Difference between revisions of "Team:Paris Bettencourt/Project/VitaminA"

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<br><br>
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<div class="column-left" align="justify">
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<h1 class="date three" id="design">The polycistron</h1>
 +
</div><div style="clear:both"></div>
 +
<div class="column-left" align="justify">
 +
<p>In 2014, Beekwilder & als. assembled the crtE, crtYB and crtI genes into a polycistronic construct where the individual Crt proteins were separated by the T2A sequences of the <i>Thosea asigna</i> virus.<br> Their polycistron is under the regulation of the strong yeast promoter TDH3, and the terminator TEF1.
 +
They were able to show that the addition of those genes to <i>Saccharomyces cerevisiae</i> was enough to make it produce ß-carotene.<br>
 +
<br><div align="center"><img src="https://static.igem.org/mediawiki/2015/9/95/ParisBettencourt_polycistron_schema.jpg" width="500px"></img></div>
 +
</div>
 +
 +
<div class="column-right" align="left"><b>2A sequences or cis-acting hydrolase element:</b> <br>
 +
2A like sequences are able to force the ribosome to "skip" a codon. The ribosome releases the part that it has already translated and to keep translating the mRNA. It allows transcription of multiple proteins from only 1 mRNA with 1 promoter, like bacterial polycistronic elements, but also with only one kozac sequence (yeast RBS) which ensures that the quantities of all the translated product are the same.<br>
 +
</div>
 +
<div style="clear:both"></div>
 +
 +
<div class="column-left" align="justify">
 +
<h1 class="date one" id="overview">Growth, blabla</h1>
 +
We used strain with polycistron from blabla.
 +
<br>cool figures
 +
</div>
 +
 +
<div class="column-right" align="left">Lorem ipsum
 +
</div>
 +
<div style="clear:both"></div>
 +
 +
 +
<div class="column-left" align="justify">
 +
<h1 class="date one" id="overview">Improvement??? (help to find cool title!)</h1></div>
 +
<div style="clear:both"></div>
 +
<div class="column-left" align="justify">
 +
<b>An optimized polycistron</b>
 +
<br>The amount of ß-carotene produced by the polycistronic strain is not enough to meet the daily requirement if the idli fermented with the engineered strain is the only source of vitamin A eaten in a day; which is why we aimed to strongly increase the ß-carotene yield of those yeast.
 +
<br>For this purpose, we designed a construct very similar to theirs, except that we moved the crtE gene to the first place of the polycistron, in order to increase the carotenoid yield. Indeed, it has been shown that the efficiency of translation decreases after every 2A sequence (de Felipe et al. 2006), and that an increase of CrtE may improve the ß-carotene production (Verwaal et al. 2007). We kept the same 2A sequences between the cistrons, as well as the same strong promoter TDH3 and the same terminator TEF1.
 +
<br>We also codon-optimized the three genes for <i>S. cerevisiae</i> in order to increase the genes expression. The study from Li et al. (2013) had shown that the optimization of 5 codons in the sequence of crtI, and 8 codons in the sequence of crtYB had increased the ß-carotene production in <i>S. cerevisiae</i> by 200%, so we had high hopes that codon-optimizing the whole genes would lead to even better yield.
 +
<br>The whole construct we designed was synthesized by IDT in 5 gBlocks.
 +
<br><br><br><div align="center"><img src="https://static.igem.org/mediawiki/2015/5/52/ParisBettencourt_new_polycistron.jpg" width="500px"></img></div>
 +
 +
<br><br>
 +
<b>An optimized HMG gene</b>
 +
<br>Additionally, we codon-optimized for <i>S. cerevisiae</i> the HMG-CoA reductase gene from <i>S. aureus</i> that had been used by Li & al. in 2013. Indeed, their study had shown that <i>S. cerevisiae</i> transformed with this gene had a better ß-carotene yield than the ones transformed by the tHMG1 from <i>S. cerevisiae</i>; it is highly probable than a codon-optimized version of this gene from <i>S. aureus</i> would produce even more ß-carotene.
 +
</div>
 +
 +
<div class="column-right" align="justify">
 +
<b>Chromosomal integration</b>
 +
<br>In the strain containing the polycistron designed by Beekwilder, the polycistronic construct is on a plasmid (pUDC082). But since in our final product we would like our yeast to grow on non selective media and to keep the polycistron, we designed a way to integrate the construct in the yeast chromosome. Our plan was to use the HO-Poly-KanMX4-HO plasmid (AddGene plasmid #51662) as a backbone for our construct: it's a yeast plasmid for chromosomal integration into the HO locus, with a selection marker for yeast (KanMX4). This plasmid also has an origin of replication for <i>E. coli</i> and a selection marker for bacteria (Ampicillin).
 +
 +
<br><br>Map of the HO-Poly-KanMX4-HO plasmid containing our optimized polycistron:
 +
<br>
 +
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 +
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<plasmid sequencelength='12010' plasmidheight="{{sample.size}}" plasmidwidth="{{sample.size}}">
 +
  <plasmidtrack width="5" trackstyle='fill:#ccc;stroke:#999;filter:url(#dropshadow)' style='fill:#FABE44;stroke:#000000'>
 +
        <tracklabel text='HO-E/YB/I-Poly-KanMX4-HO' labelstyle="font-size:13px"></tracklabel>
 +
      <tracklabel labelstyle="font-size:12px;font-weight:400;fill:#999" text="12,010 bp" vadjust="18"></tracklabel>
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 +
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 +
</trackmarker>
 +
        <trackmarker start='7818' end='7877' markerstyle='stroke:#000;fill:#666' wadjust="20" vadjust="-10">
 +
            <markerlabel text='2A' vadjust="40" hadjust="2" valign="outer" style="font-size:14px;font-weight:400;fill:#000000" showline="1" linevadjust="-15" linevadjust="-15" linelabelstyle="stroke:#cc0;stroke-dasharray:2,2;stroke-width:2px;"></markerlabel>
 +
</trackmarker>
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 +
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 +
</trackmarker>
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 +
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 +
</trackmarker>
 +
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            <markerlabel text='TEF1 terminator' vadjust="40" hadjust="2" valign="outer" style="font-size:14px;font-weight:400;fill:#000000" showline="1" linevadjust="-15" linevadjust="-15" linelabelstyle="stroke:#cc0;stroke-dasharray:2,2;stroke-width:2px;"></markerlabel>
 +
</trackmarker>
 +
 +
    </plasmidtrack>
 +
</plasmid>
 +
 +
<br><br>
 +
<b>Mutation optimization</b>
 +
<br>Another very different way to improve the sequence of the pathway would be to replace the regions that are the most likely to mutate by alternative, more stable versions. Indeed, our strain is meant to be released in the environment without containment and to be consumed by people, so if mutations were to happen in the genes we have engineered, the yeast's ability to produce ß-carotene could be greatly reduced, or lost. Uncontrolled mutations could also have undesirable consequences which could be dangerous for the environment or for the consumers' health.
 +
<br>To address this problem, we made a collaboration with the Vanderbilt iGEM Team 2015, who invented an algorithm to scan the sequences looking for regions that are likely to mutate. Thanks to their software they were able to find alternative versions of the crtE, crtI, crtYB and HMG-CoA genes that were more robust and durable.
 +
</div>
 +
<div style="clear:both"></div>
 +
 +
<br><br><br>
 +
 +
<h4>Bibliography</h4>
 +
<ul>
 +
<li>Li, Q., Sun, Z., Li, J. & Zhang, Y. Enhancing beta-carotene production in Saccharomyces cerevisiae by metabolic engineering. <i>FEMS Microbiology Letters</i> <b>345</b>, 94-101 (2013).</li>
 +
<li>Beekwilder, J. et al. Polycistronic expression of a ß-carotene biosynthetic pathway in Saccharomyces cerevisiae coupled to ß-ionone production. <i>Journal of Biotechnology</i> (2014).</li>
 +
<li>Voth, W.P., Richards, J.D., Shaw, J.M. & Stillman, D.J. Yeast vectors for integration at the HO locus. <i>Nucleic acids research</i> <b>29</b>, E59-E59 (2001).</li>
 +
<li>Gietz, R.D. & Schiestl, R.H. High-efficiency yeast transformation using the LiAc / SS carrier DNA / PEG method. <i>Nature Protocols</i> <b>2</b>, 31-35 (2008).</li>
 +
</ul>
  
  

Revision as of 21:25, 18 September 2015

Background

Aims

Results

The yeast S. cerevisiae can be engineered to produce ß-carotene, a precursor of vitamin A.
  • Evaluate the growth and vitamin production of S. cerevisiae in idli.
  • Improve the ß-carotene yield of S. cerevisiae.
    		•
  • Showed that the vitamin A producing yeast grows as fast as the wild type.
  • Showed that the engineered S. cerevisiae can significantly increase the amount of vitamin A in idli.
  • Designed a way to further improve the vitamin A synthesis.
    		•

    Motivation

    Vitamin A deficiency is a crucial issue in India, affecting millions of people.
    + numbers and consequences of deficiency
    The government developed different programs to provide people with vitamin A supplements, but they are not very convenient (people need to go to a center everyday to receive it), only help a small portion of the population, and the retinol present in the supplements is not as healthy as the ß-carotene found in food. Another solution which has been proposed is Golden Rice, a rice that have been genetically engineered to synthesize vitamin A. However, the Golden Rice is the subject of many controversies, and has not been implemented in India.
    Our idea is to have the vitamin A produced by the microbiome of fermented foods, and not by the cereal itself. It is much more easier, cheaper and faster to genetically engineer micro-organisms than plants. And for the consumer, it is much less intrusive and constraining to have a starter of yeast and bacteria which they can chose to add or not in their food at anytime, than to have to change their entire crops as proposed by the Golden Rice project.

    Design

    To produce vitamin A in idli, a popular indian rice cake that is fermented, we chose to use the yeast Saccharomyces cerevisiae since it is commonly found in idli batter (Soni and Sandhu, 1989 and Nout, 2009). So it has a better chance to grow well and not affect the taste of idli than a yeast that isn’t normally present in the batter. Though S. cerevisiae doesn’t naturally produces ß-carotene, it has been shown that with the introduction of two carotenogenic genes from the carotenoid-producing ascomycete Xanthophyllomyces dendrorhous, S. cerevisiae could synthesize ß-carotene (Verwaal et al., 2007). These two genes are crtYB which codes for phytoene synthase and lycopene cyclase, and crtI, which encodes phytoene desaturase.

    Additional overexpression of crtE (GGPP synthase) from X. dendrorhous, and an additional copy of a truncated 3-hydroxy-3-methylglutaryl-coenzyme A reductase gene (tHMG1) from S. cerevisiae were both reported to increase the carotenoid production levels in S. cerevisiae (Verwaal et al., 2007). A more recent study also showed that ß-carotene synthesis in this yeast could also be increased with codon-optimization of crtI and crtYB, and by introducing the HMG-CoA reductase (mva) from Staphyloccocus aureus rather than the truncated HMG-CoA reductase (tHMG1) from S. cerevisiae (Li, 2013).


    HMG-CoA: 3-hydroxy-3-methylglutaryl-coenzyme A
    HMG1 and HMG2 (paralogs): HMG-CoA reductase
    IPP: isopentenyl pyrophosphate
    DMAPP: dimethylallyl pyrophosphate
    GPP: geranyl diphosphate
    FPP: farnesyl pyrophosphate
    GGPP: geranylgeranyl-diphosphate
    CrtE: GGPP synthase
    CrtYB: lycopene cyclase/phytoene synthase
    CrtI: phytoene desaturase


    The polycistron

    In 2014, Beekwilder & als. assembled the crtE, crtYB and crtI genes into a polycistronic construct where the individual Crt proteins were separated by the T2A sequences of the Thosea asigna virus.
    Their polycistron is under the regulation of the strong yeast promoter TDH3, and the terminator TEF1. They were able to show that the addition of those genes to Saccharomyces cerevisiae was enough to make it produce ß-carotene.

    2A sequences or cis-acting hydrolase element:
    2A like sequences are able to force the ribosome to "skip" a codon. The ribosome releases the part that it has already translated and to keep translating the mRNA. It allows transcription of multiple proteins from only 1 mRNA with 1 promoter, like bacterial polycistronic elements, but also with only one kozac sequence (yeast RBS) which ensures that the quantities of all the translated product are the same.

    Growth, blabla

    We used strain with polycistron from blabla.
    cool figures
    Lorem ipsum

    Improvement??? (help to find cool title!)

    An optimized polycistron
    The amount of ß-carotene produced by the polycistronic strain is not enough to meet the daily requirement if the idli fermented with the engineered strain is the only source of vitamin A eaten in a day; which is why we aimed to strongly increase the ß-carotene yield of those yeast.
    For this purpose, we designed a construct very similar to theirs, except that we moved the crtE gene to the first place of the polycistron, in order to increase the carotenoid yield. Indeed, it has been shown that the efficiency of translation decreases after every 2A sequence (de Felipe et al. 2006), and that an increase of CrtE may improve the ß-carotene production (Verwaal et al. 2007). We kept the same 2A sequences between the cistrons, as well as the same strong promoter TDH3 and the same terminator TEF1.
    We also codon-optimized the three genes for S. cerevisiae in order to increase the genes expression. The study from Li et al. (2013) had shown that the optimization of 5 codons in the sequence of crtI, and 8 codons in the sequence of crtYB had increased the ß-carotene production in S. cerevisiae by 200%, so we had high hopes that codon-optimizing the whole genes would lead to even better yield.
    The whole construct we designed was synthesized by IDT in 5 gBlocks.




    An optimized HMG gene
    Additionally, we codon-optimized for S. cerevisiae the HMG-CoA reductase gene from S. aureus that had been used by Li & al. in 2013. Indeed, their study had shown that S. cerevisiae transformed with this gene had a better ß-carotene yield than the ones transformed by the tHMG1 from S. cerevisiae; it is highly probable than a codon-optimized version of this gene from S. aureus would produce even more ß-carotene.
    Chromosomal integration
    In the strain containing the polycistron designed by Beekwilder, the polycistronic construct is on a plasmid (pUDC082). But since in our final product we would like our yeast to grow on non selective media and to keep the polycistron, we designed a way to integrate the construct in the yeast chromosome. Our plan was to use the HO-Poly-KanMX4-HO plasmid (AddGene plasmid #51662) as a backbone for our construct: it's a yeast plasmid for chromosomal integration into the HO locus, with a selection marker for yeast (KanMX4). This plasmid also has an origin of replication for E. coli and a selection marker for bacteria (Ampicillin).

    Map of the HO-Poly-KanMX4-HO plasmid containing our optimized polycistron:


    Mutation optimization
    Another very different way to improve the sequence of the pathway would be to replace the regions that are the most likely to mutate by alternative, more stable versions. Indeed, our strain is meant to be released in the environment without containment and to be consumed by people, so if mutations were to happen in the genes we have engineered, the yeast's ability to produce ß-carotene could be greatly reduced, or lost. Uncontrolled mutations could also have undesirable consequences which could be dangerous for the environment or for the consumers' health.
    To address this problem, we made a collaboration with the Vanderbilt iGEM Team 2015, who invented an algorithm to scan the sequences looking for regions that are likely to mutate. Thanks to their software they were able to find alternative versions of the crtE, crtI, crtYB and HMG-CoA genes that were more robust and durable.



    Bibliography

    • Li, Q., Sun, Z., Li, J. & Zhang, Y. Enhancing beta-carotene production in Saccharomyces cerevisiae by metabolic engineering. FEMS Microbiology Letters 345, 94-101 (2013).
    • Beekwilder, J. et al. Polycistronic expression of a ß-carotene biosynthetic pathway in Saccharomyces cerevisiae coupled to ß-ionone production. Journal of Biotechnology (2014).
    • Voth, W.P., Richards, J.D., Shaw, J.M. & Stillman, D.J. Yeast vectors for integration at the HO locus. Nucleic acids research 29, E59-E59 (2001).
    • Gietz, R.D. & Schiestl, R.H. High-efficiency yeast transformation using the LiAc / SS carrier DNA / PEG method. Nature Protocols 2, 31-35 (2008).