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<div class="bs-docs-sidebar hidden-print hidden-xs hidden-sm"> | <div class="bs-docs-sidebar hidden-print hidden-xs hidden-sm"> | ||
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− | <a href="#motivation"> | + | <a href="#Connection">Connection</a> |
+ | </li> | ||
+ | <li > | ||
+ | <a href="#motivation">Why [FeFe] Hydrogenase?</a> | ||
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− | <a href="#Construction">Construction</a> | + | <a href="#Construction">Construction</a><ul> |
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− | <a href="#CPrinciple" style="font-size:14px | + | <a href="#CPrinciple" style="font-size:14px">Principle</a> |
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− | <a href="#CResult" style="font-size:14px | + | <a href="#CResult"style="font-size:14px">Result</a> |
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+ | <a href="#Expression"style="font-size:14px">Expression</a> | ||
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− | <a href="# | + | <a href="#Reference">Reference</a> |
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− | <div id="motivation" class="content"> | + | <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"> | ||
+ | <div class="row"> | ||
+ | <div class="col-lg-12"> | ||
+ | <h1 align="center">Connection to the Project</h1> | ||
+ | </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="row"> | ||
<div class="col-lg-12"> | <div class="col-lg-12"> | ||
− | <h1 align="center"> | + | <h1 align="center">Why [FeFe] Hydrogenase?</h1> |
− | <center><img src="https://static.igem.org/mediawiki/2016/0/04/T--ShanghaitechChina--hrduogenase--fangcheng.extension.jpg" ></center> | + | <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> | <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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− | + | <p id="Hydrogenases" ></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 | + | 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%;"> | <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. | <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. | ||
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<img id="hydf" class="hyd" src="https://static.igem.org/mediawiki/2016/6/6c/HydF_silence.png" style="width:100%;"> | <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 | + | <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 | + | 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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<div class="col-lg-12"> | <div class="col-lg-12"> | ||
<h1 align="center">Construction of [FeFe]-hydrogenases gene cluster</h1> | <h1 align="center">Construction of [FeFe]-hydrogenases gene cluster</h1> | ||
− | <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> | 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> | ||
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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> | 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%;"> | <img src="https://static.igem.org/mediawiki/2016/6/65/Pict2.png" style="width:100%;"> | ||
− | <p style="text-align:center"><b>Figure | + | <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/2016/4/4b/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/2016/7/7f/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/2016/4/4e/T--ShanghaitechChina--clone--hydF.jpg"> | ||
<img class="pic4x pic4" src="https://static.igem.org/mediawiki/2016/8/8d/T--ShanghaitechChina--clone--hydG.jpg"> | <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 | + | <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 | + | <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 | + | <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 | + | <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 | + | <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> | 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 | + | 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 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> | 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> | <h4><b>First step:Fusion of plasmid 1/2 and plasmid 4</b></h4> | ||
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− | < | + | <h1 align="center">Expression of the hydrogenase.</h1> |
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− | < | + | 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. 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> | + | <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>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>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> | |
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Latest revision as of 22:22, 19 October 2016