Difference between revisions of "Part:BBa K515100:Design"

(→‎Design Notes)
 
(4 intermediate revisions by 2 users not shown)
Line 5: Line 5:
  
  
−
===Design Notes===  
+
<h2>Design</h2>
−
In order to fulfill our specifications we needed to produce a construct that could express high levels of IaaH and IaaM. This was done by using the Pveg2 promoter which has a high RPU strength as well as RBS with a high translation  initiation rate. The RBS strength for the IaaM has a translation initiation rate of 18732.17. The RBS strength for the IaaH has a translation initiation rate of 33808.13 (according to the Salis labs RBS calculator).
+
<html>
−
Also, in order to make our construct more modular we have inserted 15bp insulator sequences between the promoter and RBS. These insulator sequences have been specially designed to not contain much homology with other sequences in the vector to make PCRing out the coding sequence easy. Moreover, and more importantly, these insulator sequences allow us to exchange the promoter without having to worry on the effects on the RBS.
+
<div class="imgbox" style="width:410px;margin:0 auto;">
−
Following the theme of modularity, we wanted to also be able to express the construct
+
<img src="https://static.igem.org/mediawiki/2011/7/75/ICL_auxinconstructassembly.png" width="400px"/>
−
2. bc calculator takes into account the upstream region - added insulator which allows promoter switching.
+
<p><i>Fig. 1: Assembly strategy for our Auxin Xpress construct.</i></p>
−
3. chose pVEG promoter bc it works in E. coli and B. sub. (developed program)
+
</div>
−
4. codon optimisation steps
+
<br>
 +
<p>In order to fulfill our specifications we needed to produce a construct that could express high levels of IaaH and IaaM. This was done by using the Pveg2 promoter which has a high RPU strength as well as RBS with a high translation  initiation rate. The RBS strength for the IaaM has a translation initiation rate of 18732.17. The RBS strength for the IaaH has a translation initiation rate of 33808.13 (according to the Salis labs RBS calculator).</p>
  
−
An insulator sequence has been designed upstream of the RBS (insert sequence). Its purpose is primarily to to contain no homology with the vector, thereby avoiding recombination and allowing easier PCR removal of the individual parts from the device as well as promoter switching without influencing the RBS.  
+
<p>In order to make our construct more modular we have inserted 15bp insulator sequences between the promoter and RBS. These insulator sequences have been specially designed to not contain much homology with other sequences in the vector to facilitate inverse PCR of the coding sequence. Moreover, and more importantly, these insulator sequences allow us to exchange the promoter without having to worry about the effects on the RBS.</p>
  
−
The coding regions have been optimised for B. subtilis and E. coli through the use of the program we have designed.
+
<p>Following the theme of modularity, we wanted to also be able to express the construct in <i>Escherichia coli</i> and <i>Bacillus subtilis</i>. The 2010 Imperial College team has shown that the Pveg promoter works in both <i>E. coli</i> and <i>B. subtilis</i>. Therefore we have chosen it as our promoter. Also, we have joint codon optimized our sequences so that they work efficiently in both <i>B. subtilis</i> and <i>E. coli</i>.</p>
  
−
Assembly
+
<h2>Assembly</h2>
−
1. sub parts designed and assembled by CPEC
+
<p> We ordered both the IaaM and IaaH coding sequences as two fragments to minimise cost and time (fragments 1, 2, 3, and 4). We did not want to use PCR to amplify the fragments in order to avoid introducing mutations into our final construct, and so we engineered blunt end cut sites on either side of our synthesized sequences with the MlyI restriction enzyme. Mly1 (type II restriction enzyme) cuts bluntly, 5 bp away from the recognition site. This property allowed us to cut out only the coding sequence of each fragment. Each digested fragment was then gel extracted to prepare for assembly.</p>
−
<html>
+
<p> The <a href="https://parts.igem.org/Part:pSB1C3">pSB1C3</a> vector was simultaneously inverse PCR'd to amplify the backbone vector with the required overlaps. </p>
−
The parts were assembled into pSB1C3 by <a href="http://www.nature.com/nprot/journal/v6/n2/pdf/nprot.2010.181.pdf?WT.ec_id=NPROT-201102">CPEC assembly</a>.
+
<p> We planned to combine the four fragments into the pSB1C3 vector by Gibson assembly, unfortunately our attempts failed, we postulate that this was due to homology on the backbone vector, causing it to re-anneal.</p>
 +
<p> We reverted to CPEC to assemble the construct, a method that requires more extensive use of PCR than Gibson. This said, by introducing MlyI restrictin sites, we were able to halve the number of PCR steps required, thereby reducing the potential mutation rate. </p> 
 
</html>
 
</html>
  
−
===Source===
+
<h2>Source</h2>
−
 
+
 
<p>Genomics sequence originating from <i>P. savastanoi</i>, synthesized by Eurofins.</p>
 
<p>Genomics sequence originating from <i>P. savastanoi</i>, synthesized by Eurofins.</p>
  
−
===References===
+
<h2>References</h2>

Latest revision as of 13:29, 21 September 2011

IAA biosynthetic genes under control of the Pveg2 promoter


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 547
    Illegal BamHI site found at 1492
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 254
    Illegal NgoMIV site found at 2835
  • 1000
    COMPATIBLE WITH RFC[1000]


Design

Fig. 1: Assembly strategy for our Auxin Xpress construct.


In order to fulfill our specifications we needed to produce a construct that could express high levels of IaaH and IaaM. This was done by using the Pveg2 promoter which has a high RPU strength as well as RBS with a high translation initiation rate. The RBS strength for the IaaM has a translation initiation rate of 18732.17. The RBS strength for the IaaH has a translation initiation rate of 33808.13 (according to the Salis labs RBS calculator).

In order to make our construct more modular we have inserted 15bp insulator sequences between the promoter and RBS. These insulator sequences have been specially designed to not contain much homology with other sequences in the vector to facilitate inverse PCR of the coding sequence. Moreover, and more importantly, these insulator sequences allow us to exchange the promoter without having to worry about the effects on the RBS.

Following the theme of modularity, we wanted to also be able to express the construct in Escherichia coli and Bacillus subtilis. The 2010 Imperial College team has shown that the Pveg promoter works in both E. coli and B. subtilis. Therefore we have chosen it as our promoter. Also, we have joint codon optimized our sequences so that they work efficiently in both B. subtilis and E. coli.

Assembly

We ordered both the IaaM and IaaH coding sequences as two fragments to minimise cost and time (fragments 1, 2, 3, and 4). We did not want to use PCR to amplify the fragments in order to avoid introducing mutations into our final construct, and so we engineered blunt end cut sites on either side of our synthesized sequences with the MlyI restriction enzyme. Mly1 (type II restriction enzyme) cuts bluntly, 5 bp away from the recognition site. This property allowed us to cut out only the coding sequence of each fragment. Each digested fragment was then gel extracted to prepare for assembly.

The pSB1C3 vector was simultaneously inverse PCR'd to amplify the backbone vector with the required overlaps.

We planned to combine the four fragments into the pSB1C3 vector by Gibson assembly, unfortunately our attempts failed, we postulate that this was due to homology on the backbone vector, causing it to re-anneal.

We reverted to CPEC to assemble the construct, a method that requires more extensive use of PCR than Gibson. This said, by introducing MlyI restrictin sites, we were able to halve the number of PCR steps required, thereby reducing the potential mutation rate.

Source

Genomics sequence originating from P. savastanoi, synthesized by Eurofins.

References