Part:BBa_K2132005
HydA with SpyTag, Histag and TEV site
This is a modified protein, we added Histag and TEV site to the N-terminal site of HydA, and SpyTag to the C-terminal site of HydA.
Also, we optimized [FeFe] Hydrogenases (HydA) originally from the bacterium Clostridium acetobutylicum (Original coding sequence: hydA, BBa_K535002, designed by: iGEM11_UNAM-Genomics_ Mexico.) to accept electrons and therefore enable catalytic production of hydrogen in our project. The optimized coding sequence would produce more protein, theoretically. And optimization also improved the activity of [FeFe] Hydrogenases according to the experiment that we did.
For more detail information, please visit http://2016.igem.org/Team:ShanghaitechChina/Parts, http://2016.igem.org/Team:ShanghaitechChina/Hydrogen, http://2016.igem.org/Team:ShanghaitechChina/IBS and http://2016.igem.org/Team:ShanghaitechChina/Description#p2.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 790
Illegal AgeI site found at 1300 - 1000INCOMPATIBLE WITH RFC[1000]Illegal SapI.rc site found at 1005
Optimize the codon
We optimized [FeFe] Hydrogenases (HydA) originally from the bacterium Clostridium acetobutylicum (Original coding sequence: hydA, BBa_K535002, designed by: iGEM11_UNAM-Genomics_ Mexico. Optimized coding sequence: thia part, hydA with SpyTag and Histag, BBa_K2132005) to accept electrons and therefor enable catalytic production of hydrogen in our project. The optimized coding sequence would produce more protein, theoretically. And optimization also improved the activity of [FeFe] Hydrogenases according to the experiment that we did.
>Improvement:
Codon usage bias adjustment
We analysed the Codon Adaptation Index (CAI) of the optimized coding sequence and the original one. And the distribution of codon usage frequency along the length of the gene sequence is increased from 0.33 to 0.97. A CAI of 1.0 is considered to be perfect in the desired expression organism, and a CAI of > 0.8 is regarded as good, in terms of high gene expression level.
We also compared the Frequency of Optimal Codons (FOP). The value of 100 is set for the codon with the highest usage frequency for a given amino acid in the desired expression organism. As we can see, the percentage of 91-100 increased largely, from 36 to 86, after the optimization.
What's more, we removed repeat sequences to break the Stem-Loop structures, which impact ribosomal binding and stability of mRNA.
| Max Direct Repeat | Max Inverted Repeat | Max Dyad Repeat | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| After Optimization | Size:15 Distance:3 Frequency:2 | None | None | ||||||||
| Before Optimization | Size:16 Distance:231 Frequency:2 | None | Size: 13 Tm: 34.6 Start Positions: 680, 1357 | ||||||||
| Table 1: Removed repeat sequences information | |||||||||||
>Conclusion:
A wide variety of factors regulate and influence gene expression levels, and after taking into consideration as many of them as possible, OptimumGene™ produced the single gene that can reach the highest possible level of expression.
In this case, the native gene employs tandem rare codons that can reduce the efficiency of translation or even disengage the translational machinery. We changed the codon usage bias in E. coli by upgrading the CAI from 0.33 to 0.97 . GC content and unfavorable peaks have been optimized to prolong the half-life of the mRNA. The Stem-Loop structures, which impact ribosomal binding and stability of mRNA, were broken.
Hydrogenases Expression and Enzyme Activity Assay
(1) Principles and Methods
In the activity assay of the hydrogenase in producing hydrogen, we repeated three parallel experiments to test the activity and validated the repeatability of our rudimentary system. In each parallel experiment, the system goes through three periods of “light-on and light-off”. The results (see below) shows the stability of the system and the reversible catalytic activity of the hydrogenase of the reaction, 2H+ + 2e- ⇿ H2 . The three parallel systems consist of E. coli with engineered hydrogenase (wet weight 100ug) resuspended in PBS, 200ul quantum dots/nanorods (7.72*10^-9 M) 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. Prior to the assay, the E. coli was induced with IPTG overnight at room temperature. The whole system is based on former study. In addition, we did a fourth assay with resuspended microspheres covered with quantum dots/nanorods bound biofilm in PBS, in place of the resuspended quantum dots/nanorods solution. The fourth set is the actual system we are proposing, since it is as efficient and allows the recycling of quantum dots/nanorods. 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.(2) Instrument
Figure 1 Apparatus of the hydrogen production assay.
(3) Results
a) Contribution of each component of the hydrogen production system
The first hydrogen production data using our system is the pink curve (curve 1) in Figure 1. It shows that lighting can induce hydrogen production in a closed system with nano rods (NR), mediator Methyl Viologen, and IPTG-induced bacteria transformed with fused plasmid. To prove that every element of the system is necessary and that it is our hydrogenase that produced the hydrogen rather than NR, we conducted a series of experiments. To see whether NR is necessary and whether the hydrogen is produced by the reaction between NR and water under lighting rather than our hydrogenase, we conducted the experiment where the system does not contain nano rods or contain only nano rods. The data is summarized in Figure 1A. The red curve (curve 2) represents the system with the transformed bacterial suspension but without nano rods (NR). The flat curve shows that the system without NR could not produce hydrogen with light; NR is necessary for the system. The black curve (curve 3) represents a system in which only NR and mediators are present, with no bacteria. The flat curve shows that it could not produce hydrogen, which proves that the elements of the bacteria is necessary in the synthesis of hydrogen.
Figure 2
Hydrogen production evolution curve (Sensor Data/ Hydrogen amount vs Time) with different components. The pink curve (curve 1) in all pictures is the hydrogen production with all the components, nano rods (NR), IPTG induction, and the bacteria transformed with our hydrogenase plasmid. The rest are data with one or two components missing. In particular, data in the integrated picture are categorized into Figure 2A and 2B. Figure 2A shows the system with or without nano rods or with nano rods alone, and Figure 2B represents the system with or without induction. The curve 3 in each of the specific figure is the blank control with not transformed E. coli BL21. This series of experiments show that only when both nano rods (NR) and IPTG-induced transformed bacteria are present can the system produce hydrogen in a stable way. Another step in proving that it is that the hydrogenase is indeed responsible for hydrogen production is to contrast the production level between the induced and un-induced bacteria suspension. The experiment we conducted are summarized in Figure 6B In this set of experiment, the blue line (curve 4) acts as our blank control. In this group, we use the wild type BL21 cells without plasmid. Although we can see a positive oscillation during a short time in the curve, the production was not at high rate and is likely due to the native hydrogenase in E. coli. The green curve (curve 5) represents the transformed bacterial with no induction of IPTG after 12h cultivation. The flat curve shows that it could not produce hydrogen, which proves that the induction of the hydrogenase expression is necessary. To further confirm, we did another experiment using bacteria that have grown 36 hours with no induction. The purple curve (curve 6) clearly contrasts the induced BL21 and the non-induced one. With curve 4 to 6, we have demonstrated that, with the help of NR, it was our hydrogenase in the system that produced the hydrogen we detected.b) Bidirectional catalytic property of [FeFe] hydrogenase
As mentioned earlier, hydrogenase catalyzes the reversible oxidation of molecular hydrogen (H2). Thus, when we “turn off” the production mode, we should be able to see the consumption of hydrogen by hydrogenase. In testing this bidirectional catalytic property, conducted an experiment where we turned on and turned off the light alternately. The data is shown below in Figure 7. During lighting period, 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 consumption of hydrogen. 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.
Figure 3 Verifying the bidirectional catalytic property of [FeFe] hydrogenase.
During the period under 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 consumption of hydrogen.c) Hydrogen production with nano rods suspension replaced by nano rods bound to biofilm beads.
Given the difficulty in recycling the nano rods due to their small size, we utilize biofilm to immobilize nano rods and aggregate them into larger assemblies that allow filtration or other ways of recycling including centrifugation. However, testing whether the NR aggregate work in our system is needed. We conducted experiments with nano rods suspension replaced by nano rods bound to biofilm beads. 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 were then added and given 30 min to bind to the HisTag on CsgA subunit. (The engineered SpyCatcher was used for future pure hydrogenase binding.) 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 system. The data is in Figure 3 In this experiment, we did the same “light-on light off” actions to the system and the pattern is similar to the one with NR suspension (Figure 2) During lighting, the rapid production of hydrogen can be clearly observed. Some other characteristics pertain, such as the sharp rise at the beginning of lighting.
Figure 4 Hydrogen production with nano rods suspension replaced by nano rods bound to biofilm beads.
We replaced the nanorods suspension with nano rods 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 consumption of hydrogen, as in Figure 3. Comparing Figure 2 and Figure 3 In the process of hydrogen generation, a stir bar with a necessary speed of 800 RPM was used to generate the curve in Figure 3. But in Figure 4, a stir bar was not used. It is likely because the aggregates of NR have a bigger chance in colliding with E. coli to transfer electrons. We therefore propose this model as our final model, although further optimization of the system is still under way.d) Repeatability
Figure5. Repeatability of our hydrogen production system. The three curves conform. This demonstrates our preliminary prototype as repeatable and robust.
To further prove our system as a reliable one, we did three sets of hydrogen production assays in one day in a row (Figure4, curve 10-12). The system was mainly made up of resuspended CdS nonorods, E. Coli BL21 transformed with the plasmid containing all the four [FeFe]hydrogenase subunits from Clostridium. acetobutylicum, and mediator, methyl viologen. (See Figure1 or the section of Principles and Methods for details of the reaction system.) From the data shown, we clearly see the conformation of the three curves. This demonstrates our preliminary prototype in Figure1 as repeatable and robust.
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