Applied Design

Given that our system has been proved to work with repeatability and its intrinsic characteristics for massive application, we think our project is a successful applied design. Here, we summarize the qualification and merits of our design in the following figure.

Introduction to Solar Hunter

We aimed to design a biofilm-interfaced artificial hydrogen-producing system, Solar Hunter, that harnesses the energy of sun light. Biofilm-anchored nanorods can efficiently convert photons to electrons, which seamlessly tap into the electron chain of engineered strain carrying FeFe hydrogenase gene cluster, thereby achieving high-efficiency hydrogen production. It is noteworthy that our system facilitates the recycling of the expensive nanorods as the biofilms were grown on easy-separation micro-beads to anchored NRs.

This section demonstrates the hydrogen production by integrating biofilm-anchored NRs with strain harboring hydrogenase gene clusters. Specifically, it shows that 1) the system shows high efficiency. 2) the system has some potentials that can be exploited in the future.

Method and Instrument

Method

The biofilm, whose subunit was CsgA engineered with HisTag on N-termial and SpyCachter-HisTag on C-terminal, was grown on microspheres, 25 micrometers in diameter for 48 hours. NR’s (7.72*10^-9 M) were then added and given 30 min to bind to the HisTag on CsgA subunit. (The engineered SpyCatcher was used for possible pure hydrogenase binding, our alternative proposal.) The solution was centrifuged and the sediments contained biofilm beads covered with NR. This sediment was resuspended in PBS and was added to the reaction solution consisting of E. coli with engineered hydrogenase (wet weight 100ug) resuspended in PBS, 150Mm NaCl, 100mM VitaminC, and mediator solution (5mM Paraquat dichloride, for mediating the electrons across the cell membrane). The whole solution including bacteria is adjusted to pH=4 by 100mM Tris-HCl(pH=7.0), given that the pH of 4 was reported to be an optimal environment. [1] Prior to the assay, the E. coli was induced with IPTG overnight at room temperature. In the activity assay of the hydrogenase in producing hydrogen, the system goes through three periods of “light-on and light-off”. The result (see below) shows the stability of the system and the reversible catalytic activity of the hydrogenase of the reaction, 2H+ + 2e- ⇿ H2 .

Instrument

Figure 1 Apparatus of the hydrogen production assay.

It contains (1) an anaerobic reaction container which is a transparent circular cuvette that allows light to go through; (2) a light source in our hydrogen production assay acting as a substitute for the real sun. (We chose a high-power white LED light, set 28cm away from the reaction container for a even distribution of photons); (3) a hydrogen electrode linked to its inner sensor inserted into the reaction container to measure the realtime concentration of hydrogen; (4) a data hub; (5) a computer connected to the hub to record the data and generate the curve of concentration variation within a period of time.

Results

Figure 2 Hydrogen evolution curve with nanorods bound to biofilm beads.

During the period with lighting, the hydrogen production increases, until we shut off the light at points that correspond to the tips. The curve then goes downward, showing that the hydrogen concentration is lowered, an evidence of the bidirectional catalytic activity of hydrogenase. It is noteworthy that the hydrogenase shows the greatest production rate at the beginning of lighting: a transient sharp rise can be observed at the valleys. It is also obvious that each period of “light-on light-off” gives similar curves, which implies that our hydrogenase is stable.

In our experiment, we find that despite the reported affected catalytic ability of FeFe hydrogenase due to oxygen, non-strict anaerobic and short-term exposure to oxygen does not cause detrimental effects on the enzyme activity of producing hydrogen. This can be explained by the high catalytic ability and the segregation layer from the atmosphere provided by the hydrogen it produces. Meanwhile, the electron sacrificial agent VitaminC also adds to the “protection layer” of the hydrogenase in our system.

Efficiency

Calculating the hydrogen evolution rate of our integrated system.

We are particularly interested in learning what our efficiency is compared to one study reported this year. See reference 1. In calculating the efficiency, we chose the data from the first hydrogen production period. We converted the data in mV into umol/L. The standard curve is provided by the lab who supervised our assay apparatus.

Figure Standard Relationship between voltage data and concentration.

Thus, we obtain the rate of hydrogen evolution: the tip of the first period is 7.061 mV at 500s. This corresponds to 2.179 (0.3086*7.061) umol/L at 500s. Thus the rate is 0.0126 (2.179/500*3mL*1000) umol/s, for 0.1g E. Coli. In comparison with the rate from reference 1, 0.0086mol umol/s. This 46% increase in the efficiency shows that our system not only works, but is also a progress for the study of artificial hydrogen production system.

Potential use for wider application

Our system included a SpyCatcher system which has the potential for working directly with enzymes on biofilm.

SpyTag and SpyCatcher [5]

Introduction and Motivation: SpySystem

We want to attach enzyme to biofilm, so we turn to a widely applied linkage system, SpyTag and SpyCatcher, originally discovered from Streptococcus pyogenes. By splitting its fibronectin-binding protein FbaB domain, we obtain a relatively small peptide SpyTag with 13 amino acids and a bigger protein partner, SpyCatcher, with 138 amino acids [6]. The advantage of this system lies in the following three aspects. Firstly, they can spontaneously form a covalently stable bond with each other which guarantee the viability of the permanent linkage. The second point is quick reaction within 10 min, which will stand out by its efficiency in industrial application. Besides, the whole process proceeds in mild condition (room temperature), thus set lower requirement for reaction both in lab and future practice. Therefore, we design to leverage this advantageous system to achieve the binding of biofilm with specific enzyme.

Design

Appending SpyTag to CsgA subunit is a traditional and hackneyed approach to modify biofilm posttranscriptionally. Here, we challenge to attach larger part, SpyCatcher, to CsgA to enrich the versatility of biofilm platform. For one thing, we intend to pioneer new approach. For another aspect is that we concern SpyCatcher is too large that might jeopardize the biological activity and function of the enzyme. After comprehensive consideration, we decide to append SpyTag and SpyCatcher respectively to CsgA subunits and enzyme, and successfully prove their feasibility and stability.

Construction of SpyTag-mCherry

The construction of SpyTag-mCherry, PART BBa_K2132003, (with SpyTag lying at the N-terminal of mCherry) basically involved two PCR rounds for adding the SpyTag to mCherry. Then the sequence of SpyTag-mCherry was linked to the pET22b(+) backbone between the restriction sites of NdeI, XhoI. This led to the easy induction with IPTG. For more details and the sequencing data, please click the pdf here.

The characterization of SpyTag-mCherry is below.

Characterization

As figure illustrated, His-CsgA-SpyCatcher-Histag mutant incubated with mCherry-SpyTag show a clear biofilm-associated mcherry fluorescence signal, which indicating the accurate conformation and function of the SpyTag and SpyCatcher linkage system. The third figure is merged by the first and second figures of each sample are snapped respectively under green laser field with 558 nm wavelength and bright field of fluorescence microscopy, Zeiss Axio Imager Z2. As for controls, strains secreted CsgA–Histag and ΔCsgA both are unable to specifically attach to SpyTag thus no distinct localization highlight of red fluorescence on E.coli. That to a large extent prove the specificity of our desired linkage between SpyTag and SpyCatcher system.

Fig 14. The first figures of each sample are snapped under green laser of 558 nm wavelength and mCherry-SpyTags emit red fluorescence. The second figures of each sample are snapped under bright field of fluorescence microscopy and we can clearly see a group of bacteria.. The third figures are merged by the first and second ones. All photos are taken by Zeiss Axio Imager Z2.

Conclusion

In conclusion, E. Coli strains expressing biofilm on microspheres to anchor nanorods and strains expressing hydrogenase work great together for producing hydrogen. The system achieved a fairly good hydrogen production rate compared to the similar precursor reported this year, a nearly 50% increase. The intrinsic adherence of biofilms towards various interfaces allows us to grow biofilms on easy-separation micro-beads, therefore facilitating recyclable usage of the biofilm-anchored NRs and endowing this whole system with recyclability. Notably, our hydrogen production has shown great stability compared to some precursors using hydrogenase. Practically speaking, the system comprising E. Coli and biofilms are both amenable for scalable operation, rendering itself a great potential for large-scale industrial applications. Such system can also be adapted to other energy-oriented applications by utilizing engineered new strains with a diverse spectrum of enzymes or metabolic pathways. Specifically, our SpyCatcher on the CsgA allows the binding of other proteins that may significantly improve our system. The efficiency, recyclability, stability, scalability, and versatility makes our system a design that is truly applicable.

Reference

[*] Cao Y, Bai X F. Progress in Research of Preparation of Loaded Nano-CdS and H_2 Production by Photocatalytic Decomposition of Water[J]. Imaging Science & Photochemistry, 2009, 27(3):225-232.

[1] Honda Y, Hagiwara H, Ida S, et al. Application to Photocatalytic H2, Production of a Whole-Cell Reaction by Recombinant Escherichia coli, Cells Expressing [FeFe]-Hydrogenase and Maturases Genes[J]. Angewandte Chemie, 2016

@@ Line 16: / Line 16: @@
 </li>
 <li>
-<a href="#Demonstration">Introduction</a>
+<a href="#Demonstration" style="font-size:14px;margin-left:15px;">Demonstration</a>
 </li>
 <li>
-<a href="#Method and Instrument">Method and Instrument</a>
+<a href="#Method and Instrument" style="font-size:14px;margin-left:15px;">Method and Instrument</a>
 </li>
 <li>
-<a href="#AResults">Results</a>
+<a href="#AResults" style="font-size:14px;margin-left:15px;">Results</a>
 </li>
 <li>
-<a href="#Efficiency" >Efficiency</a>
+<a href="#Efficiency" style="font-size:14px;margin-left:15px;">Efficiency</a>
 </li>
 <li>
-<a href="#Conclusion">Conclusion</a>
+<a href="#Potential use for wider application" style="font-size:14px;margin-left:15px;">Potential use for wider application</a>
 </li>
 <li>
-<a href="#Ref">Reference</a>
+<a href="#Conclusion" style="font-size:14px;margin-left:15px;">Conclusion</a>
 </li>
 </ul>
@@ Line 72: / Line 72: @@
-<p id="Method and Instrument"></p>
 <p id="Assay"></p>
 <div  class="content">
    <div class="row">
+<p id="Method and Instrument"></p>
      <div class="col-lg-12">      <center> <h1 > Method and Instrument</h1></center>
 <h2> Method </h2>
@@ Line 98: / Line 98: @@
 </div></div></div></div>
 <p id="Assay"></p>
-<p id="AResults"></p>
 <div  class="content">
    <div class="row">
      <div class="col-lg-12">
+<p id="AResults"></p>
          <center> <h1 > Results</h1></center>
@@ Line 144: / Line 143: @@
    <div class="row">
      <div class="col-lg-12" >
-          <h1 align="center"  >Efficiency</h1>
+          <h1 align="center"  >Potential use for wider application</h1>
 <b> Our system included a SpyCatcher system which has the potential for working directly with enzymes on biofilm.</b><p></p>
-For the construction and the characterization of SpyCatcher on biofilm, please refer to https://2016.igem.org/Team:ShanghaitechChina/Biofilm#p5.
+ <div class="col-lg-12">
+              <h3 class="bg" >SpyTag and SpyCatcher [5]</h3>
+<h4><b>Introduction and Motivation: SpySystem</b></h4>
+We want to attach enzyme to biofilm, so we turn to a widely applied linkage system, SpyTag and SpyCatcher, originally discovered from Streptococcus pyogenes. By splitting its fibronectin-binding protein FbaB domain, we obtain a relatively small peptide SpyTag with 13 amino acids and a bigger protein partner, SpyCatcher, with 138 amino acids [6]. The advantage of this system lies in the following three aspects. Firstly, they can spontaneously form a covalently stable bond with each other which guarantee the viability of the permanent linkage. The second point is quick reaction within 10 min, which will stand out by its efficiency in industrial application. Besides, the whole process proceeds in mild condition (room temperature), thus set lower requirement for reaction both in lab and future practice. Therefore, we design to leverage this advantageous system to achieve the binding of biofilm with specific enzyme. <p></p>
+<center>
+<img src="https://static.igem.org/mediawiki/parts/c/c5/Shanghaitechchina_spy1.png" style="width:50%;">
+</center>
+<h4><b> Design</b></h4>
+Appending SpyTag to CsgA subunit is a traditional and hackneyed approach to modify biofilm posttranscriptionally. Here, we challenge to attach larger part, SpyCatcher, to CsgA to enrich the versatility of biofilm platform. For one thing, we intend to pioneer new approach. For another aspect is that we concern SpyCatcher is too large that might jeopardize the biological activity and function of the enzyme. After comprehensive consideration, we decide to append SpyTag and SpyCatcher respectively to CsgA subunits and enzyme, and successfully prove their feasibility and stability.<p></p>
+<center>
+<img src="https://static.igem.org/mediawiki/parts/0/07/Shanghaitechchina_spy2.png" style="width:50%;">
+</center>
+       </div>
+<div>
+<h4><b>Construction of SpyTag-mCherry</b></h4>
+The construction of SpyTag-mCherry, <a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K2132003">PART BBa_K2132003</a>, (with SpyTag lying at the N-terminal of mCherry) basically involved two PCR rounds for adding the SpyTag to mCherry. Then the sequence of SpyTag-mCherry was linked to the pET22b(+) backbone between the restriction sites of NdeI, XhoI. This led to the easy induction with IPTG. For more details and the sequencing data, please click the <a href="https://static.igem.org/mediawiki/2016/f/f6/MCherrySpyTagProtocol.pdf">pdf </a>here.<p></p> The characterization of  SpyTag-mCherry is below.
+<p></p><p></p>
+<h4><b>Characterization</b></h4>
+As figure illustrated, His-CsgA-SpyCatcher-Histag mutant incubated with mCherry-SpyTag show a clear biofilm-associated mcherry fluorescence signal, which indicating the accurate conformation and function of the SpyTag and SpyCatcher linkage system. The third figure is merged by the first and second figures of each sample are snapped respectively under green laser field with 558 nm wavelength and bright field of fluorescence microscopy, Zeiss Axio Imager Z2. As for controls, strains secreted CsgA–Histag and ΔCsgA both are unable to specifically attach to SpyTag thus no distinct localization highlight of red fluorescence on E.coli. That to a large extent prove the specificity of our desired linkage between SpyTag and SpyCatcher system. <p></p>
+<center>
+<img src="https://static.igem.org/mediawiki/parts/5/5c/Shanghaitechchina_mcherry-SpyTag%2BCsgA-SpyCatcher.png" style="width:100%;">
+</center>
+<p style="text-align:center"><b>Fig 14. </b> The first figures of each sample are snapped under green laser of 558 nm wavelength and mCherry-SpyTags emit red fluorescence. The second figures of each sample are snapped under bright field of fluorescence microscopy and we can clearly see a group of bacteria.. The third figures are merged by the first and second ones. All photos are taken by Zeiss Axio Imager Z2.</p>
+</div>
 </div></div></div>
@@ Line 160: / Line 184: @@
 </div></div></div>
-<p id="Ref">
-<div class="content">
+<div id="p9" class="content">
    <div class="row">
      <div class="col-lg-12">

Difference between revisions of "Team:ShanghaitechChina/Design"

Revision as of 18:31, 19 October 2016