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   <p>Metallothioneins (MTs) are a group of small (6-8 kDa) promiscuous metal-chelating proteins that have an affinity toward a wide range of divalent cations including Zn(II), Ni(II), Pb(II), Hg(II) and Cd(II) and trivalent cations like As(III) [11,12]. Furthermore, one MT molecule can bind 6-9 metal ions [13]. This is because they are rich in thiol groups (high cysteine content) that form complexes with metal ions. MTs are dominated by Cys-Cys, Cys-X-Cys and Cys-X-X-Cys metal-binding motifs [14]. Their high metal-binding capacity and affinity for heavy metal ions when compared to other proteins like phytochelatins which have a very narrow binding specificity and are only able to bind 1 to 2 metal ions [15] are why we chose MTs as our candidate protein for our cell-free heavy metal bioremediation system. </p>
   <p>The MT sequence we used comes from the blue mussel species, <i>Mytilus edulis</i>, due to the notoriety of mussels for their heavy metal bioaccumulation and therefore, use as natural heavy metal pollution indicators in marine settings [14] which is the setting we plan on using our bioremediation device. </p>
   <h3 id="2.4" class="anchor">Metallothionein-Displaying 3C Hydrogels</h3>
-  <p>For our bioremediation device, we created ‘3C hydrogels’. They are named ‘3C hydrogels’ as they are made of three components:</p>
+
+  <div class="row">
+    <div class="column" style="width:50%;float:left;">
+      <br>
+      <p>For our bioremediation device, we created ‘3C hydrogels’ (See Figure 3). They are named ‘3C hydrogels’ as they are made of three components:</p>
   <ul>
     <li>Carboxymethylcellulose (CMC) as the base</li>
     <li>Citric acid (CA) for crosslinking</li>
@@ -168,14 +172,22 @@
   <p>CMC was used as it is a cellulose-based compound which is earth-abundant, inexpensive and sustainable, it therefore meets all the design criteria for PETALUTION. However, CMC polymers alone are soluble in water due to their hydrophilic carboxymethyl groups but mixing a solution of CMC with CA crosslinks the polymers to form an insoluble CMC-CA hydrogel matrix [16]. The first two components are edible therefore creating no risk to wildlife and ensure the hydrogel is biodegradable. </p>
   <p>The CBD sequence we used is of CenA, the cellulose-binding domain of the cellulase endoglucanase A from <i>Cellulomonas fimi</i> [17]. We attached the CBD to the N-terminus of our MTs via a glycine-serine linker. The CBD binds to the beta-1,4 glycosidic bonds of cellulose and its derivatives like CMC [17], allowing attachment of the fused MT to the hydrogel matrix. </p>
   <p>We expressed CBD-tagged <i>M. edulis</i> MTs in the non-pathogenic laboratory <i>E. coli</i> strain, BL21(DE3). Afterwards, we attached our recombinant MTs to our hydrogels by incubating the hydrogels in the lysates of the <i>E. coli</i> cultures expressing the CBD-tagged MTs. </p>
+</div>
+
+  
+  <div class="column" style="width:50%;float:left;">
+    <img src="https://static.igem.wiki/teams/4390/wiki/diagrams/hydrogel-design.png" class="column" style="width:100%;display:block;left:0;right:0;margin:auto;">
+    <p style="text-align:center;"><b>Figure 3.</b> A general schematic diagram of how our 3C Hydrogels are constructed. </p>
+    </div>
+  </div>
 
 
   <h3 id="2.5" class="anchor">Directed Evolution</h3>
   <p>The use of MTs was explored as a method to bioaccumulate toxic metals via hydrogels in the bioremediation aspect of our project. The idea of using metal-chelating proteins inspired us to also explore the potential for improving MTs binding capacity and thus their function, through Directed Evolution.</p>
-  <p>We wanted to establish a novel screening and selection system that could indicate improved MT function. We hypothesised that if we grow MT expressing bacteria in toxic metal concentrations, the bacteria will have to utilise MTs for metal chelation, critical for its survival. Therefore, bacteria that survive at an increasingly toxic heavy metal concentration, will express MTs that would be potentially interesting to characterise and study. Our experimental plan is outlined in Figure 3.</p>
+  <p>We wanted to establish a novel screening and selection system that could indicate improved MT function. We hypothesised that if we grow MT expressing bacteria in toxic metal concentrations, the bacteria will have to utilise MTs for metal chelation, critical for its survival. Therefore, bacteria that survive at an increasingly toxic heavy metal concentration, will express MTs that would be potentially interesting to characterise and study. Our experimental plan is outlined in Figure 4.</p>
   <figure>
     <img src="https://static.igem.wiki/teams/4390/wiki/results/screenshot-2022-10-11-at-23-45-28.png" style="width:70%;left:0;right:0;margin:auto;display:block;">
-    <figcaption style="width:70%;left:0;right:0;margin:auto;text-align:center;"><b>Figure 3.</b> Our planned workflow for the directed evolution of MTs.</figcaption>
+    <figcaption style="width:70%;left:0;right:0;margin:auto;text-align:center;"><b>Figure 4.</b> Our planned workflow for the directed evolution of MTs.</figcaption>
   </figure>
   <h5>Random mutagenesis</h5>
   <p>Error prone PCR can be used for generating mutant libraries by using a low-fidelity DNA polymerase (Taq M0267) which lacks 3’ to 5’ exonuclease proof-reading abilities [27]. Increasing MgCl<sub>2</sub> concentrations is another way to increase mutation rates by reducing DNA polymerase fidelity. To manipulate the kinds of mutations being incorporated, the concentrations of dNTPs can be varied to increase the likelihood that dNTPs present at higher concentrations are incorporated into the newly replicated strand.</p>
@@ -211,10 +223,10 @@
   <p>Like every other part of PETULATION, we designed our polyethylene terephthalate (PET) biodegradation device to be cell-free and sustainable. However, we are designing a tool for the PET plastic recycling industry which is not designed to be used directly in water bodies like our biosensor and bioremediation device, but, rather by industrial plastic recycling facilities. We have therefore had to tailor our design to reflect this different use case. </p>
   <h3 id="3.2" class="anchor">Silica immobilisation  </h3>
   <p>Silica is a cheap and robust material that has been commonly used in the laboratory for immobilization since 2006, however, it is not a biodegradable or renewable material. Despite this, we believe that silica for this use case is better as silica has enhanced stability which increases the usability of the enzymes bound to it when compared to a biodegradable matrix like hydrogels. Silica features are therefore more suited to an industrial setting like the one we plan to use the biodegradation device in.  </p>
-  <p>Through our literature search, we found two silica tags which would allow us to attach our enzymes (PETase and MHETase) to silica. The conserved <i>E. coli</i> L2 ribosomal protein (L2NC) bound very tightly to the silanol moiety of mesoporous silica [19], which provided an opportunity for the L2 fusion protein to be immobilized on the surface of unmodified silica. Our second silica tag was the Car9 protein which was originally thought to bind to carbonaceous substrates and was found to bind to silica as well [20]. These two silica tags were also used by the Edinburgh 2021 iGEM team (Super Grinder), however, we wanted to evaluate L2NC and Car9 more systematically. To do this we attached the silica tags to the N terminus and C terminus of different PETases (Figure 3) and assessed the effect of this attachment on the solubility as well as the activity of the enzymes. For the MHETase tagging we found there was a ∼60 Å long intrinsically disordered tether structure (residues 1–25) at the N-terminus of the MHETase [21]. Therefore, we assumed N-terminal silica tags are more suitable than C-terminus for MHETase (Figure 3). </p>
+  <p>Through our literature search, we found two silica tags which would allow us to attach our enzymes (PETase and MHETase) to silica. The conserved <i>E. coli</i> L2 ribosomal protein (L2NC) bound very tightly to the silanol moiety of mesoporous silica [19], which provided an opportunity for the L2 fusion protein to be immobilized on the surface of unmodified silica. Our second silica tag was the Car9 protein which was originally thought to bind to carbonaceous substrates and was found to bind to silica as well [20]. These two silica tags were also used by the Edinburgh 2021 iGEM team (Super Grinder), however, we wanted to evaluate L2NC and Car9 more systematically. To do this we attached the silica tags to the N terminus and C terminus of different PETases (Figure 6) and assessed the effect of this attachment on the solubility as well as the activity of the enzymes. For the MHETase tagging we found there was a ∼60 Å long intrinsically disordered tether structure (residues 1–25) at the N-terminus of the MHETase [21]. Therefore, we assumed N-terminal silica tags are more suitable than C-terminus for MHETase (Figure 3). </p>
   <figure>
     <img src="https://static.igem.wiki/teams/4390/wiki/pet/pet-design-parts.jpeg" style="display: block; left: 0; right: 0; margin: auto; width:60vw;">
-    <figcaption><b>Figure 3. </b>The schematic representation of the composite part designed for PETase and MHETase immobilization. Dou-PETase: Double mutant PETase (S238F/ W159H); Tri-PETase: Triple mutant PETase (T140D/R224Q/N233K); FAST-PETase: Quintuple mutant PETase (S121E/D186H/R224Q/N233K/R280A)  </figcaption>
+    <figcaption><b>Figure 6. </b>The schematic representation of the composite part designed for PETase and MHETase immobilization. Dou-PETase: Double mutant PETase (S238F/ W159H); Tri-PETase: Triple mutant PETase (T140D/R224Q/N233K); FAST-PETase: Quintuple mutant PETase (S121E/D186H/R224Q/N233K/R280A)  </figcaption>
   </figure>
   <h3 id="3.3" class="anchor">PETase and MHETase </h3>
   <p>PETase was discovered in 2016 in Ideonella sakaiensis, which can use PET as a single carbon source [22]. The PETase hydrolyses PET polymers and produces four products terephthalic acid (TPA), mono(2-hydroxyethyl) terephthalate (MHET), and bis(2-hydroxyethyl) terephthalate (BHET), ethylene glycol (EG). PETase will mainly produce MHET from PET; the highest yield of MHET is 2.5 times more than that of TPA. TPA is much more usable than MHET as TPA can be converted into high-value products like vanillin. MHET also has an inhibitory effect on the hydrolysis of PET. However, since only a very small amount of MHET can be continued to be hydrolysed to TPA by PETase, we needed to add an MHETase to convert MHET to TPA to increase TPA yield and purity [23]. </p>
@@ -223,10 +235,10 @@
   <p>Increased crystallinity limits the movement/fluctuation of polymer chains and decreases the availability of polymer chains for enzymatic attack. PET molecules with low crystallinity have amorphous substrates, which are easier for the enzyme to bind to the substrate [25]. Highly crystalline (>20%) PET molecules have crystalline substrates that are difficult for enzymes to bind to, so the yield of degrading highly crystalline PET molecules with mixed enzymes is low. Currently the industry pre-treats highly crystalline PET by first melting it at 290°C and then cooling it rapidly to reduce the crystallinity of the PET [26]. The use of these high temperatures to degrade the PET would require lots of energy and would not match our design criteria for PETULATION being sustainable.  </p>
   <p>To combat this, we found the RolA hydrophobin protein which can be found in fungi. Hydrophobins can increase the hydrophilicity of the PET product surface, thereby increasing the affinity of the substrate for PETase and thus the release of the final product [23][26]. So, we either pre-treated the PET raw materials with RolA hydrophobin or fused RolA with PETase to see if we could mitigate the effect of high crystallinity levels on PETase function and use our device at room temperature to make it a sustainable product.  </p>
   <h3 id="3.5" class="anchor">PET biodegradation device </h3>
-  <p>After designing the silica beads decorated with PETase and MHETase enzymes we wanted to create a device with these immobilised enzymes with enzymes such that they could be used easily by a recycling facility (Figure 4). Silica beads have completed their reaction with the PET, the solution is passed through a large pore size filter membrane to separate (enzymes and reaction products) from (large impurities, undegraded PET). The initially filtered solution is then passed through a smaller pore size membrane to separate the working enzyme from the reaction substrate (TPA & EG), this step also allows the working enzyme to be recovered for reuse. The isolated TPA and EG substrates can be chemically purified or specifically taken up by engineered organisms for downstream use. </p>
+  <p>After designing the silica beads decorated with PETase and MHETase enzymes we wanted to create a device with these immobilised enzymes with enzymes such that they could be used easily by a recycling facility (Figure 7). Silica beads have completed their reaction with the PET, the solution is passed through a large pore size filter membrane to separate (enzymes and reaction products) from (large impurities, undegraded PET). The initially filtered solution is then passed through a smaller pore size membrane to separate the working enzyme from the reaction substrate (TPA & EG), this step also allows the working enzyme to be recovered for reuse. The isolated TPA and EG substrates can be chemically purified or specifically taken up by engineered organisms for downstream use. </p>
   <figure>
     <img src="https://static.igem.wiki/teams/4390/wiki/main-page/pet-main-page-one.jpeg" style="display: block; left: 0; right: 0; margin: auto; width:60vw;">
-    <figcaption><b>Figure 4.</b> A schematic diagram of our proposed PET biodegradation device, showing how our device can used to recycle PET plastic into more usable products.</figcaption>
+    <figcaption><b>Figure 7.</b> A schematic diagram of our proposed PET biodegradation device, showing how our device can used to recycle PET plastic into more usable products.</figcaption>
   </figure>