Difference between revisions of "Team:ZJU-China/Part Collection"

 
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{{ZJU-China}}
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<h1> Part Collection </h1>
 
  
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<p>Did your team make a lot of great parts? Is there a theme that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection, or a collection of awesome pigment parts? Describe your parts collection on this page, so the judges can evaluate you for the Best Part Collection award.</p>
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While you should put all the characterization information for your parts on the Registry, you are encouraged to explain how all your parts form a collection on this page.
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<br>
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<h3>Best Part Collection Special Prize</h3>
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<p>Did your team make a lot of great parts? Is there a team that ties all your parts together? Do you have more than 10 parts in this collection? Did you make a CRISPR collection, a MoClo collection or a collection of awesome pigment parts? Tell the judges you should be evaluated for the Best Parts Collection award! To be eligible for this award, these parts must adhere to <a href="http://parts.igem.org/DNA_Submission">Registry sample submission guidelines</a> and have been sent to the Registry of Standard Biological Parts.
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<br><br>
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If you have a collection of parts you wish to nominate your team for this <a href="https://2017.igem.org/Judging/Awards">special prize</a>, make sure you add your part numbers to your <a href="https://2017.igem.org/Judging/Judging_Form">judging form</a> and delete the box at the top of this page.</p>
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<h4>Note</h4>
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<p>This page should list all the parts in the collection your team made during your project. You must add all characterization information for your parts on the Registry. You should not put characterization information on this page.</p>
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                          <a href="#" class="dropdown-toggle link" data-toggle="dropdown">Overview<b class="caret"></b></a>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Overview">Description</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Demonstrate">Demonstrate</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Applied_Design">Applied Design</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Achievements">Achievements</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Improve">Improve Parts</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/InterLab">InterLab</a></li>
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                          </ul>
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                      </li>
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                          <a href="#" class="dropdown-toggle link" data-toggle="dropdown">Project<b class="caret"></b></a>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Project/tp">Trichoderma Proof</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Project/voc">VOC sensors</a></li>
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                              <li><a style="font-size: 0.7em!important;" href="https://2017.igem.org/Team:ZJU-China/Project/st">Chemical Signal Transduction</a></li>
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                              <li><a style="font-size: 0.7em!important;" href="https://2017.igem.org/Team:ZJU-China/Project/mt">Medium Wave Transduction</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Project/Downstream">Downstream</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Project/conclusion">Conclusions</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Notebook">Notebook</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Protocols">Protocols</a></li>
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                          </ul>
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                      </li>
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                      <li class="m_nav_item dropdown" >
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                          <a href="#" class="dropdown-toggle link" data-toggle="dropdown">Model<b class="caret"></b></a>
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                          <ul class="dropdown-menu ">
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                              <!--<li><a href="https://2017.igem.org/Team:ZJU-China/Model">Summery</a></li>-->
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Model">VOC analysis</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Model/Coculture">Coculture</a></li>
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                          </ul>
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                      </li>
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                      <li class="m_nav_item dropdown">
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                          <a href="#" class="dropdown-toggle link" data-toggle="dropdown">Parts<b class="caret"></b></a>
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                          <ul class="dropdown-menu ">
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Parts">All Parts</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Basic_Part">Basic Parts</a></li>
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                              <li><a href="https://2017.igem.org/Team:ZJU-China/Composite_Part">Composite Parts</a></li>
 +
                              <li><a href="https://2017.igem.org/Team:ZJU-China/Part_Collection">Part Collection</a></li>
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          <h1 id="improve" class="page-header ArticleHead GreenAH">Part Collection</h1>
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          <p class="PP"><br/>It is well known that T7 promoter is a kind of common promoter used for expression of heterogenous protein in some E.coli strains such as BL21(DE3). Though the wild-type T7 promoter is of high efficiency, in order to meet some specific demands, we need a series of modified T7 promoters with different strength of expression. Hence, we tried to transform the wild-type T7 promoter to get a collection of modified T7 promoters.</p>
 +
          <p class="PP">T7 RNA polymerase promoters consist of a highly conserved 23 base-pair sequence that spans the site of the initiation of transcription (+ 1) and extends from -17 to +6. As reported in some papers, the sequence specificty of T7 promoter is so strong that some mutation may make T7 promoter fail to work. Thus, with the help of some previous research, we carefully chose the site which would be mutated by PCR. These sites mainly distribute in the range from -20 to -12. The sequences of these modified promoters are shown in the Table below.</p>
 +
          <h2 id="sms" class="H2Head">Sequences of Modified Promoters</h2>
 +
          <table class="table">
 +
              <tr><th class="yellowTable">Part number</th><th class="yellowTable">Sequence(-20~+6)</th></tr>
 +
              <tr><th class="grayTable">BBa_K525998(wild type)</th><th>gagtaatacgactcactatagggaaa</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207024</th><th><a class="redgene">t</a>agtaatacgactcactatagggaaa</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207025</th><th>aa<a class="redgene">g</a>taatacgactcactatagggaaa</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207026</th><th>ga<a class="redgene">a</a>taatacgactcactatagggaaa</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207027</th><th>ga<a class="redgene">t</a>taatacgactcactatagggaaa</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207028</th><th>ga<a class="redgene">t</a>taata<a class="redgene">a</a>gactcactatagggaaa</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207029</th><th>ga<a class="redgene">t</a>taata<a class="redgene">t</a>gactcactatagggaaa</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207030</th><th><a class="redgene">t</a>a<a class="redgene">t</a>taatacgactcactatagggaaa</th></tr>
 +
          </table>
 +
 +
          <h2 id="test" class="H2Head">Test</h2>
 +
          <p class="PP">To test the function of mutant promoters, we chose the <a class="cite" href="http://parts.igem.org/Part:BBa_E1010">mRFP</a> as our reporter. By assessing the absolute fluorescence units(RFU) and OD600, we can conclude the relative strength of all promoters. When the E.coli BL21(DE3) is cultured at the stage of logarithmic phase, we added IPTG to induce the expression of mRFP in strains BL21(DE3) for 4 hours. And the result is shown as Figure and Table below.</p>
 +
          <div class="imgdiv"><img class="textimg" src="https://static.igem.org/mediawiki/2017/2/23/ZJU_China_imporve_1.png"></div>
 +
          <p class="capture">Fig.1 Relative Strength of wildtype T7 promoter and mutant promoters</p>
 +
 +
          <table class="table">
 +
              <tr><th class="yellowTable">Part number</th><th class="yellowTable">Relative Strength</th></tr>
 +
              <tr><th class="grayTable">BBa_K525998(wild type)</th><th>1</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207024</th><th>0.26</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207025</th><th>11.44</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207026</th><th>9.15</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207027</th><th>7.57</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207028</th><th>8.41</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207029</th><th>3.65</th></tr>
 +
              <tr><th class="grayTable">BBa_K2207030</th><th>6.79</th></tr>
 +
          </table>
 +
 +
          <p class="PP">As we can see from the figure, except the part K2207024, all mutant promoters showed increased strength compared with wild type T7 promoter. Therefore, our part collection enables users to control the expression of protein using T7 promoter, especially offering more opportunity for increasing the efficiency of protein expression.</p>
 +
 +
          <h2 id="ref" class="H2Head">Reference</h2>
 +
          <p class="ref">[1] Ikeda R A, Ligman C M, Warshamana S, et al. T7 promoter contacts essential for promoter activity in vivo[J]. Nucleic Acids Research, 1992, 20(10): 2517-2524.</p>
 +
          <p class="ref">[2] Tang G, Bandwar R P, Patel S S, et al. Extended Upstream A-T Sequence Increases T7 Promoter Strength[J]. Journal of Biological Chemistry, 2005, 280(49): 40707-40713.</p>
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Latest revision as of 15:18, 1 November 2017

Part Collection


It is well known that T7 promoter is a kind of common promoter used for expression of heterogenous protein in some E.coli strains such as BL21(DE3). Though the wild-type T7 promoter is of high efficiency, in order to meet some specific demands, we need a series of modified T7 promoters with different strength of expression. Hence, we tried to transform the wild-type T7 promoter to get a collection of modified T7 promoters.

T7 RNA polymerase promoters consist of a highly conserved 23 base-pair sequence that spans the site of the initiation of transcription (+ 1) and extends from -17 to +6. As reported in some papers, the sequence specificty of T7 promoter is so strong that some mutation may make T7 promoter fail to work. Thus, with the help of some previous research, we carefully chose the site which would be mutated by PCR. These sites mainly distribute in the range from -20 to -12. The sequences of these modified promoters are shown in the Table below.

Sequences of Modified Promoters

Part numberSequence(-20~+6)
BBa_K525998(wild type)gagtaatacgactcactatagggaaa
BBa_K2207024tagtaatacgactcactatagggaaa
BBa_K2207025aagtaatacgactcactatagggaaa
BBa_K2207026gaataatacgactcactatagggaaa
BBa_K2207027gattaatacgactcactatagggaaa
BBa_K2207028gattaataagactcactatagggaaa
BBa_K2207029gattaatatgactcactatagggaaa
BBa_K2207030tattaatacgactcactatagggaaa

Test

To test the function of mutant promoters, we chose the mRFP as our reporter. By assessing the absolute fluorescence units(RFU) and OD600, we can conclude the relative strength of all promoters. When the E.coli BL21(DE3) is cultured at the stage of logarithmic phase, we added IPTG to induce the expression of mRFP in strains BL21(DE3) for 4 hours. And the result is shown as Figure and Table below.

Fig.1 Relative Strength of wildtype T7 promoter and mutant promoters

Part numberRelative Strength
BBa_K525998(wild type)1
BBa_K22070240.26
BBa_K220702511.44
BBa_K22070269.15
BBa_K22070277.57
BBa_K22070288.41
BBa_K22070293.65
BBa_K22070306.79

As we can see from the figure, except the part K2207024, all mutant promoters showed increased strength compared with wild type T7 promoter. Therefore, our part collection enables users to control the expression of protein using T7 promoter, especially offering more opportunity for increasing the efficiency of protein expression.

Reference

[1] Ikeda R A, Ligman C M, Warshamana S, et al. T7 promoter contacts essential for promoter activity in vivo[J]. Nucleic Acids Research, 1992, 20(10): 2517-2524.

[2] Tang G, Bandwar R P, Patel S S, et al. Extended Upstream A-T Sequence Increases T7 Promoter Strength[J]. Journal of Biological Chemistry, 2005, 280(49): 40707-40713.


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