Team:SCUT/Project/System Construction/n-Butanol Prod

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Latest revision as of 20:47, 17 October 2014

Overview>>>

CO₂ Fixation>>>

Introduction

Design

Construction

Leading Peptide Test

References

n-Butanol Prod>>>

Introduction

Design

Construction

Localization Test

References

Introduction

Simulation

Reference

Outline

Reference

Introduction

n-Butanol

Soaring energy costs and increased awareness of global warming have motivated production of renewable, bio-mass-derived fuels and chemicals. Since butanol has a longer chain length than ethanol, it has a higher energy density than ethanol and can be blended up to 85% with gasoline; while ethanol can only be blended up to 10% due to limits set by regulation and requirements of engine modification. The high percentage of butanol-blending renders it an attractive biofuel (Figure 1).
n-Butanol can be produced either chemically from petroleum or fermentatively in a variety of Clostridial species. Clostridia are not ideal because of the relative lack of genetic tools to manipulate their metabolism, their slow growth, their intolerance to n-butanol above 1–2% and oxygen, and their production of butyrate, ace-tone, and ethanol as byproducts.

Figure 1 | Advantages of n-butanol Butanol is a potential eco fuel in the future.Compared to ethanol, n-butanol is more hydrophobic, has a higher energy density, can be transported through existing pipeline infrastructure and mixed with gasoline at any ratio.

Here we engineered Saccharomyces cerevisiae with an n-butanol biosynthetic pathway. We chose Saccharomyces cerevisiae as a host for n-butanol production because it is a genetically tractable, well-characterized organism, the current industrial strain alcohol (ethanol)producer, and it has been previously manipulated to produce other heterologous metabolites . Recently, S. cerevisiae has been demonstrated to have tolerance to n-butanol.

Mitochondrial matrix

The environment within the mitochondrial matrix differs from the cytoplasm, including '''higher pH, lower oxygen concentration, and a more reducing redox potential''', which may more closely match the optimal for maximal activity of many enzymes. Besides, the smaller volume of mitochondria, could concentrate substrates favoring faster reaction rates and productivity and confine metabolic intermediates avoiding repressive regulatory responses, diversion of intermediates into competing pathways or even toxic effects of intermediates to cytoplasmic or nuclear processes (Figure 2).

Figure 2 | Physicochemical properties of mitochondrial matrix a. powerful coenzyme generation system; b. higher concentration of substrates because of its small volume; c. avoiding competing pathways or toxic effects.

Mitochondrial matrix leading peptide

Most mitochondrial proteins are synthesized in the cytosol as larger precursors carrying mitochondria targeting signals. In this pathway, the precursor is bound by cytosolic chaperones and then delivered to a set of receptors on the outer surface of mitochondria. Then, the polypeptide chain is passed through the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. Insertion into the inner membrane is driven electrophoretically by the electrochemical potential across the membrane. Finally, the precursor is pulled completely across the membrane into the matrix by an ATP-powered translocation motor attached to the inner side of the TIM23complex. After that, the protein will be refolded by mitochondrial chaperone, and the mitochondria targeting signal will be cleaved (Figure 3).

Figure 3 | The mechanism of CoxVI signal peptide

Design

Aimed to take advantage of the potential attributes of the mitochondrial environment, we engineered Saccharomyces cerevisiae mitochondria with a n-butanol biosynthetic pathway original from Clostridium beijerinckii in which isozymes from a number of different organisms (Figure 4) were substituted for the Clostridial enzymes.

Figure 4 | The n-butanol biosynthetic pathway Enzymes are from these organisms: Erg10, S. cerevisiae; Hbd, Crt, AdhE2, Clostridium beijerinckii; Ccr, Streptomyces collinus.

As the pathway showed above, there are three reactions involving NADH (NADPH) as cofactors that are abundant in mitochondrial matrix. Additionally, production of HbCoA by 3-hydroxybutyryl-CoA dehydrogenase is the rate-limiting reaction that determines the n-butanol production in this context. All these suggest the pathway will be more efficient when translocated in mitochondria.
To accomplish our proposal, we must first translocate the n-butanol biosynthetic pathway into the mitochondrial matrix.
After reading lots of literatures about leading peptide, we chose to use the N-terminal mitochondrial localization signal from subunit VI of the yeast cytochrome c oxidase (CoxVI) (Shown in Figure 3), to target the pathway to the mitochondrial matrix.

Construction

The five genes encoding these six enzymes were cloned into two different plasmids -----YEplac181 and YEp352 (Figure 5), which can coexist in one cell. Considering our multiple-enzyme system, it is necessary to use those compatible plasmids. Most genes were synthesized by Genewiz: Hbd, Crt, AdhE2 (C. beijerinckii), and Ccr ((Streptomyces collinus). While S. cerevisiae gene: Erg10 were cloned from genomic DNA. And all enzymes were under control of GAL1 promoter with CYC1 or ADH1 terminator.

Figure 5 | Profile of reconstructed plasmids in n-butanol project

Besides targeting the n-butanol biosynthesis pathway to mitochondrial matrix with the help of CoxVI, we constructed other two plasmids without CoxVI, which locate the pathway to the cytoplasm as a control group. (Figure 6) The different n-butanol productions of the two parallel assemblies will prove whether the environment of mitochondrial matrix can make the target reactions more efficient.

Figure 6 | Construction scheme for the pathwaty targeting to cytoplasm and mitochondrial matrix

Localization Test

Leading Peptide Verification

To justify the localization ability of CoxVI, the C-terminus of CoxVI was fused to GFP; while the control group was without CoxVI (Figure 7). We use MitoTracker Red®CMXRos to stain the mitochondria and do an overlap with GFP. By observing the coefficient value, we can judge that if our leading peptide works.

Figure 7 | Construction scheme for leading peptide verification (a)positive control, (b)negative control.

To verify the localization function of CoxVI, the C-terminus of CoxVI was fused with GFP. We adopted fluorescence test to have a visible look at where the GFP is located. The following microscope images were captured (Figure 8). We can observe that the green fluorescence concentrates in a specific area , instead of diffusing homogeneously in the cytosol.The reult proves that CoxVI can perform its function properly.

Figure 8 | COXVI function verification GFP fused with COXVI is concentrated in a specific area of the cytoplasm,while GFP without COXVI diffuses in the cytoplasm of the cell.

Enzyme location confirmation

To justify whether the enzymes can be transported into mitochondrial matrix correctly with the help of CoxVI, we fused GFP to the C- terminus of all five enzymes. And of course, we set up two parallel groups, one with CoxVI targeting to the mitochondrial matrix, another without CoxVI targeting to the cytoplasm (Figure 9).

Figure 9 | Construction scheme for enzyme location verification (a)positive control, (b)negative control.

Under the confocal microscope, we can observe the location of green fluorescence, thus to confirm the exact subcellular localization of target proteins (Figure 10).

Figure 10 | Views under Ion confocal microscopy By comparing the confocal images of GAL1-Enzymes-TE and GAL1-COXVI-Enzymes-TE, we can confirm that our enzymes have been directed to mitochondria.

The result proved that fusion protein with construction strategy could be effectively localized into mitochondrial matrix of yeast.

References

[1]KOSTAS TOKATLIDIS, Directing Proteins to Mitochondria by Fusion to Mitochondrial Targeting Signals, METHODS IN ENZYMOLOGY, VOL. 321.

[2]José L. Avalos et al. (2013). Compartmentalization of metabolic pathways in yeast mitochondria improves production of branched chain alcohols. Nature Biotechnology 2059.

[3]Masayuki Inui, et al. (2008). Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biotechnol 77:1305–1316.

[4]Fischer CR, et al. (2008). Selection and optimization of microbial hosts for biofuels production. Metabolic Engineering.

[5]Eric J Steen, et al. (2008). Metabolic engineering of Saccharomyces cerevisiae for theproduction of n-butanol, Microbial Cell Factories, 7:36.

[6] DavidR.Nielsen, et al. (2009). Engineering alternative butanol production platforms in heterologous bacteria. Metabolic Engineering11, 262–273.

@@ Line 80: / Line 80: @@
-<p>Soaring energy costs and increased awareness of global warming have motivated production of renewable, bio-mass-derived fuels and chemicals. Since butanol has a longer chain length than ethanol, it has a higher energy density than ethanol and can be blended up to 85% with gasoline; while ethanol can only be blended up to 10% due to limits set by regulation and requirements of engine modification. The high percentage of butanol-blending renders it an attractive biofuel. (Figure 1)</br>
+<p>Soaring energy costs and increased awareness of global warming have motivated production of renewable, bio-mass-derived fuels and chemicals. Since butanol has a longer chain length than ethanol, it has a higher energy density than ethanol and can be blended up to 85% with gasoline; while ethanol can only be blended up to 10% due to limits set by regulation and requirements of engine modification. The high percentage of butanol-blending renders it an attractive biofuel (Figure 1).</br>
-N-Butanol can be produced either chemically from petroleum or fermentatively in a variety of Clostridial species. Clostridia are not ideal because of the relative lack of genetic tools to manipulate their metabolism, their slow growth, their intolerance to n-butanol above 1–2% and oxygen, and their production of butyrate, ace-tone, and ethanol as byproducts.</br>
+n-Butanol can be produced either chemically from petroleum or fermentatively in a variety of Clostridial species. Clostridia are not ideal because of the relative lack of genetic tools to manipulate their metabolism, their slow growth, their intolerance to n-butanol above 1–2% and oxygen, and their production of butyrate, ace-tone, and ethanol as byproducts.</br>
 </p>
+<p>
+</p>
 <p class="image">
 <img style="width:500px;"src="https://static.igem.org/mediawiki/parts/6/6e/Application_of_n-butanol.png"/>
 </p>
-<p class="zhujie"><b>Figure 1</b>
+<p class="zhujie"><b>Figure 1 | Advantages of n-butanol</b>
 Butanol is a potential eco fuel in the future.Compared to ethanol, n-butanol is more hydrophobic, has a higher energy density, can be transported through existing pipeline infrastructure and mixed with gasoline at any ratio.
 </p>
+<p>
+</p>
 <p>Here we engineered Saccharomyces cerevisiae with an n-butanol biosynthetic pathway. We chose Saccharomyces cerevisiae as a host for n-butanol production because it is a genetically tractable, well-characterized organism, the current industrial strain alcohol (ethanol)producer, and it has been previously manipulated to produce other heterologous metabolites . Recently, S. cerevisiae has been demonstrated to have tolerance to n-butanol.
 </p>
@@ Line 98: / Line 102: @@
 <p>
-The environment within the mitochondrial matrix differs from the cytoplasm, including '''higher pH, lower oxygen concentration, and a more reducing redox potential''', which may more closely match the optimal for maximal activity of many enzymes. Besides, the smaller volume of mitochondria, could concentrate substrates favoring faster reaction rates and productivity and confine metabolic intermediates avoiding repressive regulatory responses, diversion of intermediates into competing pathways or even toxic effects of intermediates to cytoplasmic or nuclear processes. (Figure 2)
+The environment within the mitochondrial matrix differs from the cytoplasm, including '''higher pH, lower oxygen concentration, and a more reducing redox potential''', which may more closely match the optimal for maximal activity of many enzymes. Besides, the smaller volume of mitochondria, could concentrate substrates favoring faster reaction rates and productivity and confine metabolic intermediates avoiding repressive regulatory responses, diversion of intermediates into competing pathways or even toxic effects of intermediates to cytoplasmic or nuclear processes (Figure 2).
 </p>
@@ Line 104: / Line 108: @@
 <img style="width:600px;"src="https://static.igem.org/mediawiki/parts/0/09/Physicochemical_property_of_mitochondrial_matrix.png"/>
 </p>
-<p class="zhujie"><b>Figure 2</b>
+<p class="zhujie"><b>Figure 2 | Physicochemical properties of mitochondrial matrix</b>
-Physicochemical property of mitochondrial matrix: a. powerful coenzyme generation system; b. higher concentration of substrates; c. avoiding competing pathways
+ a. powerful coenzyme generation system; b. higher concentration of substrates because of its small volume; c. avoiding competing pathways
 or toxic effects.
@@ Line 114: / Line 118: @@
-Mitochondrial matrix leading peptide ---- CoxVI
+Mitochondrial matrix leading peptide
 <p>
-Most mitochondrial proteins are synthesized in the cytosol as larger precursors carrying mitochondria targeting signals. In this pathway, the precursor is bound by cytosolic chaperones and then delivered to a set of receptors on the outer surface of mitochondria. Then, the polypeptide chain is passed through the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. Insertion into the inner membrane is driven electrophoretically by the electrochemical potential across the membrane. Finally, the precursor is pulled completely across the membrane into the matrix by an ATP-powered translocation motor attached to the inner side of the TIM23complex. After that, the protein will be refolded by mitochondrial chaperone, and the mitochondria targeting signal will be cleaved.(Figure 3)
+Most mitochondrial proteins are synthesized in the cytosol as larger precursors carrying mitochondria targeting signals. In this pathway, the precursor is bound by cytosolic chaperones and then delivered to a set of receptors on the outer surface of mitochondria. Then, the polypeptide chain is passed through the TOM complex in the outer membrane and the TIM23 complex in the inner membrane. Insertion into the inner membrane is driven electrophoretically by the electrochemical potential across the membrane. Finally, the precursor is pulled completely across the membrane into the matrix by an ATP-powered translocation motor attached to the inner side of the TIM23complex. After that, the protein will be refolded by mitochondrial chaperone, and the mitochondria targeting signal will be cleaved (Figure 3).
 </p>
@@ Line 123: / Line 127: @@
 <img style="width:600px;"src="https://static.igem.org/mediawiki/parts/4/48/COX6_leading_peptide_mechanism.jpg"/>
 </p>
-<p class="zhujie"><b>Figure 3</b>
+<p class="m-zhujie"><b>Figure 3 | The mechanism of CoxVI signal peptide</b>
-The mechanism of CoxVI signal peptide.
 </p>
@@ Line 140: / Line 144: @@
 <img style="width:600px;"src="https://static.igem.org/mediawiki/parts/0/00/Pathway_of_butanol.jpg"/>
 </p>
-<p class="zhujie"><b>Figure 4</b>
+<p class="zhujie"><b>Figure 4 | The n-butanol biosynthetic pathway</b>
-The n-butanol biosynthetic pathway. Enzymes are from these organisms: Erg10, S. cerevisiae; Hbd, Crt, AdhE2, Clostridium beijerinckii; Ccr, Streptomyces collinus.
+ Enzymes are from these organisms: Erg10, S. cerevisiae; Hbd, Crt, AdhE2, Clostridium beijerinckii; Ccr, Streptomyces collinus.
 </p>
@@ Line 164: / Line 168: @@
 <img style="width:600px;"src="https://static.igem.org/mediawiki/parts/4/4d/352.png"/>
 </p>
-<p class="zhujie"><b>Figure 5</b>
+<p class="m-zhujie"><b>Figure 5 | Profile of reconstructed plasmids in n-butanol project</b>
-Profile of reconstructed plasmids in n-butanol project.
 </p>
@@ Line 177: / Line 181: @@
 <img style="width:600px;"src="https://static.igem.org/mediawiki/parts/a/ac/Project11-01-1.png"/>
 </p>
-<p class="zhujie"><b>Figure 6</b>
+<p class="m-zhujie"><b>Figure 6 | Construction scheme for the pathwaty targeting to cytoplasm and mitochondrial matrix</b>
-Biobricks of cytoplasm pathwaty and mitochondria pathway.
 </p>
@@ Line 190: / Line 194: @@
 <span class="xiaobiaoti">Leading Peptide Verification<span>
-<p>To justify the localization ability of CoxVI, the C-terminus of CoxVI was fused to GFP; while the control group was without CoxVI. (Figure 7) We use MitoTracker Red®CMXRos to stain the mitochondria and do an overlap with GFP. By observing the coefficient value, we can judge that if our leading peptide works.
+<p>To justify the localization ability of CoxVI, the C-terminus of CoxVI was fused to GFP; while the control group was without CoxVI (Figure 7). We use MitoTracker Red®CMXRos to stain the mitochondria and do an overlap with GFP. By observing the coefficient value, we can judge that if our leading peptide works.
 </p>
@@ Line 197: / Line 201: @@
 </p>
 <p class="image">
-<img style="width:600px;"src="https://static.igem.org/mediawiki/parts/a/a1/Project16-01-bb.png"/>
+<img style="width:600px;"src="https://static.igem.org/mediawiki/parts/4/4f/Gal1-GFP-T-b.png"/>
 </p>
-<p class="zhujie"><b>Figure 7</b>
+<p class="zhujie"><b>Figure 7 | Construction scheme for leading peptide verification</b>
-Construction scheme for leading peptide verification: (a)positive control, (b)negative control.
+ (a)positive control, (b)negative control.
 </p>
-<p>We adopted fluorescence test to have a visible look at where the fusion protein is located. The following microscope images were obtained. (Figure 8) It was observed that green fluorescence concentrated in mitochondria stained by MitoTracker Red®CMXRos, instead of diffusing in the cytosol. Figure 8(a) proves that CoxVI can locate GFP into the mitochondrial matrix.
+<p>To verify the localization function of CoxVI, the C-terminus of CoxVI was fused with GFP. We adopted fluorescence test to have a visible look at where the GFP is located. The following microscope images were captured (Figure 8). We can observe that the green fluorescence concentrates in a specific area , instead of diffusing homogeneously in the cytosol.The reult proves that CoxVI can perform its function properly.
+</p>
+<p class="image">
+<img style="width:600px;"src="https://static.igem.org/mediawiki/parts/b/b0/G6GT.jpg"/>
+</p>
+<p class="zhujie"><b>Figure 8 | COXVI function verification</b>
+ GFP fused with COXVI is concentrated in a specific area of the cytoplasm,while GFP without COXVI diffuses in the cytoplasm of the cell.
 </p>
 Enzyme location confirmation
 <p>
-To justify whether the enzymes can be transported into mitochondrial matrix correctly with the help of CoxVI, we fused GFP to the C- terminus of all five enzymes. And of course, we set up two parallel groups, one with CoxVI targeting to the mitochondrial matrix, another without CoxVI targeting to the cytoplasm. (Figure 9)
+To justify whether the enzymes can be transported into mitochondrial matrix correctly with the help of CoxVI, we fused GFP to the C- terminus of all five enzymes. And of course, we set up two parallel groups, one with CoxVI targeting to the mitochondrial matrix, another without CoxVI targeting to the cytoplasm (Figure 9).</p>
+<p class="image">
+<img style="width:600px;"src="https://static.igem.org/mediawiki/parts/6/6d/Project14-01-aa.png"/>
+</p>
+<p class="image">
+<img style="width:600px;"src="https://static.igem.org/mediawiki/parts/a/a1/Project16-01-bb.png"/>
+</p>
+<p class="zhujie"><b>Figure 9 | Construction scheme for enzyme location verification</b>
+(a)positive control, (b)negative control.
+</p>
-<br>Under the confocal microscope, we can observe the location of green fluorescence, thus to confirm the exact subcellular localization of target proteins. (Figure 10) </br>
+<p>Under the confocal microscope, we can observe the location of green fluorescence, thus to confirm the exact subcellular localization of target proteins (Figure 10). </p>
+<p class="image">
+<img style="width:700px;"src="https://static.igem.org/mediawiki/parts/7/72/Total_%E5%89%AF%E6%9C%AC.jpg"/>
+</p>
+<p class="zhujie"><b>Figure 10 | Views under Ion confocal microscopy</b>
+ By comparing the confocal images of GAL1-Enzymes-TE and GAL1-COXVI-Enzymes-TE, we can confirm that our enzymes have been directed to mitochondria.
+</p>
-The result proved that fusion protein with construction strategy could be effectively localized into mitochondrial matrix of yeast.
+<p>The result proved that fusion protein with construction strategy could be effectively localized into mitochondrial matrix of yeast.
 </p>
 </div>
@@ Line 226: / Line 248: @@
 </p>
 <p>
-[1]KOSTAS TOKATLIDIS, Directing Proteins to Mitochondria by Fusion to Mitochondrial Targeting Signals, METHODS IN ENZYMOLOGY, VOL. 321.</br>
+[1]KOSTAS TOKATLIDIS, <b>Directing Proteins to Mitochondria by Fusion to Mitochondrial Targeting Signals</b>, METHODS IN ENZYMOLOGY, VOL. 321.</p><p>
-[2]José L. Avalos et al. (2013). Compartmentalization of metabolic pathways in yeast mitochondria improves production of branched chain alcohols. Nature Biotechnology 2059.</br>
+[2]José L. Avalos et al. (2013). <b>Compartmentalization of metabolic pathways in yeast mitochondria improves production of branched chain alcohols</b>. Nature Biotechnology 2059.</p><p>
-[3]Masayuki Inui, et al. (2008). Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biotechnol 77:1305–1316.</br>
+[3]Masayuki Inui, et al. (2008). <b>Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli</b>. Appl Microbiol Biotechnol 77:1305–1316.</p><p>
-[4]Fischer CR, et al. (2008). Selection and optimization of microbial hosts for biofuels production. Metabolic Engineering.</br>
+[4]Fischer CR, et al. (2008). <b>Selection and optimization of microbial hosts for biofuels production</b>. Metabolic Engineering.</p><p>
-[5]Eric J Steen, et al. (2008). Metabolic engineering of Saccharomyces cerevisiae for theproduction of n-butanol, Microbial Cell Factories, 7:36.</br>
+[5]Eric J Steen, et al. (2008).<b> Metabolic engineering of Saccharomyces cerevisiae for theproduction of n-butanol</b>, Microbial Cell Factories, 7:36.</p><p>
-[6] DavidR.Nielsen, et al. (2009). Engineering alternative butanol production platforms in heterologous bacteria. Metabolic Engineering11, 262–273.</br>
+[6] DavidR.Nielsen, et al. (2009).<b> Engineering alternative butanol production platforms in heterologous bacteria</b>. Metabolic Engineering11, 262–273.</p>
-</p>
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