explored the possibilities of <strong><em>Saccharomyces spp.</em></strong> as a cell factory by
−
                 <section id="overview">
+
                    testing enzymes from different organisms; <strong><em>Bacillus subtilis, Bacillus amyloliquefaciens,
−
                    <div class="section-header">
+
                            Bacillus licheniformis</em></strong> and <strong><em>Aspergillus
−
                        <h2 class="headline">Parts overview</h2>
+
                            oryzae</em></strong><strong>.</strong></p>
−
                    </div>
+
                <p>It is sometimes hard to predict which <strong>combination</strong> of promoter, secretion signal and
−
                    <p>Achieving the highest alpha amylase activity is the main engineering goal of the team this year. We explored the possibilities of <strong><em>Saccharomyces spp.</em></strong> as a cell factory by testing enzymes from different organisms; <strong><em>Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis</em></strong> and <strong><em>Aspergillus oryzae</em></strong><strong>.</strong></p>
+
                    gene will lead to<strong> better yield</strong>. Therefore, we aimed to test as many promoters,
−
                    <p>It is sometimes hard to predict which <strong>combination</strong> of promoter, secretion signal and gene will lead to<strong> better yield</strong>. Therefore, we aimed to test as many promoters, secretion signal peptides and genes as possible. For this purpose, we used Golden Gate Assembly and took advantage of its <strong>modularity</strong> to clone our genes into a vector, creating 60 different combinations of promoters, secretion peptides and genes.</p>
+
                    secretion signal peptides and genes as possible. For this purpose, we used Golden Gate Assembly and
−
                    <p>The native sequence of alpha amylase codes for a secretion signal that is used in the native host to secrete the enzyme (as these enzymes act extracellularly). To increase the possibilities of achieving higher yields of <strong>extracellular protein,</strong> besides testing for the native secretion peptide, we isolate the CDS (coding sequence) of alpha amylase and add a different secretion peptide that has been proven to work on yeast<sup>[1]</sup>. To know more about the genetic design approach go to the <a href="https://2021.igem.org/Team:Groningen/Engineering">engineering page</a>.</p>
+
                    took advantage of its <strong>modularity</strong> to clone our genes into a vector, creating 60
−
                </section>
+
                    different combinations of promoters, secretion peptides and genes.</p>
−
                <section id="overview">
+
                <p>The native sequence of alpha amylase codes for a secretion signal that is used in the native host to
−
                    <div class="section-header">
+
                    secrete the enzyme (as these enzymes act extracellularly). To increase the possibilities of
−
                        <h2 class="headline">Basic parts</h2>
+
                    achieving higher yields of <strong>extracellular protein,</strong> besides testing for the native
−
                    </div>
+
                    secretion peptide, we isolate the CDS (coding sequence) of alpha amylase and add a different
−
                    <p>The sequences of alpha amylase from 4 different organisms were codon optimized for the chassis. The basic parts were designed from the native sequence and synthesized <em>de novo. </em>The basic parts can be found in <strong>Table 1</strong>.</p>
+
                    secretion peptide that has been proven to work on yeast<sup>[1]</sup>. To know more about the
−
                 </section>
+
                    genetic design approach go to the <a
−
                 <section id="overview">
+
                        href="https://2021.igem.org/Team:Groningen/Engineering">engineering page</a>.</p>
−
                    <div class="section-header">
+
            </section>
−
                        <h2 class="headline">Composite parts - Groningen Collection</h2>
+
            <section id="overview">
−
                    </div>
+
                <div class="section-header">
−
                </section>
+
                    <h2 class="headline">Basic parts</h2>
−
            </div>
+
                </div>
−
        </main>
+
                <p>The sequences of alpha amylase from 4 different organisms were codon optimized for the chassis. The
−
    </body>
+
                    basic parts were designed from the native sequence and synthesized <em>de novo. </em>The basic parts
−
    <script>
+
                    can be found in <strong>Table 1</strong>.</p>
 +
                 <table>
 +
                    <tbody>
 +
                        <tr>
 +
                            <td>
 +
                                <p><span>Name</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Type&nbsp;</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Description</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Designer</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Length</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748000"><span>BBa_K3748000</span></a></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Alpha amylase from </span><em><span>Bacillus amyloliquefaciens.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1545</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748001"><span>BB_K3748001</span></a></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Alpha amylase from </span><em><span>Bacillus licheniformis.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1539</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748002"><span>BB_K3748002</span></a></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Alpha amylase from </span><em><span>Bacillus subtilis.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1980</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748003"><span>BB_K3748003</span></a></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Alpha amylase from </span><em><span>Aspergillus Oryzae.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1500</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748004"><span>BBa_K3748004</span></a></p>
 +
                                <br /><br />
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Secreted Alpha amylase from </span><em><span>Bacillus amyloliquefaciens.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1545</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748005"><span>BB_K3748005</span></a></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Secreted Alpha amylase from </span><em><span>Bacillus licheniformis.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1539</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748006"><span>BB_K3748006</span></a></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Secreted Alpha amylase from </span><em><span>Bacillus subtilis.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1980</span></p>
 +
                            </td>
 +
                        </tr>
 +
                        <tr>
 +
                            <td>
 +
                                <p><a href="http://parts.igem.org/Part:BBa_K3748007"><span>BB_K3748007</span></a></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Coding</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>Secreted Alpha amylase from </span><em><span>Aspergillus Oryzae.</span></em></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>iGEM Groningen</span></p>
 +
                            </td>
 +
                            <td>
 +
                                <p><span>1500</span></p>
 +
                            </td>
 +
                        </tr>
 +
                    </tbody>
 +
                 </table>
 +
            </section>
 +
            <section id="overview">
 +
                <div class="section-header">
 +
                    <h2 class="headline">Composite parts - Groningen Collection</h2>
 +
                </div>
 +
            </section>
 +
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{{Groningen/Footer}}
 
{{Groningen/Footer}}

Revision as of 22:37, 18 October 2021

Parts

Parts overview

Achieving the highest alpha amylase activity is the main engineering goal of the team this year. We explored the possibilities of Saccharomyces spp. as a cell factory by testing enzymes from different organisms; Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis and Aspergillus oryzae.

It is sometimes hard to predict which combination of promoter, secretion signal and gene will lead to better yield. Therefore, we aimed to test as many promoters, secretion signal peptides and genes as possible. For this purpose, we used Golden Gate Assembly and took advantage of its modularity to clone our genes into a vector, creating 60 different combinations of promoters, secretion peptides and genes.

The native sequence of alpha amylase codes for a secretion signal that is used in the native host to secrete the enzyme (as these enzymes act extracellularly). To increase the possibilities of achieving higher yields of extracellular protein, besides testing for the native secretion peptide, we isolate the CDS (coding sequence) of alpha amylase and add a different secretion peptide that has been proven to work on yeast[1]. To know more about the genetic design approach go to the engineering page.

Basic parts

The sequences of alpha amylase from 4 different organisms were codon optimized for the chassis. The basic parts were designed from the native sequence and synthesized de novo. The basic parts can be found in Table 1.

Name

Type 

Description

Designer

Length

BBa_K3748000

Coding

Alpha amylase from Bacillus amyloliquefaciens.

iGEM Groningen

1545

BB_K3748001

Coding

Alpha amylase from Bacillus licheniformis.

iGEM Groningen

1539

BB_K3748002

Coding

Alpha amylase from Bacillus subtilis.

iGEM Groningen

1980

BB_K3748003

Coding

Alpha amylase from Aspergillus Oryzae.

iGEM Groningen

1500

BBa_K3748004

Coding

Secreted Alpha amylase from Bacillus amyloliquefaciens.

iGEM Groningen

1545

BB_K3748005

Coding

Secreted Alpha amylase from Bacillus licheniformis.

iGEM Groningen

1539

BB_K3748006

Coding

Secreted Alpha amylase from Bacillus subtilis.

iGEM Groningen

1980

BB_K3748007

Coding

Secreted Alpha amylase from Aspergillus Oryzae.

iGEM Groningen

1500

Composite parts - Groningen Collection