Difference between revisions of "Team:BostonU/Parts"

 
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<h3>Part Submissions</h3>
 
<h3>Part Submissions</h3>
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<p> Here is a link to our parts:
 
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<a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2015&group=BostonU" style="color:#FF9966;">Our parts page</a>
 
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</p>
 
  
 
<p>As an iGEM team, we wanted to contribute novel and functional parts to the iGEM Registry. </p>
 
<p>As an iGEM team, we wanted to contribute novel and functional parts to the iGEM Registry. </p>
  
−
<p>We submitted 3 parts integral to our experiments as BioBricks. Here is a link to our parts page on the Registry. Below we describe these parts in more detail.</p>
+
<p>We submitted 3 parts integral to our experiments as BioBricks. Here is a link to <a href="http://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2015&group=BostonU" style="color:#FF9966;">our parts page on the Registry</a>. Below we describe these parts in more detail.</p>
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<p><b>Recombination Directionality Factors:</b></p>
 +
<p><a href="http://parts.igem.org/Part:BBa_K1733000" style="color:#FF9966;">orf7</a></p>
  
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<p>Recombination Directionality Factors:</p>
 
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<p>orf7</p>
 
 
<p>This part (K1733000) contains the orf7 recombination directionality factor, corresponding to the TP901-1 integrase. It catalyzes the unidirectional inverse reaction of the TP901-1 integrase, allowing for the inversion, deletion, and cassette exchange of sequences of DNA flanked by specific recombination sites.
 
<p>This part (K1733000) contains the orf7 recombination directionality factor, corresponding to the TP901-1 integrase. It catalyzes the unidirectional inverse reaction of the TP901-1 integrase, allowing for the inversion, deletion, and cassette exchange of sequences of DNA flanked by specific recombination sites.
 
</p>
 
</p>
 
<p>Orf7 recognizes AttL and AttR recombination sites that flank sequences of interest, and, when both TP901-1 and orf7 are present, the sequence within the recombination sites can be manipulated. After performing the reaction, orf7 will no longer recognize the recombination sites, since they change to AttB and AttP sites, so the sequence cannot be reverted as such.</p>
 
<p>Orf7 recognizes AttL and AttR recombination sites that flank sequences of interest, and, when both TP901-1 and orf7 are present, the sequence within the recombination sites can be manipulated. After performing the reaction, orf7 will no longer recognize the recombination sites, since they change to AttB and AttP sites, so the sequence cannot be reverted as such.</p>
 +
 
<p>We characterized functionality of the intact orf7 against a fluorescent reporter plasmid. This plasmid encoded for an mRuby protein in the inverse orientation, between AttL and AttR sites. We transfected this reporter with an intact TP901-1 protein and the orf7 protein, and the proteins catalyzed the inversion reaction to yield expression of mRuby. Below is the characterization data of our orf7 part:</P>
 
<p>We characterized functionality of the intact orf7 against a fluorescent reporter plasmid. This plasmid encoded for an mRuby protein in the inverse orientation, between AttL and AttR sites. We transfected this reporter with an intact TP901-1 protein and the orf7 protein, and the proteins catalyzed the inversion reaction to yield expression of mRuby. Below is the characterization data of our orf7 part:</P>
  
 +
<center><img src="https://static.igem.org/mediawiki/2015/thumb/1/11/Orf7_data_set_a.png/489px-Orf7_data_set_a.png" style="width:25%;height:25%;"/><center>
  
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<center><img src="https://static.igem.org/mediawiki/2015/thumb/7/73/Aba_tp901_.png/800px-Aba_tp901_.png" style="width:50%;height:50%;"/><center>
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<p>Importantly, our part was characterized in a mammalian expression system. We have not characterized this part in other chassis.</p>
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+
−
<p>Importantly, our part was characterized in a mammalian expression system. We have not characterized this part in other chasses.</p>
+
  
 
<p><b>Dimerization Domains:</b></p>
 
<p><b>Dimerization Domains:</b></p>
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<p>These parts (K1733001 and K1733002) contain the ABI (ABA insensititve 1) and PYL (pyrabactin resistance like) protein domains that dimerize in the presence of the small molecule abscisic acid (ABA). By fusing these dimerization domains to inert halves of a protein, and adding or removing ABA, we were able to control the function and activities of several split proteins. We believe that other iGEM teams can take advantage of this conditional dimerization system to regulate their own protein activities.</p>
 
<p>These parts (K1733001 and K1733002) contain the ABI (ABA insensititve 1) and PYL (pyrabactin resistance like) protein domains that dimerize in the presence of the small molecule abscisic acid (ABA). By fusing these dimerization domains to inert halves of a protein, and adding or removing ABA, we were able to control the function and activities of several split proteins. We believe that other iGEM teams can take advantage of this conditional dimerization system to regulate their own protein activities.</p>
−
<p>Both ABI and PYL are found in plants1. Thus, they can be implemented in mammalian cells, since the system is orthogonal. We tested our system using split integrase proteins in mammalian cells. </p>
 
−
<p>We characterized functionality of this domain in several split amino acid locations. One example shown below included splitting the TP901-1 protein and fusing halves to ABI and PYL respectively. We added ABA into our media to induce dimerization of the domains and protein halves, and measured the protein activity of TP901-1 afterwards. We were able to characterize some functional splits, since we regained TP901-1 activity after inducing dimerization. One functional split site (between amino acids 326-327) is shown below:</p>
 
  
−
<p></p>
+
<p>Both ABI and PYL are found in plants. Thus, they can be implemented in mammalian cells, since the system is orthogonal. We tested our system using split integrase proteins in mammalian cells. </p>
  
−
<p>In the above experiment, we tested both domain fusion orientations. Proper TP901-1 activity led to expression of our mRuby fluorescent protein, which can be seen in both cases above. Read more about our fluorescent reporter experiment here.</p>
+
<p>We characterized functionality of this domain in several split amino acid locations. One example shown below included splitting the TP901-1 protein and fusing halves to ABI and PYL respectively. We added ABA into our media to induce dimerization of the domains and protein halves, and measured the protein activity of TP901-1 afterwards. We were able to characterize some functional splits, since we regained TP901-1 activity after inducing dimerization. One functional split site (between amino acids 326-327) is shown below:</p>
  
−
<p>Importantly, our parts were characterized in a mammalian expression system. We have not characterized these part in other chasses.</p>
 
  
−
<p><b>Recombination Directionality Factors:</b></p>
+
<center><img src="https://static.igem.org/mediawiki/2015/thumb/7/73/Aba_tp901_.png/800px-Aba_tp901_.png" style="width:50%;height:50%;"/><center>
−
<p><a href="http://parts.igem.org/Part:BBa_K1733000" style="color:#FF9966;">orf7</a></p>
+
  
−
<p>This part contains orf7, which is the corresponding recombination directionality factor to the TP901-1 integrase. It catalyzes the unidirectional inverse reaction of the TP901-1 integrase, allowing for the inversion, deletion, and cassette exchange of sequences of DNA.</p>
+
<p>In the above experiment, we tested both domain fusion orientations. Proper TP901-1 activity led to expression of our mRuby fluorescent protein, which can be seen in both cases above. Read more about our fluorescent reporter experiment <a href="https://2015.igem.org/Team:BostonU/App_1/Design" style="color:#FF9966;">here</a>.</p>
−
<p>Orf7 recognizes AttL and AttR recombination sites that flank some sequence of interest, and, when both TP901-1 and orf7 are present, the sequence within the recombination sites is can be inverted, deleted, or undergo cassette exchange with another sequence of DNA. After performing the reaction, orf7 will no longer recognize the recombination sites (AttP and AttB), so the sequence will not continually inverting.</p>
+
−
<p>To test this part within our project, we used a reporter that contained a gene that codes for a fluorescent protein flanked by the AttL and AttR recombination sites. Originally, this fluorescent protein is unexpressed, but when we add TP901-1 and orf7 to the system, the proteins catalyze the inversion reaction, the sequence in between the recombination sites is flipped, and the fluorescent protein is expressed. Below is the fluorescence expressed for the full orf7 RDF.</p>
+
  
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<center><img src="https://static.igem.org/mediawiki/2015/thumb/1/11/Orf7_data_set_a.png/489px-Orf7_data_set_a.png" style="width:25%;height:25%;"/><center>
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<p>Considerations with other parts:
 +
We intended to submit more parts to the iGEM registry, including other dimerization domains that we used (FKBP and FRB, CRY2 and CIBN), other integrases and RDFs (TP901-1, PhiC31, and gp3). Some of these were already in the Registry. However several of these protein domains were extremely large and did not conform with the BioBrick standard since they contained several internal restriction sites.  
 +
</p>
  
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<p>Orf7 and TP901-1 can be used in further applications to create a switch to flip and knock out a gene of interest.</p>
+
<p><b>Considerations with other parts</b><p>
  
−
<p>We had intended to submit more parts, including the other dimerization domains that we'd used (FKBP/FRB and CRY2/CIBN) and the other integrases and RDFs that we had split (TP901-1, Phic31, and gp3). However, these protein domains were large and were not up to the Biobrick standard, containing at least one of the restriction sites within the protein sequence. Often these proteins in mammalian cells do not conform to the Biobrick restrictions. Luckily, orf7 and PYL were up to Biobrick standards. ABI had one restriction site, so we had to introduce a silent mutation and had IDT synthesize a new part for us to Biobrick. We recognize that working with mammalian parts often leads to problems with Biobricking, and so we have proposed some solutions to this issue on our <a href="https://2015.igem.org/Team:BostonU/Mammalian_synbio/Solutions" style="color:#FF9966;">Mammalian Syn Bio Research solutions page here</a>.<p>
+
<p>We intended to submit more parts to the iGEM registry, including other dimerization domains that we used (FKBP and FRB, CRY2 and CIBN), other integrases and RDFs (TP901-1, PhiC31, and gp3). Some of these were already in the Registry. However several of these protein domains were extremely large and did not conform with the BioBrick standard since they contained several internal restriction sites. <p>
 +
 
 +
<p>We were able to introduce a silent mutation into ABI such that it was BioBrick compatible (thanks to IDT for the synthesis offer). We were also easily able to submit orf7 and PYL because these were BioBrick compatible. We recognize that working with large parts pose such BioBrick issues, and we discuss possible ways to mitigate this on <a href="https://2015.igem.org/Team:BostonU/Mammalian_synbio/Current_Challenges" style="color:#FF9966;">our mammalian synthetic biology challenges page</a>.
 +
</p>
  
−
<p>Additionally, we had intended to characterize an SpCas9 part from the 2013 Freiburg team using flow cytometry. We had wanted to add an NLS (nuclear localization sequence) to the part in order to improve its function. The NLS tags the SpCas9 for transport into the nucleus, and since SpCas9 performs its function into the nucleus, this NLS would allow for optimal SpCas9 activity. However, this part was difficult to clone. We wanted to characterize and submit our human codon optimized SpCas9 with an NLS; however, this was not up to Biobrick standards.</p>
+
<p>We also intended to characterize the spCas9 part from the 2013 Freiburg team using flow cytometry, in part to also have an intact spCas9 control for our own experiments. This part was a bacterial-optimized part; we aimed to add a Nuclear Localization Sequence (NLS) to the spCas9 protein such that it would function better in our mammalian system, as the protein needs to be in the nucleus to have proper functionality. However, we had difficulties cloning this part, and furthermore, found it difficult to re-BioBrick.</p>
  
 
<h4 style="font-size:16px; text-align:center;">Citations</h4>
 
<h4 style="font-size:16px; text-align:center;">Citations</h4>

Latest revision as of 00:26, 19 September 2015

Parts

Part Submissions

As an iGEM team, we wanted to contribute novel and functional parts to the iGEM Registry.

We submitted 3 parts integral to our experiments as BioBricks. Here is a link to our parts page on the Registry. Below we describe these parts in more detail.

Recombination Directionality Factors:

orf7

This part (K1733000) contains the orf7 recombination directionality factor, corresponding to the TP901-1 integrase. It catalyzes the unidirectional inverse reaction of the TP901-1 integrase, allowing for the inversion, deletion, and cassette exchange of sequences of DNA flanked by specific recombination sites.

Orf7 recognizes AttL and AttR recombination sites that flank sequences of interest, and, when both TP901-1 and orf7 are present, the sequence within the recombination sites can be manipulated. After performing the reaction, orf7 will no longer recognize the recombination sites, since they change to AttB and AttP sites, so the sequence cannot be reverted as such.

We characterized functionality of the intact orf7 against a fluorescent reporter plasmid. This plasmid encoded for an mRuby protein in the inverse orientation, between AttL and AttR sites. We transfected this reporter with an intact TP901-1 protein and the orf7 protein, and the proteins catalyzed the inversion reaction to yield expression of mRuby. Below is the characterization data of our orf7 part:

Importantly, our part was characterized in a mammalian expression system. We have not characterized this part in other chassis.

Dimerization Domains:

ABI and PYL

These parts (K1733001 and K1733002) contain the ABI (ABA insensititve 1) and PYL (pyrabactin resistance like) protein domains that dimerize in the presence of the small molecule abscisic acid (ABA). By fusing these dimerization domains to inert halves of a protein, and adding or removing ABA, we were able to control the function and activities of several split proteins. We believe that other iGEM teams can take advantage of this conditional dimerization system to regulate their own protein activities.

Both ABI and PYL are found in plants. Thus, they can be implemented in mammalian cells, since the system is orthogonal. We tested our system using split integrase proteins in mammalian cells.

We characterized functionality of this domain in several split amino acid locations. One example shown below included splitting the TP901-1 protein and fusing halves to ABI and PYL respectively. We added ABA into our media to induce dimerization of the domains and protein halves, and measured the protein activity of TP901-1 afterwards. We were able to characterize some functional splits, since we regained TP901-1 activity after inducing dimerization. One functional split site (between amino acids 326-327) is shown below:

In the above experiment, we tested both domain fusion orientations. Proper TP901-1 activity led to expression of our mRuby fluorescent protein, which can be seen in both cases above. Read more about our fluorescent reporter experiment here.

Considerations with other parts: We intended to submit more parts to the iGEM registry, including other dimerization domains that we used (FKBP and FRB, CRY2 and CIBN), other integrases and RDFs (TP901-1, PhiC31, and gp3). Some of these were already in the Registry. However several of these protein domains were extremely large and did not conform with the BioBrick standard since they contained several internal restriction sites.

Considerations with other parts

We intended to submit more parts to the iGEM registry, including other dimerization domains that we used (FKBP and FRB, CRY2 and CIBN), other integrases and RDFs (TP901-1, PhiC31, and gp3). Some of these were already in the Registry. However several of these protein domains were extremely large and did not conform with the BioBrick standard since they contained several internal restriction sites.

We were able to introduce a silent mutation into ABI such that it was BioBrick compatible (thanks to IDT for the synthesis offer). We were also easily able to submit orf7 and PYL because these were BioBrick compatible. We recognize that working with large parts pose such BioBrick issues, and we discuss possible ways to mitigate this on our mammalian synthetic biology challenges page.

We also intended to characterize the spCas9 part from the 2013 Freiburg team using flow cytometry, in part to also have an intact spCas9 control for our own experiments. This part was a bacterial-optimized part; we aimed to add a Nuclear Localization Sequence (NLS) to the spCas9 protein such that it would function better in our mammalian system, as the protein needs to be in the nucleus to have proper functionality. However, we had difficulties cloning this part, and furthermore, found it difficult to re-BioBrick.

Citations

  1. Liang, Fu-Sen, Ho, Wen Qi, Crabtree, Gerald R., “Engineering the ABA Stress Pathway for Regulation of Induced Proximity”, Sci Signal, 2011.