Team:Minnesota/Project/Insulin

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<div style="position:absolute;top:0px;margin-left:50px; width:600px; height:450px; overflow-y:scroll; text-align:left; overflow-x:hidden;"> <!---START HERE--->
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<h1>Designing a BioBrick Compatible Pichia Expression System</h1><br>
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<h1>Constructing Parts to Express Active Human Insulin</h1><br>
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<p>Laboratory and industrial projects that involve the high volume production of a protein often select E. coli as an expression system due to its rapid growth. However, bacterial expression systems are not always a viable option. In the case where proper folding of the protein of interest requires post-translational modification such as the addition of disulfide bonds or glycosylation, a eukaryote must be used. Although several well-defined eukaryotic options exist, yeast is often selected for its ease of use in the laboratory. One yeast species in particular, P. pastoris, has gained popularity as an expression system for recombinant human proteins. P. pastoris has a glycosylation pattern that is more compatible with the human immune system, when compared to the glycosylation pattern of Saccharomyces cerevisiae. P. pastoris is also known for its ability to grow in high densities with methanol as its only food source. Despite the usefulness of yeast species such as P. pastoris there are currently few items in the parts registry that are designed for use within yeast, and none that are specifically designed to be used with P. pastoris. Our team intends on producing pBB3G1 and pBB1Z1, two BioBrick compatible P. pastoris-E. coli shuttle vectors.
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<b><font size="4"> Insulin: Basic Background </font></b><br>
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pBB3G1 and pBB1Z1 include features that increase its ease-of-use and versatility, such as optional inducibility, optional product secretion, trans-kingdom conjugation (TKC), and episomal maintenance of the vector in the host organism.
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<br>
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The vectors vary in their expression level. Constitutive expression is achieved in pBB1Z1 by the pGAP promoter. Methanol-induced expression is available in pBB3G1 by means of the pAOX1 promoter.
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Product secretion may be had by inserting an alpha secretion signal in the cloning site preceding the have been provided in both vectors.
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TKC involves the transfer of DNA from a bacterial cell to a eukaryotic cell, by means of conjugation. Harnessing the ability to shuttle plasmids between E. coli and P. pastoris through TKC would simplify transformation protocols. Currently, transformation methods using shuttle plasmids cloned in E. coli is a time consuming process, requiring isolation of the cloned plasmid, and transformation into yeast. Transformation using TKC shortens the process by transferring the plasmid directly into the yeast cell. Utilizing TKC as a transformation protocol would translate to faster results in the laboratory, and reduced costs in an industrial setting. Currently there are no BioBrick vectors in the parts registry that enable TKC between E. coli and P. pastoris.
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TKC functionality is provided by the OriT¬P sequence which hosts the nick site that will be cleaved at during the initiation of conjugation in order to linearize the plasmid, and ligated once transferred to the recipient. Importantly, the OriT¬P sequence, compared to other variations of OriT, does not require the presence of a helper plasmid within the recipient to complete the final ligation step of conjugal transfer. 
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One limitation to using P. pastoris as an expression system is that most shuttle plasmids must be integrated into the yeast chromosome. This results in lower expression of desired protein products, as well as lower transformation efficiency. We hope to improve the functionality of the pBB3G1/pBB1Z1 system, by allowing the plasmid, once transferred to the yeast cell, to remain as an episomal plasmid. This is made possible by the inclusion of the PARS1 yeast autonomous replication sequence. This sequence ensures that the plasmid is maintained through several (~200) generations.
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Transformant selection is simplified by the inclusion of antibiotic resistance genes that are effective in both E. coli and P. pastoris. The backbones that will be submitted to the parts registry will include either Zeocin or Geneticin, however the resistance genes have been cloned into a KpnI site, and may be swapped for any selective marker specific to the user’s needs.
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</p>
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<p><b>Goal</b><br> To design a BioBrick compatible <i>E. coli</i>-<i>P. pastoris</i> shuttle vector.</p>
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<p>
 +
<i><u><font size="3"></font>What is the role of Insulin in the Human body?</u></i>
 +
<br>
 +
&nbsp; &nbsp; &nbsp; Insulin is a hormone produced by the pancreas that removes glucose from the blood. In healthy individuals, excess glucose is readily removed from the blood stream by a proportional production of insulin. In persons with diabetes mellitus however; the body is either resistant to insulin, or it has a reduced capacity to produce insulin. Those individuals require an external source of insulin.
 +
<br><br>
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<p><b>Background</b><br>
 
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</p>
 
 +
<i><u><font size="3">• </font>Why are we expressing human Insulin?</u></i>
 +
<br>
 +
&nbsp; &nbsp; &nbsp; The ability to produce recombinant human Insulin cheaply has long been a lucrative goal. There are millions of people worldwide who are dependent on Insulin derived from production methods that make the product expensive -and further yet- potentially dangerous.Our team thinks that the current production methods for human Insulin are inefficient and can be optimized by being expressed in Pichia pastoris.
 +
<br><br>
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<!--2013 edit <img style="width:500px;" src="http://i1158.photobucket.com/albums/p607/iGEM_MN/caffeine_synth_resize.png">
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<i><u><font size="3">• </font>What is the current method for Human Insulin production?</u></i>
 +
<br>
 +
&nbsp; &nbsp; &nbsp; Saccharomyces cerevisiae and Escherichia coli have historically been the preferred host cells to produce recombinant human insulin; however, each one of these organisms has great disadvantages. E. coli lack secretory mechanisms, thus the cells must be lysed and processed to isolate the insulin. Another concern with E.coli is the lactose operon acting as an inducible system to control gene expression. S. cerevisiae, on the other hand, have the necessary secretory machinery to secrete insulin, but they produce it at very low yields compared to E. coli. 
 +
<br><br>
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<p><b>Figure 1.  Scheme showing proposed caffeine biosynthetic pathway in S. cerevisiae. </b></p>
 
-
  -->
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<i><u><font size="3">• </font>Why are we using Pichia pastoris to express Human Insulin?</u></i>
 +
<br>
 +
&nbsp; &nbsp; &nbsp; P. pastoris is a eukaryotic organism in the yeast family that overcomes both obstacles encountered by the aforementioned organisms. P. pastoris has been shown to excrete proteins at a rate of approximately five times that of S. cerevisiae with higher qualitative value as well. Recombinant human insulin has been produced in P. pastoris, but the harvesting and processing procedures are long, complex, and would be greatly simplified through the application of the BioBrick system. P. pastoris is already utilized by the Chinese for various industrial tasks, lending more promise to it as our choice, as industrial application would require very little change to our system. 
 +
<br><br>
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<p><b>Methods</b><br>
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<i><u><font size="3">• </font>What are some risks associated with this design?</u></i>
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<!-- 2013 edit
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<br>
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After settling on the two genes, the sequences were taken from NCBI and finalized for synthetic synthesis (XMT1 accession number DQ422954 and DXMT1 accession number DQ422955). A program was designed to optimize these plant genes for yeast use. Because of the similarity of the two genes (~88% similarity) the program was also designed to identify regions of homology between the two genes and adjust the codon usage such that homologous recombination will not occur at the nucleotide level while the overall protein sequence would be retained. The codons were chosen in descending order of complementary tRNA abundance. Any BioBrick cut sites found within the gene sequences were also removed.</p>
+
&nbsp; &nbsp; &nbsp; Our system poses a hopeful future for diabetes sufferers, but, as with any medical breakthrough there are some risks to be aware of.  Although the risk of allergy or rejection will be reduced, there may still be adverse side effects that we cannot foresee despite careful testing in the laboratory, until the synthetically secreted protein is actually trial tested in humans.  Although great caution can be taken to solidify the safety of our synthetic system, unpredictable mutations may still occur that, again, cannot be foreseen until human trials are conducted. The proposal of human trials alone poses a dilemma for ethical reasons.  
 +
<br><br><br>
 +
</p>
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<p>To synthesize the overall plasmid backbone, PCR primers were designed to amplify five desired fragments (with 25-30 bp overlap) from different plasmids, which could be joined by Gibson Assembly:<br>
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<b><font size="4"> PCSK1 </font></b><br>
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1.&nbsp;&nbsp;BioBrick destination plasmid pSB1C3 containing the MCS and rep (pMB1).<br>
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<br>
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2.&nbsp;&nbsp;BioBrick destination plasmid pSB1C3 containing the Chloramphenical resistance gene. <br>
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3.&nbsp;&nbsp;2u Gibson Extract provided by the Schmidt-Dannert lab (University of Minnesota) containing the&nbsp;&nbsp;2u ORI for yeast. <br>
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4.&nbsp;&nbsp;pkT127 provided by the Schmidt-Dannert lab containing G418 resistance genes and tTEF1.<br>
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5.&nbsp;&nbsp;ATCC plasmid provided by the Schmidt-Dannert lab containing the ADH1 promoter to drive the &nbsp;&nbsp;&nbsp;&nbsp;G418 R gene.</p>
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-->
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<p><b>Parts List</b><br>
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-
<!-- 2013 edit
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BBa_K814000&nbsp;&nbsp;dehydroquinate synthase (DHQS) generator<br>
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BBa_K814001&nbsp;&nbsp;    ATP-grasp (ATPG) generator<br>
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BBa_K814002&nbsp;&nbsp;     dehydroquinate O-methyltrasferase (O-MT) generator<br>
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<p>
 +
<i><u><font size="3">• </font>What is PCSK1?</u></i>
 +
<br>
 +
&nbsp; &nbsp; &nbsp; PCSK1 encodes for preprotein convertase type I, which is regarded as the most important enzyme in the first step of insulin processing in humans. Since our model organism P. pastoris lacks this enzyme it is hypothesized that its addition will increase efficiency of Insulin over the lineage.</p>
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BBa_K814003&nbsp;&nbsp;    shinorine non-ribosomal peptide synthase (NRPS) generator<br>
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</p>
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BBa_K814004&nbsp;&nbsp;    mycosporine-glycine biosynthetic pathway<br>
 
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BBa_K814005&nbsp;&nbsp;     shinorine biosynthetic pathway<br>
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<br>
 +
<p><b>Methods</b><br><br>
 +
&nbsp;&nbsp;&nbsp;Insulin and PCSK1 Open Reading Frame Design
 +
Sequences for insulin and its chaperone PCSK1 were obtained through NCBI. Both insulin and PCSK1 were codon optimized for expression in P. pastoris using the online Codon Optimization tool from IDT. The BioBrick consensus sequence was added to both insulin and PCSK1 in preparation for cloning into the shipping vector. Restriction sites that were incompatible with the BioBrick standard, as well as our Pichia pastoris expression system pMNBB were eliminated by altering single nucleotides while maintaining the proper amino acid sequence. Both genes were synthesized by IDT. Insulin was obtained as one 333 bp fragment, while the longer PCSK1 was split into three, roughly 750 bp fragments.
 +
<br><br>
 +
&nbsp;&nbsp;&nbsp;Fragments for insulin and PCSK1 were amplified by polymerase chain reaction (PCR). Insulin was cloned into the shipping vector. The three PCSK1 fragments were joined into the the full 2300 bp product using overlap extension PCR. The full PCSK1 product was cloned into the shipping vector. Cloning primers were not designed for PCSK1 with flanking BioBrick consensus sequences. PCSK1 was cloned into the pCR®Blunt II-TOPO® vector, provided by Invitrogen.
 +
<br><br>
 +
E. coli C2566 cultures were transformed with PCSK1- pCR®Blunt II-TOPO®. PCSK1- pCR®Blunt II-TOPO® was isolated  from transformation cultures and used as a template for PCR amplification of PCSK1 with our insulin primers that contained the BioBrick consensus sequence.
 +
<br><br>
 +
Two transformations were performed using Escherichia coli C2566, one with pSB1C3-Insulin and another with pSB1C3-PCSK1. Both constructs were submitted for sequencing.
 +
<br><br>
 +
<b>Results</b>
 +
<br><br>
 +
The products that were cloned into the shipping vector were verified by gel electrophoresis (Figure 1).
 +
<br><br>
 +
Several colonies were identified in colony screens for PCSK1 and insulin in transformants containing the shipping vector. Seen below are verification gels for PCSK1 and insulin.
 +
<br><br>
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<img src="http://i791.photobucket.com/albums/yy194/GopheriGEM/09-17-2013PCSK1ColonyScreen_zps3855c144.jpg" width=40% height=40%>
 +
<br>
 +
Figure 1. PCR colony screen of PCSK1-pSB1C3 transformants. Note the banding in each lane at roughly 750 bp, consistent with the second fragment of PCSK1.
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BBa_K814006&nbsp;&nbsp;    negative control for mycosporine-like amino acid biosynthesis<br>
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<br><br>
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<imb src="http://i791.photobucket.com/albums/yy194/GopheriGEM/9-13-2013pSB1C3-InsColonyScreen_zps8e2db536.jpg" width=40% height=40%>
 +
<br>
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BBa_K814007&nbsp;&nbsp;    ScyA (acetolactate synthase) generator<br>
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Figure 2. PCR colony screen of Ins-pSB1C3 transformants. Banding can be seen at roughly 333 bp, consistent with the full insulin ORF.
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BBa_K814008&nbsp;&nbsp;    ScyB (leucine dehydrogenase) generator<br>
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Sequencing data received for both PCSK1 and insulin was inconclusive.
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BBa_K814009&nbsp;&nbsp;    ScyC generator<br>
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<br><br>
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BBa_K814010&nbsp;&nbsp;    partial scytonemin biosynthetic pathway, scyCB<br>
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<p><b>Parts List</b><br>
 +
BBa_K1187001&nbsp;&nbsp;    Human insulin, codon optimized for expression in <i>P. pastoris</i><br><br>
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BBa_K814011&nbsp;&nbsp;    scytonemin biosynthetic pathway, scyBAC<br>
 
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BBa_K814012&nbsp;&nbsp;    XMT1 protein generator<br>
 
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BBa_K814013&nbsp;&nbsp;    DXMT1 protein generator
 
</p>
</p>
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<p><b>Figure 2:</b>  Pieces for Gibson assembly of our novel, shuttle backbone.  The individual pieces relate to the described components enumerated above. 1.  Purple arrow; 2.  Orange arrow; 3.  Green arrow; 4.  Blue arrow; 5.  Light green arrow.</p>
 
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<img src="http://i1158.photobucket.com/albums/p607/iGEM_MN/cells.jpg
 
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">
 
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<p><b>Figure 3. Creation of a shuttle vector designed for BioBrick components.</b>  A), Overnight culture of the pSB1C3 shipping vector showing RFP expression (a blank LB tube is shown as a control on the right).  B), RFP expression in the pGHMM2012 shuttle vector.  Cell pellets clearly indicate expression of RFP from this plasmid.  C), PCR screening for caffeine biosynthetic components into pGHMM2012.  The panels from left to right are positive clones for Xmt, Dxmt and controls for each of these components.</p>
 
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<img style="width:500px;" src="http://i1158.photobucket.com/albums/p607/iGEM_MN/growth_curve_resize.png">
 
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<p><b>Figure 4. Investigation of caffeine toxicity in yeast. </b>The yeast were resilient in the presence of caffeine and there was no significant decrease in growth overtime at each different concentration.  For reference, the concentration of caffeine in coffee is roughly 600mg/L.</p>
 
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<img src="http://i1158.photobucket.com/albums/p607/iGEM_MN/hplccaffeine-1_resize.jpg">
 
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<p><b>Figure 5. HPLC Data. </b>description.</p>
 
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<p><b>Conclusions</b><br>
 
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We were able to design and synthesize a novel yeast- E. coli hybrid plasmid which was optimized to prevent homologous recombination in our two synthetic genes: XMT1 and DXMT1. </p>
 
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<p>If the HPLC results can confirm the presence of caffeine in the yeast cultures, we would confirm the presence of the two target proteins by SDS-PAGE, possibly even performing antibody detection if there is difficulty confirming the presence.</p>
 
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<p>If the HPLC results cannot confirm the presence of caffeine, the first step would be to sequence our genes and align them with the sequences submitted to IDT for the gBlocks. We could also measure the production of the intermediates compared to the cultures to test whether caffeine synthesis is being arrested in the pathway.</p>
 
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<a href="https://2013.igem.org/Main_Page">iGEM Home</a> | <a href="https://igem.org/Team.cgi?id=814">Team Minnesota Info</a> |  
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<a href="https://2013.igem.org/Main_Page">iGEM Home</a> | <a href="https://igem.org/Team.cgi?id=1187">Team Minnesota Info</a> |  
<a href="http://www1.umn.edu/twincities/index.html">University of Minnesota Home</a> |  <a href="https://2013.igem.org/Team:Minnesota/Contact">Contact Us!</a>
<a href="http://www1.umn.edu/twincities/index.html">University of Minnesota Home</a> |  <a href="https://2013.igem.org/Team:Minnesota/Contact">Contact Us!</a>
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Latest revision as of 03:40, 28 September 2013

Team:Minnesota - Main Style Template Team:Minnesota - Template

Constructing Parts to Express Active Human Insulin


Insulin: Basic Background

What is the role of Insulin in the Human body?
      Insulin is a hormone produced by the pancreas that removes glucose from the blood. In healthy individuals, excess glucose is readily removed from the blood stream by a proportional production of insulin. In persons with diabetes mellitus however; the body is either resistant to insulin, or it has a reduced capacity to produce insulin. Those individuals require an external source of insulin.

Why are we expressing human Insulin?
      The ability to produce recombinant human Insulin cheaply has long been a lucrative goal. There are millions of people worldwide who are dependent on Insulin derived from production methods that make the product expensive -and further yet- potentially dangerous.Our team thinks that the current production methods for human Insulin are inefficient and can be optimized by being expressed in Pichia pastoris.

What is the current method for Human Insulin production?
      Saccharomyces cerevisiae and Escherichia coli have historically been the preferred host cells to produce recombinant human insulin; however, each one of these organisms has great disadvantages. E. coli lack secretory mechanisms, thus the cells must be lysed and processed to isolate the insulin. Another concern with E.coli is the lactose operon acting as an inducible system to control gene expression. S. cerevisiae, on the other hand, have the necessary secretory machinery to secrete insulin, but they produce it at very low yields compared to E. coli.

Why are we using Pichia pastoris to express Human Insulin?
      P. pastoris is a eukaryotic organism in the yeast family that overcomes both obstacles encountered by the aforementioned organisms. P. pastoris has been shown to excrete proteins at a rate of approximately five times that of S. cerevisiae with higher qualitative value as well. Recombinant human insulin has been produced in P. pastoris, but the harvesting and processing procedures are long, complex, and would be greatly simplified through the application of the BioBrick system. P. pastoris is already utilized by the Chinese for various industrial tasks, lending more promise to it as our choice, as industrial application would require very little change to our system.

What are some risks associated with this design?
      Our system poses a hopeful future for diabetes sufferers, but, as with any medical breakthrough there are some risks to be aware of. Although the risk of allergy or rejection will be reduced, there may still be adverse side effects that we cannot foresee despite careful testing in the laboratory, until the synthetically secreted protein is actually trial tested in humans. Although great caution can be taken to solidify the safety of our synthetic system, unpredictable mutations may still occur that, again, cannot be foreseen until human trials are conducted. The proposal of human trials alone poses a dilemma for ethical reasons.


PCSK1

What is PCSK1?
      PCSK1 encodes for preprotein convertase type I, which is regarded as the most important enzyme in the first step of insulin processing in humans. Since our model organism P. pastoris lacks this enzyme it is hypothesized that its addition will increase efficiency of Insulin over the lineage.


Methods

   Insulin and PCSK1 Open Reading Frame Design Sequences for insulin and its chaperone PCSK1 were obtained through NCBI. Both insulin and PCSK1 were codon optimized for expression in P. pastoris using the online Codon Optimization tool from IDT. The BioBrick consensus sequence was added to both insulin and PCSK1 in preparation for cloning into the shipping vector. Restriction sites that were incompatible with the BioBrick standard, as well as our Pichia pastoris expression system pMNBB were eliminated by altering single nucleotides while maintaining the proper amino acid sequence. Both genes were synthesized by IDT. Insulin was obtained as one 333 bp fragment, while the longer PCSK1 was split into three, roughly 750 bp fragments.

   Fragments for insulin and PCSK1 were amplified by polymerase chain reaction (PCR). Insulin was cloned into the shipping vector. The three PCSK1 fragments were joined into the the full 2300 bp product using overlap extension PCR. The full PCSK1 product was cloned into the shipping vector. Cloning primers were not designed for PCSK1 with flanking BioBrick consensus sequences. PCSK1 was cloned into the pCR®Blunt II-TOPO® vector, provided by Invitrogen.

E. coli C2566 cultures were transformed with PCSK1- pCR®Blunt II-TOPO®. PCSK1- pCR®Blunt II-TOPO® was isolated from transformation cultures and used as a template for PCR amplification of PCSK1 with our insulin primers that contained the BioBrick consensus sequence.

Two transformations were performed using Escherichia coli C2566, one with pSB1C3-Insulin and another with pSB1C3-PCSK1. Both constructs were submitted for sequencing.

Results

The products that were cloned into the shipping vector were verified by gel electrophoresis (Figure 1).

Several colonies were identified in colony screens for PCSK1 and insulin in transformants containing the shipping vector. Seen below are verification gels for PCSK1 and insulin.


Figure 1. PCR colony screen of PCSK1-pSB1C3 transformants. Note the banding in each lane at roughly 750 bp, consistent with the second fragment of PCSK1.


Figure 2. PCR colony screen of Ins-pSB1C3 transformants. Banding can be seen at roughly 333 bp, consistent with the full insulin ORF. Sequencing data received for both PCSK1 and insulin was inconclusive.

Parts List
BBa_K1187001   Human insulin, codon optimized for expression in P. pastoris


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