Team:Valencia Biocampus/Yeast

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(MOLECULAR MECHANISMS)
(INDUSTRIAL APPLICATIONS)
 
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<h2>Yeast Subteam</h2>
<h2>Yeast Subteam</h2>
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=== '''THE IDEA''' ===
=== '''THE IDEA''' ===
<br>
<br>
 +
Our aim in this part of the project is to detect when the yeast starts fermenting. At the end of the project we will be able to “ask”  the yeast if there is still any glucose in the medium or not through the addition of H2O2. Furthermore, we will be able to know for how long the media has been running out of  glucose.
 +
In conclusion, this project allows us to know how much time has elapsed since the fermentation began.
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<br>
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To do this, we are going to use two gene constructions:<br><br>
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• '''The ADH2 promoter is fused to the YAP1 protein coding sequence.''' The YAP1 protein is a yeast transcription factor regulator of H2O2 adaptive response. It is stored in the cytoplasm in normal conditions and, in the presence of H2O2, it is transported to the nucleus where it acts as a transcription factor. The ADH2 promoter is activated in the absence of glucose.
-
Our aim in this part of the project is to detect when the yeast starts to ferment. At the end of the project we will be capable of “asking”  the yeast if there is still any glucose in the media  or not by the addition of H2O2. Furthermore we will be able to know how long the media has ran out of  glucose.
+
Thus, complete disappearance of glucose triggers the production of YAP1 in the cytoplasm, and YAP1 concentration increases if the lack of glucose continues. Notice that we are working with a delta-yap1 mutant strain as a recipient of our construct.
-
In conclution, this project allows us to know how much time has elipsed since the fermentation began.
+
-
 
+
-
To do this, we are going to use two gene constructions:
+
-
 
+
-
'''The ADH2 promoter fused to the YAP1 protein coding sequence'''. The protein YAP1 is a yeast transcription factor regulator of  H2O2 adaptative response. It is stored in the citoplasm in normal conditions and, in presence of H2O2, is transported to the nucleous actting as a transcription factor.  The ADH2 promoter is activated in abscence of glucose.
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+
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So, complete disappearence of glucose [] the production of YAP1 in the citoplasm whose concentration increases if the lack of glucose continues (we work with delta-yap1 strain).
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'''The TRR promoter is fused to the GFP (Green Fluorescence Protein) coding sequence'''. The green fluorescent protein can be detected by fluorencent emission. The tiorredoxin reducase promoter  is activated by two transcriptional factors (YAP1 and SKN7 in the oxidative form), both only bind to the promoter if  H2O2 is previously added to the media.
+
 +
• '''The TRR promoter is fused to the GFP (Green Fluorescence Protein) coding sequence.''' The green fluorescent protein can be detected by fluorescent emission. The tiorredoxin reductase promoter is activated by two transcriptional factors, YAP1 and SKN7 in the oxidative form. Both of them can only bind to the promoter if H2O2 has been previously added to the culture medium.
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<br>
 +
<br><br>
=== '''MOLECULAR MECHANISMS''' ===
=== '''MOLECULAR MECHANISMS''' ===
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         <td><html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Yeast#Fermentative_response">
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         <td><html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Molecular#Yeast">
         <img src="https://static.igem.org/mediawiki/2012/f/fe/Yeast_fermentative.png" width="300" height="280" BORDER=0</a></html></td>
         <img src="https://static.igem.org/mediawiki/2012/f/fe/Yeast_fermentative.png" width="300" height="280" BORDER=0</a></html></td>
          
          
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         <td><html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Yeast#Oxidative_stress_response">
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         <td><html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Molecular#OXIDATIVE_STRESS_RESPONSE">
         <img src="https://static.igem.org/mediawiki/2012/9/9e/Yeast_oxidative.png" width="300" height="280" BORDER=0</a></html></td>
         <img src="https://static.igem.org/mediawiki/2012/9/9e/Yeast_oxidative.png" width="300" height="280" BORDER=0</a></html></td>
          
          
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Each construction was carried in different plasmids for their expression in yeast:
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==='''Fermentative response'''===
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<br><br>
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-
This construction has three parts: (1) the first transcription factor binding site inside the promoter (UAS1), (2) the second transcription factor binding site (UAS2/CSRE), (3) the coding sequence which contains the yeast AP-1 protein (YAP1). We use the promoter of the ADH2 regulated by two trans-acting elements, both necessary for maximal promoter expression in absence of a fermentable carbon source [1].
+
-
 
+
-
When is the protein synthesized? Our construction is repressed several hundred-fold in the presence of glucose so, the transcription of YAP1 protein is initiated once the glucose in the medium is exhausted. 
+
-
 
+
-
The molecular mechanism underlying this phenomenon is as follows: There are two transcriptional factors which regulates the promoter: ADR1 a carbon source-responsibe zinc-finger [2] and CAT8 [3]. In the absence of glucose both cis-acting sites in the promoter are bound cooperatively by the transcriptional activators. ADR1 binds to the UAS1 site while CAT8 binds to the UAS2/CSRE site and regulates positively the transcription of YAP1 protein by the activation of the ADH2 promoter [4]. The presence of glucose downregulates the levels of the transcription factors (ADR1 and CAT8) which results in the depletion of the production of YAP1 protein by the repression of the ADH2 promoter.
+
-
 
+
<br>
<br>
 +
'''YEplac181 carried the Fermentative response construction'''. To see further information about the vector, <html><a href="http://www.addgene.org/vector-database/4893/">click here</a></html>.
 +
<br>
 +
'''YEp352 carried the Oxidative response construction'''. To see further information about the vector, <html><a href="http://www.addgene.org/vector-database/4867/">click here</a></html>.
 +
<br><br><br>
 +
 +
=== '''INDUSTRIAL APPLICATIONS''' ===
<html>
<html>
-
<ol>
+
<br>
-
    <li>Tachibana C, et al.  (2005) Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8.Mol Cell Biol 25(6):2138-46
+
<div id="DerSup2">
-
    <li>Denis CL and Young ET  (1983) Isolation and characterization of the positive regulatory gene ADR1 from Saccharomyces cerevisiae. Mol Cell Biol3(3):360-70.
+
</html>[[Image:Aplicacionesindustriales.jpg|250px|right]]
-
 
+
</div>
-
    <li>Hedges D, et al. (1995) CAT8, a new zinc cluster-encoding gene necessary for derepression of gluconeogenic enzymes in the yeast Saccharomyces cerevisiae. Mol Cell Biol 15(4):1915-22
+
The main industrial application of our talking yeast is to know the moment at which fermentation started. This is possible because we can calculate the time elapsed since the medium ran out of glucose according to the fluorescence intensity. Taking this into account, we could ask the yeast, through the addition of hydrogen peroxide: <b>“How long have you been fermenting?”</b> And the cells would answer telling us how long it has been since all the glucose was consumed. One possible answer could be <b>“I have been fermenting for 1 hour”</b>
-
 
+
-
    <li>Walther K and Schuller HJ  (2001) Adr1 and Cat8 synergistically activate the glucose-regulated alcohol dehydrogenase gene ADH2 of the yeast Saccharomyces cerevisiae. Microbiology 147(Pt 8):2037-44
+
-
</ol>
+
-
</html>
+
<br><br>
<br><br>
-
 
+
There is also a second possible application, but it needs a more detailed explanation:
-
==='''Oxidative stress response'''===
+
<br><br>
<br><br>
-
This construction is made up of two parts: (1) a transcriptional factor binding site inside the promoter, (2) the coding sequence which contains a synthetic fluorescent (green) protein. The expression of the thioredoxin reductase (TRR) promoter is regulated by two transcription factors, YAP1 and SKN7, which work together in response to oxidative stress [1].
+
There are several factors affecting yeast ethanol production during alcoholic fermentation. <i>Saccharomyces cerevisiae</i> seems to have adapted all along its evolution to optimize its growing rate in environments that are rich in easily assimilable nutrients, such as sugars and amino acids.
 +
<br><br>
 +
There are two important characteristics responsible of <i>S. cerevisiae</i> adaptation to this particular niche. One of them is its capability of metabolizing glucose and fructose through both the respiration and the fermentation pathways. The second one is its ability to grow in aerobic and anaerobic conditions. All of this makes this species exhibit some metabolic peculiarities, such as the Pasteur and the Crabtree effects. The Crabtree effect, described in <i>S. cerevisiae</i> and in a few other yeast species, must be taken into account when ethanol production is being studied or modified during fermentation. This effect causes that, even under high concentration of oxygen and with a relatively low amount of glucose, a considerable fraction of the consumed sugar is used to produce ethanol through the fermentative pathway. This is why in every industrial process which requires yeast growth (such as starter yeast production) it is necessary to provide the optimum amount of glucose that permits its direct consumption through the respiratory pathway (or the other way round if fermentation is desirable, such in bioethanol production).  
 +
<br><br>
 +
We present here one way of monitoring the fate of glucose in the medium. By adding a small amount of hydrogen peroxide as a chemical input, we plan to ask our culture: <b>“Is there any glucose left?”</b>, and the culture would answer -according to the amount of glucose already present in the medium- what concentration would be necessary to optimize either yeast growth or fermentation through the Crabtree effect. In this way, the Crabtree effect could be monitored (perhaps even online) by measuring fluorescence and used to regulate the amount of glucose to be fed.  
 +
<br>
 +
<br>
-
When is the protein synthesized? We obtain the green fluorescent protein by the addition of hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>).
+
=== '''EXPERIMENTAL OUTLINE''' ===
-
 
+
-
The molecular mechanism underlying this phenomenon is as follows: YAP1 transcription factor is regulated by subcellular localization. Under normal conditions an exporting receptor (Crm1) escorts YAP1 from the nucleus to the cytoplasm where it is stored. In the presence of hydrogen peroxide, another protein (Hyr1) catalyzes the formation of an intramolecular disulfide bond in YAP1 [2]. This conformational change allows YAP1 to accumulate in the nucleus and binds to the TRR promoter by a bZIP DNA-binding domain. In the other side, Skn7 transcriptional factor is constitutively nuclear. In the presence of hydrogen peroxide it is able to associate with the TRR promoter. Some studies suggest that the formation of the kn7+ yap1+ DNA complex requires more than both transcription factor binding to the promoter in close proximity, and the fact that both proteins interact directly. In conclusion, the two transcriptional factors require only one biding site in the promoter [3]. Once the two proteins are bound to the TRR promoter the transcription of the green fluorescent protein starts.
+
 +
- We ordered the DNA constructions: pADH2-YAP1 protein and pTRR-GFP protein that were cloned in plasmid pUC57 with a bacterial origin of replication.
 +
<br>
 +
- We obtain the Yeplac181 and Yep352 yeast vectors by our laboratory.
 +
<br>
 +
- We carried out four transformations of <i>E. coli</i> strain DH5, one for each plasmid DNA (the two constructions and the two vectors), in order to amplify them. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Heat_Shock_Protocol_for_bacteria_transformation"> Transformation Protocol Using Heat Shock </a></html>.
 +
<br>
 +
- We obtained several <i>E. coli</i> transformants in four plates and took some colonies of each DNA construction (from both constructions and both vectors) and cultured them in liquid medium over night at 37ºC in shaking flasks.
 +
<br>
 +
- A day after, we extracted the plasmid DNA. See the Mini-preps protocol. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Mini-prep">Mini-prep Protocol</a></html>.
 +
<br>
 +
- We obtained the purified constructions (both in pUC57 plasmid) and the vectors for yeast (YEplac181 and YEp352) also purified. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Protocol_for_Gel_Extraction"> Protocol for Gel Extraction </a></html>
 +
<br>
 +
- We digested the four DNAs with restriction enzymes EcoRI and PstI in order to obtain compatible ends. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Digestion_Protocol_For_Plasmid_pUC57_.2B_Construction_Using_EcoRI_and_PstI"> Digestion Protocol </a></html>.
 +
<br>
 +
- We ligated the pTRR-GFP construction with the Yep352 vector and the ADH2-YAP1 construction with the Yeplac181 vector. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Ligation">ligation Protocol</a></html>.
 +
<br>
 +
- The day after that we transformed <i>E. coli</i> with the results of the ligation in order to amplify the final constructions (pTRR-GFP/Yep352 and pADH2-YAP1/YEplac181). We located the recombinant constructs using X-Gal and white/blue selection. 
 +
<br>
 +
- We took some of these white colonies and cultured them in liquid medium overnight at 37ºC in shaking flasks.
 +
<br>
 +
- The day after we extracted the plasmid DNA. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Mini-prep">Mini-prep Protocol</a></html>.
 +
<br>
 +
- After this, we checked the final purified recombinant constructs by electrophoresis, restriction digest and DNA capilar sequencing.
 +
<br>
 +
- We introduced the first of the DNA recombinant plasmids in the yeast. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Yeast_transformation">Yeast transformation protocol</a></html>.
 +
<br>
 +
- We selected the transformants by growth in solid and liquid mineral medium attending to the auxotrophic markers and checked the presence of the construction by PCR. See the protocol <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Colony_PCR">here</a></html>.
 +
<br>
 +
- We used the transformed yeast obtained at that moment and transformed it with the second recombinant construct. See the yeast transformation protocol. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Yeast_transformation">Yeast transformation protocol</a></html>.
 +
<br>
 +
- Once again we identified the transformants by growth in selective medium and after that we used a PCR protocol to check the presence of both constructions.
 +
<br>
 +
- In order to detect fluorescence, we carried out a protocol to induce the expression of GFP. See the <html><a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Yeast_Induction_protocol"> Yeast induction protocol </a></html>.
<br>
<br>
-
<html>
 
-
<ol>
 
-
    <li>Jaekwon Lee, Christian Godon, Gilles Lagniel, Daniel Spector, Jérome Garin, Jean Labarre and B. Toledano (1999) Yap1 and Skn7 control two specialized oxidative stress response regulons in yeast. The journal of biological chemistry 23(274): 16040-16046.
 
-
 
-
    <li>Kuge S, et al.  (1997) Regulation of yAP-1 nuclear localization in response to oxidative stress. EMBO J 16(7):1710-20
 
-
    <li>K. E. Mulford and J. S. Fassler (2011) Association of the Skn7 and Yap1 transcriptiom factors in the Saccharomyces cerevisiae oxidative Stress response. Eukaryotic cell 10(6):761
+
</div>
-
</ol>
+
-
</html>
+
-
<br><br>
+
-
 
+
-
=== '''OUTLINE''' ===
+
-
<html>
+
-
<ol>
+
-
    <li> We ordered the DNA constructions: pADH2-YAP1 protein and pTRR-GFP protein which comes in the bacterium plasmid pUC57.
+
-
    <li> We already had the Yeplac181 and Yep352 yeast vectors in our laboratory.
+
-
    <li> We carried out four transformations in E. coli, one for each DNA molecules (the two constructions and the two vectors),
+
-
        in order to clone them.See the <a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Heat_Shock"> Transformation Protocol Using Heat Shock </a>
+
-
    <li> We obtained several E. coli colonies in four dishes and took some colonies of each DNA (two constructions and two vectors) to grow them in liquid medium
+
-
        overnight  at 37 ºC in a shake chamber.
+
-
    <li> The next day we extracted the DNA molecules. See the <a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Mini-prep">Mini-prep Protocol</a>.
+
-
    <li> We obtained the purified constructions (both in pUC57 plasmid) and the purified yeast vector (YEplac181 and YEp352).
+
-
    <li> We digested the four DNA molecules with restriction enzymes EcoRI and PstI. See the
+
-
        <a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Digestion">digestion protocol</a>.
+
-
    <li> We ligated the pTRR-GFP construction with the Yep352 vector and the ADH2-YAP1 construction with the Yeplac181 vector.
+
-
        See the <a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Ligation">ligation Protocol</a>.
+
-
    <li> The day after, we transformed E.Coli with the ligation in order to amplify and store the final constructions (pTRR-GFP/Yep352 and pADH2-YAP1/YEplac181)
+
-
    <li> We took some of the colonies to grow them in liquid medium overnight at 37ºC in a shake chamber
+
-
    <li> The next day, we extracted the DNA. See the <a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Mini-prep">Mini-prep Protocol</a>.
+
-
    <li> After the final purified constructions were obtained, we checked it by electrophoresis and sequenced them.
+
-
    <li> We introduced one of the DNA constructions in yeast. See the <a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Yeast_transformation">Yeast transformation protocol</a>.
+
-
 
+
-
    <li> We checked the presence of the construction by PCR. See the protocol here.
+
-
 
+
-
    <li> We used the obtained yeast in that moment and transformed it with the second construction. See the <a href="https://2012.igem.org/Team:Valencia_Biocampus/Protocols#Yeast_transformation">Yeast transformation protocol</a>.
+
-
 
+
-
    <li> After that, we used a PCR protocol to check the presence of both constructions. In that moment, we transferred some colonies of these yeast to grow them in YPD
+
-
    <li> We measured the fluorescence at different glucose concentrations.
+
-
    <li> We obtained a curve relating these values.
+
-
</html>
+

Latest revision as of 23:15, 26 September 2012




    Yeast Subteam


    THE IDEA


    Our aim in this part of the project is to detect when the yeast starts fermenting. At the end of the project we will be able to “ask” the yeast if there is still any glucose in the medium or not through the addition of H2O2. Furthermore, we will be able to know for how long the media has been running out of glucose. In conclusion, this project allows us to know how much time has elapsed since the fermentation began.

    To do this, we are going to use two gene constructions:



    The ADH2 promoter is fused to the YAP1 protein coding sequence. The YAP1 protein is a yeast transcription factor regulator of H2O2 adaptive response. It is stored in the cytoplasm in normal conditions and, in the presence of H2O2, it is transported to the nucleus where it acts as a transcription factor. The ADH2 promoter is activated in the absence of glucose.

    Thus, complete disappearance of glucose triggers the production of YAP1 in the cytoplasm, and YAP1 concentration increases if the lack of glucose continues. Notice that we are working with a delta-yap1 mutant strain as a recipient of our construct.

    The TRR promoter is fused to the GFP (Green Fluorescence Protein) coding sequence. The green fluorescent protein can be detected by fluorescent emission. The tiorredoxin reductase promoter is activated by two transcriptional factors, YAP1 and SKN7 in the oxidative form. Both of them can only bind to the promoter if H2O2 has been previously added to the culture medium.


    MOLECULAR MECHANISMS


    Click on each plasmid to learn how our constructions work!


    Each construction was carried in different plasmids for their expression in yeast:
    YEplac181 carried the Fermentative response construction. To see further information about the vector, click here.
    YEp352 carried the Oxidative response construction. To see further information about the vector, click here.


    INDUSTRIAL APPLICATIONS


    Aplicacionesindustriales.jpg

    The main industrial application of our talking yeast is to know the moment at which fermentation started. This is possible because we can calculate the time elapsed since the medium ran out of glucose according to the fluorescence intensity. Taking this into account, we could ask the yeast, through the addition of hydrogen peroxide: “How long have you been fermenting?” And the cells would answer telling us how long it has been since all the glucose was consumed. One possible answer could be “I have been fermenting for 1 hour”.

    There is also a second possible application, but it needs a more detailed explanation:

    There are several factors affecting yeast ethanol production during alcoholic fermentation. Saccharomyces cerevisiae seems to have adapted all along its evolution to optimize its growing rate in environments that are rich in easily assimilable nutrients, such as sugars and amino acids.

    There are two important characteristics responsible of S. cerevisiae adaptation to this particular niche. One of them is its capability of metabolizing glucose and fructose through both the respiration and the fermentation pathways. The second one is its ability to grow in aerobic and anaerobic conditions. All of this makes this species exhibit some metabolic peculiarities, such as the Pasteur and the Crabtree effects. The Crabtree effect, described in S. cerevisiae and in a few other yeast species, must be taken into account when ethanol production is being studied or modified during fermentation. This effect causes that, even under high concentration of oxygen and with a relatively low amount of glucose, a considerable fraction of the consumed sugar is used to produce ethanol through the fermentative pathway. This is why in every industrial process which requires yeast growth (such as starter yeast production) it is necessary to provide the optimum amount of glucose that permits its direct consumption through the respiratory pathway (or the other way round if fermentation is desirable, such in bioethanol production).

    We present here one way of monitoring the fate of glucose in the medium. By adding a small amount of hydrogen peroxide as a chemical input, we plan to ask our culture: “Is there any glucose left?”, and the culture would answer -according to the amount of glucose already present in the medium- what concentration would be necessary to optimize either yeast growth or fermentation through the Crabtree effect. In this way, the Crabtree effect could be monitored (perhaps even online) by measuring fluorescence and used to regulate the amount of glucose to be fed.

    EXPERIMENTAL OUTLINE

    - We ordered the DNA constructions: pADH2-YAP1 protein and pTRR-GFP protein that were cloned in plasmid pUC57 with a bacterial origin of replication.
    - We obtain the Yeplac181 and Yep352 yeast vectors by our laboratory.
    - We carried out four transformations of E. coli strain DH5, one for each plasmid DNA (the two constructions and the two vectors), in order to amplify them. See the Transformation Protocol Using Heat Shock .
    - We obtained several E. coli transformants in four plates and took some colonies of each DNA construction (from both constructions and both vectors) and cultured them in liquid medium over night at 37ºC in shaking flasks.
    - A day after, we extracted the plasmid DNA. See the Mini-preps protocol. See the Mini-prep Protocol.
    - We obtained the purified constructions (both in pUC57 plasmid) and the vectors for yeast (YEplac181 and YEp352) also purified. See the Protocol for Gel Extraction
    - We digested the four DNAs with restriction enzymes EcoRI and PstI in order to obtain compatible ends. See the Digestion Protocol .
    - We ligated the pTRR-GFP construction with the Yep352 vector and the ADH2-YAP1 construction with the Yeplac181 vector. See the ligation Protocol.
    - The day after that we transformed E. coli with the results of the ligation in order to amplify the final constructions (pTRR-GFP/Yep352 and pADH2-YAP1/YEplac181). We located the recombinant constructs using X-Gal and white/blue selection.
    - We took some of these white colonies and cultured them in liquid medium overnight at 37ºC in shaking flasks.
    - The day after we extracted the plasmid DNA. See the Mini-prep Protocol.
    - After this, we checked the final purified recombinant constructs by electrophoresis, restriction digest and DNA capilar sequencing.
    - We introduced the first of the DNA recombinant plasmids in the yeast. See the Yeast transformation protocol.
    - We selected the transformants by growth in solid and liquid mineral medium attending to the auxotrophic markers and checked the presence of the construction by PCR. See the protocol here.
    - We used the transformed yeast obtained at that moment and transformed it with the second recombinant construct. See the yeast transformation protocol. See the Yeast transformation protocol.
    - Once again we identified the transformants by growth in selective medium and after that we used a PCR protocol to check the presence of both constructions.
    - In order to detect fluorescence, we carried out a protocol to induce the expression of GFP. See the Yeast induction protocol .