Difference between revisions of "Team:ShanghaitechChina/Hydrogen"

Latest revision as of 22:22, 19 October 2016

igem2016:ShanghaiTech

Construction of [FeFe]-hydrogenases gene cluster

Principle of Molecular Cloning

To ensure normal enzyme activity, we need to make sure that these four enzymes are simultaneously expressed in E. coli with a moderate amount. The well-established high-efficiency Acembl system [5] came into our sight.

We adopted this Acembl system as a multi-expression system with special DNA replication origin and Cre-loxP site, which utilizes Cre recombinase to integrate four basic plasmid backbones into one. (Figure 3) Descriptions are as follows.

The Acembl system in our project involves four plasmids, pACE, pDC, pDS, and pDk, and each contains one of the four gene sequences we would like to fuse (Figure 3A-D).

Figure 3A Integration of four basic plasmid backbones into one.

Figure 3B 1.Histag-TEV-HydA-Spytag in pACE(pACE-HydA-Tag in abbreviaFon/pladmid 1) Figure 3C 3.HydE in pDC(pDC-HydE in abbreviaFon/plasmid3) Figure 3D 4. HydF in pDK (pDK-HydF in abbreviaFon/plasmid4) Figure 3E 5. HydG in pDS(pDS-HydG in abbreviaFon/plasmid5)

Figure 3B-E The single plasmids to fuse by Acembl system. We obtained five sequence-confirmed single plasmids including the RBS, promoter region and loxP site. All those functional sequence have been sequenced.

(Click to see the detail sequenced information: HydA-SpyCatcher, HydA-SpyTag, HydE, HydF, HydG)

In particular, pACE is the “acceptor” plasmid with hydA sequence, while others are the “donor” plasmids with the auxiliary protein sequences. With one-step Cre recombination and subsequent transformation into BL21 or DH5a, we would obtain strictly fused plasmid with either all gene circuits integrated in one big plasmid or non-fused single plasmids. The screening of successful assembly involves different resistance (Ampicillin / Chloramphenicol / spectinomycin) and different kinds of origin. In pACE1, it has a replication origin that can be recognized by common DH5a or BL21. In pDC,pDS,pDk, it has a special origin (R6K gamma ori) can be recognized only by a mutation strain of E. coli. (PirHC or PirLC, which can express pir gene product for its replication.) Only a successful fusion into the acceptor plasmid can it propagate, using the accepters ori. Therefore, we efficiently put all four hyd sequences on one single plasmid, avoiding the potential problems imposed by the two-plasmid system.

The basis of our constructs, the four sequences, are not directly obtained from bacteria. But they are all codon-optimized to ensure high-level expression. (The original sequences of hydrogenase are found on www.genome.jp.)

Results of cloning

As mentioned before, we basically relied on the Acembl system for hydrogenases gene cluster construction. In using the system, however, we can either fuse 4 single plasmids with one step of Cre recombination or do it step by step, integrating each plasmid one at a time. In order to gain higher success rate, we choose the second way.

First step:Fusion of plasmid 1/2 and plasmid 4

We fused pACE-Histag-TEV-HydA-Spytag/pACE-Histag-TEV-HydA-Spycatcher with pDK-HydF together as the first step. To test if we successfully fused the two, we use single restricted endonuclease digestion of XhoI. The restriction gives two bands on a 1% TAE Gel, in accordance with the band predicted by SnapGene®.

Figure 4A Fusion of plasmid 1 and plasmid 4.

Single restricted-endonuclease digestion of Xhol in pACE-Histag-TEV-HydA-Spytag x pDK-HydF gives two bands. The left pic refers to expected results based on SnapGene® software prediction, with two bands at 5427bp and 2146bp, respectively. The right figure refers to the experimental results, which is in good agreement with the software prediction.

Figure 4B Fusion of plasmid 2 and plasmid 4.

Single restricted-endonuclease digestion of Xhol in pACE-Histag-TEV-HydA-Spycatcher x pDK-HydF gives two bands. The left pic refers to expected results based on SnapGene® software prediction, with two bands at 5427bp and 2455bp, respectively. The 2455bp is larger than 2146bp due to the larger SpyCatcher. The right figure refers to the experimental results, which is in good agreement with the software prediction.

Figure 4A/B shows that plasmid1/2 and 4 are successfully fused.

Second step:Fusion of plasmid in step one and plasmid 3.

We test through the selection of LB solid plate with three resistance, Ampicillin, Chloramphenicol, and kanamycin. Then we use single restricted endonuclease digestion of XhoI. There should be two kinds of ways in fusing. Comparing our electrophoresis band with the prediction by SnapGene®, we confirmed the kind we obtained.

Figure 4C Fusion of the plasmid in step one(4A) and plasmid 3.

After the fusion of the plasmid in step one and plasmid 3, there will be one more enzyme restriction site of XhoI. Single restricted-endonuclease digestion of Xhol in pACE-Histag-TEV-HydA-SpyTag x pDK-HydF x pDC-HydE gives two bands. The left pic refers to expected results based on SnapGene® software prediction, with three bands at 5427bp, 2897bp and 2249bp, respectively. The right figure refers to the experimental results, which is in good agreement with the software prediction.

Figure 4D Fusion of the plasmid in step one(4B) and plasmid 3.

After the fusion of the plasmid in step one and plasmid 3, there will be one more enzyme restriction site of XhoI. Single restricted-endonuclease digestion of Xhol in pACE-Histag-TEV-HydA-SpyCatcher x pDK-HydF x pDC-HydE gives two bands. The left pic refers to expected results based on SnapGene® software prediction, with three bands at 5427bp, 2897bp and 2558bp, respectively. The right figure refers to the experimental results, which is in good agreement with the software prediction.

Figure 1C/D shows that plasmids obtained in step 1 and plasmid 3 are successfully fused.

Final step:Fusion of plasmid in step 2 and 5.

This fusion was conferred many possibilities due to the multiple loxP sites that are potentially recognized by Cre, and the fact that some fused loxP sites are reversely separated. However, since the plasmid in step 2 and plasmid 5 are put into the reaction in equal molar, the fully fused plasmid has a better chance. In parallel, we mixed four (plasmid 1/2, 3, 4, 5) plasmids together. After characterization by endonuclease restriction, we obtained the final plasmid. In addition, we find that the mixing of four in one reaction is not efficient.

Figure 4E Fusion of the plasmid in step (4C) and plasmid 3.

For a whole fused plasmid, It becomes hard to analyze it with just Xho I single enzyme. The bar at 3k actually accounts for two bars, with a separation of 20bp. In the picture, although the four bands predicted by SnapGene® can be found on our real gel, it is less clear.

Given the inconvenience with testing by restriction, we turned to resistance screening. The result is that it is resistant to four antibodies (Ampicillin, Chloramphenicol, kanamycin and Spectinomycin). Figure 4E shows that plasmids obtained in step 2 and plasmid 4 are successfully fused. Thus, we obtained a plasmid with all four subunits, HydA, HydE, HydF, HydG, fused together. The next step is to induce the expression of the hydrogenase.

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+<a href="#motivation">Why [FeFe] Hydrogenase?</a>
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+<a href="#CPrinciple" style="font-size:14px">Principle</a>
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-<a href="#CResult" style="font-size:14px;margin-left:15px;">Result</a>
+<a href="#CResult"style="font-size:14px">Result</a>
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-<a href="#Expression">Expression</a>
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-<a href="#E-Catcher" style="font-size:14px;margin-left:15px;">Histag-tev-HydA-Spycatcher</a>
+<a href="#Expression"style="font-size:14px">Expression</a>
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-<a href="#E-Tag" style="font-size:14px;margin-left:15px;">Histag-tev-HydA-Spytag</a>
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+<img class="imgnav" src="https://static.igem.org/mediawiki/2016/7/7c/T--ShanghaitechChina--member--bf--Hydrogenase_Gene_Clusters.png">
+<p id="Connection"></p>
+<div  class="content">
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-         <h1 align="center">Motivation of Hydrogenase</h1>
+  <h1 align="center">Connection to the Project</h1>
-           <center><img src="https://static.igem.org/mediawiki/2016/0/04/T--ShanghaitechChina--hrduogenase--fangcheng.extension.jpg"  style="width:30%;"></center>
+</div><div class="col-lg-3"><img src="https://static.igem.org/mediawiki/2016/7/76/T--ShanghaitechChina--member--qlc--hydrogenase.jpg" style="width:100%"></div><divclass="col-lg-9">
+In our sun-powered biofilm-interfaced hydrogen-producing system, <strong>hydrogenase  harnessed in engineered <i>E.coli</i> are conceived to efficiently catalyze proton reduction upon receiving electrons originally donated by semiconductor nanomaterials</strong>. Electron transportation from semiconductors to hydrogenase could be bridged and facilitated by the use of mediators, methyl viologen. To achieve efficient enzymatic activities, we codon-optimized and constructed the whole hydrogenase gene clusters (from <i>Clostridium acetobutylicum</i>) by leveraging the multi-expression Acembl System. <p></p>
+</div></div></div>
+<p  id="motivation" ></p>
+<div class="content">
+  <div class="row">
+    <div class="col-lg-12">
+         <h1 align="center">Why [FeFe] Hydrogenase?</h1>
+           <center><img src="https://static.igem.org/mediawiki/2016/0/04/T--ShanghaitechChina--hrduogenase--fangcheng.extension.jpg"  style="width:20%;"></center>
           <p style="text-align:center"><b>Figure 1A</b>  Hydrogenase is an enzyme that catalyses the reversible oxidation of molecular hydrogen (H2)</p>
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-             At molecular level, the gene sequences involved in producing hydrogenase in different species vary wildly. In our study, we focus on hydrogenase gene cluster from Clostridium. acetobutylicum. The important genes include hydA, hydEF, hydG, which are expressed as HydA, HydE and HydF, HydG respectively.  We will briefly introduce these enzymes below. （Tip：click enzymes to have fun:）<p></p>
+             At molecular level, the gene sequences involved in producing hydrogenase in different species vary wildly. In our study, we focus on hydrogenase gene cluster from <i>Clostridium acetobutylicum</i>. The important genes include hydA, hydEF, hydG, which are expressed as HydA, HydE and HydF, HydG respectively.  We will briefly introduce these enzymes below. （Tip：click enzymes to have fun:）<p></p>
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 <img id="hyde" class="hyd" src="https://static.igem.org/mediawiki/2016/3/34/HydE_silence.png" style="width:100%;">
 <b>Figure 2B</b> HydE, as well as HydG have a radical-SAM motif. In most of the cases, these two enzymes might form a complex to fulfill their functions in helping the HydA mature.
+<p></p><p></p>
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 <img  id="hydf"  class="hyd" src="https://static.igem.org/mediawiki/2016/6/6c/HydF_silence.png" style="width:100%;">
-<b>Figure 2C</b> HydF, whose N-termiatal domain is homoligous to the GTPase family and C-terminatal domain putatively contains a iron-sulfur center bingding motif CxHx45HCxxC,is considered to provide energy during the process.
+<b>Figure 2C</b> HydF, whose N-termiatal domain is homoligous to the GTPase family and C-terminatal domain putatively contains a iron-sulfur center binding motif CxHx45HCxxC,is considered to provide energy during the process.
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-Our goal is to transplant the gene clusters of [FeFe]-hydrogenase from Clostridium. acetobutylicum into <em>E. coli</em>, and produce a strain that could effectively produce hydrogen. This seemingly novel idea has been actually fulfilled by Yuki Honda, et al. [4] However, the methods and the result of gene manipulation was not efficient. They used the pETDuet-1+pCDFDuet-1 system to carry the hydEA and hydFG sequence separately. This method in cloning is not only laborious but also inefficient. Firstly, the expression of HydA, HydE, HydF, HydG are not controlled in a synchronized way; secondly, the two-plasmid system runs certain risk in the stability of the strain[4]. Thus to explore the strength of synthetic biology, we made certain improvements on the system from the level of gene manipulation.<p></p>
+Our goal is to transplant the gene clusters of [FeFe]-hydrogenase from <i>Clostridium acetobutylicum</i> into <em>E. coli</em>, and engineer a strain that could effectively produce hydrogen. Previous work for transferring [FeFe]-hydrogenase into <i>E.coli</i> using a two-plasmid system been demonstrated by Yuki Honda, et al. [4]  Specifically, they used the pETDuet-1 and pCDFDuet-1 system to carry the hydEA and hydFG sequence separately.  However, their method for gene manipulation was laborious and the results were not efficient, as expression of HydA, HydE, HydF, HydG is not controlled in a synchronized way. In addition, the two-plasmid system runs certain risk in the stability of the strain[4]. We made significant improvements on the system using a high-efficiency and multi-expression Acembl system by leveraging the power of synthetic biology, .<p></p>
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+<p  id="Construction"></p>
-<div id="Construction" class="content">
+<div class="content">
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+    <div class="row"><p id="CPrinciple"></p>
         <div class="col-lg-12">
             <h1 align="center">Construction of [FeFe]-hydrogenases gene cluster</h1>
-           <h3 id="CPrinciple">Principle of Molecular Cloning</h3>
+           <h3 class="bg" >Principle of Molecular Cloning</h3>
                To ensure normal enzyme activity, we need to make sure that these four enzymes are simultaneously expressed in <em>E. coli</em> with a moderate amount. The well-established high-efficiency Acembl system [5] came into our sight.<p></p>
-We adopted this Acembl system as a multi-expression system with special DNA replication origin and Cre-loxP site, which utilizes Cre recombinase to integrate four basic plasmid backbones into  one. (Figure 3A-D) Descriptions are as follows.<p></p>
+We adopted this Acembl system as a multi-expression system with special DNA replication origin and Cre-loxP site, which utilizes Cre recombinase to integrate four basic plasmid backbones into  one. (Figure 3) Descriptions are as follows.<p></p>
 The Acembl system in our project involves four plasmids, pACE, pDC, pDS, and pDk, and each contains one of the four gene sequences we would like to fuse (Figure 3A-D).<p></p>
 <img src="https://static.igem.org/mediawiki/2016/6/65/Pict2.png" style="width:100%;">
-<p style="text-align:center"><b>Figure 3</b> Integration of four basic plasmid backbones into one.</p>
+<p style="text-align:center"><b>Figure 3A</b> Integration of four basic plasmid backbones into one.</p>
 <img class="pic4x pic4" src="https://static.igem.org/mediawiki/2016/4/4b/T--ShanghaitechChina--clone--hydA.jpg">
 <img class="pic4x pic4" src="https://static.igem.org/mediawiki/2016/7/7f/T--ShanghaitechChina--clone--hydE.jpg">
 <img class="pic4x pic4" src="https://static.igem.org/mediawiki/2016/4/4e/T--ShanghaitechChina--clone--hydF.jpg">
 <img class="pic4x pic4" src="https://static.igem.org/mediawiki/2016/8/8d/T--ShanghaitechChina--clone--hydG.jpg">
-<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3A</b> 1.Histag-TEV-HydA-Spytag in pACE(pACE-HydA-Tag in abbreviaFon/pladmid 1)</span>
+<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3B</b> 1.Histag-TEV-HydA-Spytag in pACE(pACE-HydA-Tag in abbreviaFon/pladmid 1)</span>
-<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3B</b> 3.HydE in pDC(pDC-HydE in abbreviaFon/plasmid3)</span>
+<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3C</b> 3.HydE in pDC(pDC-HydE in abbreviaFon/plasmid3)</span>
-<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3C</b> 4. HydF in pDK (pDK-HydF in abbreviaFon/plasmid4)</span>
+<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3D</b> 4. HydF in pDK (pDK-HydF in abbreviaFon/plasmid4)</span>
-<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3D</b> 5. HydG in pDS(pDS-HydG in abbreviaFon/plasmid5)</span>
+<span style="display:inline-block;width:24%;font-size:12px;"><b>Figure 3E</b> 5. HydG in pDS(pDS-HydG in abbreviaFon/plasmid5)</span>
-<p style="text-align:center"><b>Figure 3. The single plasmids to fuse by Acembl system. We obtained five sequence-confirmed single plasmids including the RBS, promoter region and loxP site. More detailed information about the sequence files could be seen on our wiki_parts.)</b></p>
+<p style="text-align:center"><b>Figure 3B-E</b> The single plasmids to fuse by Acembl system. We obtained five sequence-confirmed single plasmids including the RBS, promoter region and loxP site. All those functional sequence have been sequenced. </p>
+<h5><p style="text-align:center">
+(Click to see the detail sequenced information: <a href="https://static.igem.org/mediawiki/2016/7/75/G_HydA_SpyCatcher.pdf">HydA-SpyCatcher</a>, <a href="https://static.igem.org/mediawiki/2016/d/db/G_HydA_SpyTag.pdf">HydA-SpyTag</a>, <a href="https://static.igem.org/mediawiki/2016/9/91/G_HydE.pdf">HydE</a>, <a href="https://static.igem.org/mediawiki/2016/9/98/G_HydF.pdf">HydF</a>, <a href="https://static.igem.org/mediawiki/2016/b/bf/G_HydG.pdf">HydG</a>)</p></h5>
 In particular, pACE is the “acceptor” plasmid with hydA sequence, while others are the “donor” plasmids with the auxiliary protein sequences. With one-step Cre recombination and subsequent transformation into BL21 or DH5a, we would obtain strictly fused plasmid with either all gene circuits integrated in one big plasmid or non-fused single plasmids. The screening of successful assembly involves different resistance (Ampicillin / Chloramphenicol / spectinomycin) and different kinds of origin. In pACE1, it has a replication origin that can be recognized by common DH5a or BL21. In pDC,pDS,pDk, it has a special origin (R6K gamma ori) can be recognized only by a mutation strain of <em>E. coli</em>. (PirHC or PirLC, which can express pir gene product for its replication.) Only a successful fusion into the acceptor plasmid can it propagate, using the accepters ori. Therefore, we efficiently put all four hyd sequences on one single plasmid, avoiding the potential problems imposed by the two-plasmid system.<p></p>
-The basis of our constructs, the four sequences, are not directly obtained from bacteriaBut they are all codon-optimized to ensure high-level expression.  (The original sequences of hydrogenase are found on <a href="http://www.genome.jp">www.genome.jp.</a>)<p></p>
+The basis of our constructs, the four sequences, are not directly obtained from bacteria. But they are all codon-optimized to ensure high-level expression.  (The original sequences of hydrogenase are found on <a href="http://www.genome.jp">www.genome.jp.</a>)<p></p>
+<p id="CResult" style="margin-bottom:80px"></p>
-<h3 id="CResult"> Results of cloning</h3>
+<h3 class="bg"> Results of cloning</h3>
 As mentioned before, we basically relied on the Acembl system for hydrogenases gene cluster construction. In using the system, however, we can either fuse 4 single plasmids with one step of Cre recombination or do it step by step, integrating each plasmid one at a time. In order to gain higher success rate, we choose the second way.<p></p>
 <h4><b>First step:Fusion of plasmid 1/2 and plasmid 4</b></h4>
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+<p id="Expression" ></p>
+<div class="content">
+  <div class="row">
+    <div class="col-lg-12">
+         <h1 align="center">Expression of the hydrogenase.</h1>
+<p></p>
+As we had successfully get the device,the next step is to induce the expression of the hydrogenase.<p></p>
+<center><img src="https://static.igem.org/mediawiki/2016/8/8e/T--ShanghaitechChina--hrduogenase--paojiao.jpg"></center>
+To see, we use the antibody of Histag to show the specific of HydA-spycatcher and HydA-spytag and got the result. While we can not avoid the other protein with a similar affinity.
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-         <p>[1]Madden C, Vaughn MD, Díez-Pérez I, Brown KA, King PW, Gust D, Moore AL, Moore TA (January 2012). "Catalytic turnover of [FeFe]-hydrogenase based on single-molecule imaging". Journal of the American Chemical Society. 134 (3): 1577–82. doi:10.1021/ja207461t. PMID 21916466.</p>
+<p>1.	C. Bieniossek et al., Automated unrestricted multigene recombineering for multiprotein complex production. Nature methods 6, 447-450 (2009).</p>
+<p>2.	Y. Honda, H. Hagiwara, S. Ida, T. Ishihara, Application to Photocatalytic H2 Production of a Whole‐Cell Reaction by Recombinant Escherichia coli Cells Expressing [FeFe]‐Hydrogenase and Maturases Genes. Angewandte Chemie,  (2016).</p>
-<p>[2] Smith PR, Bingham AS, Swartz JR (2012). "Generation of hydrogen from NADPH using an [FeFe] hydrogenase". Int. J. Hydrogen Energy. 37: 2977–2983.</p>
+<p>3.	P. W. King, M. C. Posewitz, M. L. Ghirardi, M. Seibert, Functional studies of [FeFe] hydrogenase maturation in an Escherichia coli biosynthetic system. Journal of bacteriology 188, 2163-2172 (2006).</p>
-<p>[3] Madden C, Vaughn MD, Díez-Pérez I, Brown KA, King PW, Gust D, Moore AL, Moore TA (January 2012). "Catalytic turnover of [FeFe]-hydrogenase based on single-molecule imaging". Journal of the American Chemical Society. 134 (3): 1577–82. doi:10.1021/ja207461t. PMID 21916466.] </p>
+<p>4.	C. Madden et al., Catalytic turnover of [FeFe]-hydrogenase based on single-molecule imaging. Journal of the American Chemical Society 134, 1577-1582 (2011).</p>
-<p>[4] Honda, Y., Hagiwara, H., Ida, S., & Ishihara, T. (2016). Application to photocatalytic h 2, production of a whole-cell reaction by recombinant escherichia coli, cells expressing [fefe]-hydrogenase and maturases genes. Angewandte Chemie.</p>
+<p>5.	P. R. Smith, A. S. Bingham, J. R. Swartz, Generation of hydrogen from NADPH using an [FeFe] hydrogenase. international journal of hydrogen energy 37, 2977-2983 (2012).</p>
-<p>[5] Bieniossek, C., Nie, Y., Frey, D., Olieric, N., Schaffitzel, C., & Collinson, I., et al. (2009). Automated unrestricted multigene recombineering for multiprotein complex production. Nature Methods, 6(6), 447-450.</p>
-<p>[6] King, P. W., Posewitz, M. C., Ghirardi, M. L., & Seibert, M. (2006). Functional studies of [fefe] hydrogenase maturation in an escherichia coli biosynthetic system. Journal of Bacteriology, 188(6), 2163-72.</p>
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