Difference between revisions of "Part:BBa K5034217"
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<partinfo>BBa_K5034217 short</partinfo>
 
<partinfo>BBa_K5034217 short</partinfo>
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===Basic Description===
 
===Basic Description===
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This composite part includes the PPK2 gene from Pseudomonas aeruginosa and the NADK gene from Mycobacterium tuberculosis H37Rv, both we performed codon optimization on and are expressed in the PYYDT plasmid together. The PPK2 enzyme facilitates the reversible conversion between inorganic polyphosphate (PolyP) and inorganic phosphate (Pi), while the NADK enzyme converts PolyP to NADP. Importing them separately was successful, thus we intend to proceed with continued optimisation by their combination.
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This composite part includes the <i>PPK2</i> gene from <i>Pseudomonas aeruginosa</i> and the <i>NADK</i> gene from <i>Mycobacterium tuberculosis</i> H37Rv, both we performed codon optimization on and are expressed in the <html><a href="https://parts.igem.org/Part:BBa_K5034201">pBBR1MCS-terminator</a></html> plasmid together. The PPK2 enzyme facilitates the reversible conversion between inorganic polyphosphate (PolyP) and inorganic phosphate (Pi), while the NADK enzyme converts PolyP to NADP. Importing them separately was successful, thus we intend to proceed with continued optimisation by their combination.
 
This part consists of two enzymes, one is a reversible enzyme that converts Pi and Polyp, and the other is an enzyme that converts Polyp to NADK. The tandem connection of the two enzymes actually promoted the synthesis of NADK, and by maintaining some polyp reserves, it was able to improve the efficiency of electrical production and improve the phosphorus accumulation capacity of Shewanella.
 
This part consists of two enzymes, one is a reversible enzyme that converts Pi and Polyp, and the other is an enzyme that converts Polyp to NADK. The tandem connection of the two enzymes actually promoted the synthesis of NADK, and by maintaining some polyp reserves, it was able to improve the efficiency of electrical production and improve the phosphorus accumulation capacity of Shewanella.
  
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<p><i>PPK2</i> Coding Sequence: Encodes the polyphosphate kinase 2 enzyme.</p>
 
<p><i>PPK2</i> Coding Sequence: Encodes the polyphosphate kinase 2 enzyme.</p>
 
<p><i>NADK</i> Coding Sequence: Encodes the NAD kinase enzyme.</p>
 
<p><i>NADK</i> Coding Sequence: Encodes the NAD kinase enzyme.</p>
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<p>Terminator: Efficient transcription terminator to ensure proper mRNA processing. We use T7Te terminator in our experiment.</p>
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<p>Terminator: Efficient transcription terminator to ensure proper mRNA processing. We use a double terminator rrnBT1-T7TE(BBa_B0015) in our experiment.
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</p>
 
</html>
 
</html>
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
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===Origin (Organism)===
 
===Origin (Organism)===
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<i>PPK2</i> Gene: Pseudomonas aeruginosa PAO1 strain.
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<i>PPK2</i> Gene: <i>Pseudomonas aeruginosa</i> PAO1 strain.
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<i>NADK</i> Gene: Mycobacterium tuberculosis H37Rv strain.
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<i>NADK</i> Gene: <i>Mycobacterium tuberculosis</i> H37Rv strain.
  
 
===Experimental Characterization and results===
 
===Experimental Characterization and results===
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Students from dry lab group using mathematical modelling to introduce the two enzymes and found an enhancement in the polyphosphate and electroproduction capabilities of Shewanella.
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Students from dry lab group using mathematical modelling to simulate the introduction of the two enzymes and found an enhancement in the polyphosphate and electroproduction capabilities of <i>Shewanella</i>.
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Using half-cell reaction(electrochemistry) to measure the electricity production ability and conducting molybdate assays to determine Pi concentration, we also found a notable enhancement in the polyphosphate, ATP and electroproduction capabilities.
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The results of the half-cell experiments indicated an elevated electron transfer activity, with currents of 137.4 ± 16.34 µA/cm² for the SPPK2 strain, 134.56 ± 17.01 µA/cm² for the SNADK strain, and 164.2 ± 17.64 µA/cm² for the SPPK2-NADK strain.
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−
 
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<html>
 
<html>
 
<div align="center">
 
<div align="center">
 
<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/engineering/fig21.png">
 
<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/engineering/fig21.png">
 
<p>
 
<p>
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Figure 1: statistical data on electricity production capacity and phosphorus accumulation capacity of Shewanella with the introduction of PPK2-NADK
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Figure 1: Experimental modeling proves that importing PPK2 and NADK simultaneously is better than importing PPK2 or NADK separately
 
</p>
 
</p>
 
</div>
 
</div>
 
</html>
 
</html>
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Then, the students in the wet experiment constructed a component that linked two enzymes in series, and the results of colony PCR confirmed the success of our construction. （Fig.2）
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<html>
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<div align="center">
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<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/results/figure16.png">
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<p>
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Figure 2: Clony PCR to prove that PPK2-NADK plasmid is introduced to <i>S.oneidensis</i>
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</p>
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</div>
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</html>
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After successful construction, we transferred it into Shewanella and conducted measurements of its electricity production and phosphorus accumulation effects. We found that after transferring into the Shewanella bacterium, both the electricity production and phosphorus accumulation efficiency were significantly improved compared to the wild type.
 +
<html>
 +
<div align="center">
 +
<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/engineering/fig21.png">
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<p>
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Figure 3: statistical data on electricity production capacity and phosphorus accumulation capacity of Shewanella with the introduction of PPK2-NADK
 +
</p>
 +
</div>
 +
</html>
 +
The phosphorus aggregation effect was measured in M9 cultural medium, and the electricity generation effect was measured in LB medium, because M9 medium is the medium used in practical applications and can be better combined with practical applications.
 +
 +
Subsequently, we also investigated the reasons for the improvement in electricity generation and phosphorus aggregation efficiency. We found that the levels of ATP and NADH inside the cell were significantly increased(Fig.4), indicating that the metabolic level of Shewanella increased, leading to an increase in electricity production and phosphorus accumulation levels.
  
 
<html>
 
<html>
 
<div align="center">
 
<div align="center">
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<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/engineering/fig23.png">
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<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/results/figure18.png">
 
<p>
 
<p>
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Figure 2: statistical data on ATP and NADH level of Shewanella with the introduction of PPK2-NADK
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Figure 4: levels of ATP and NADH/NAD<sup>+<sup> of S.oneidensis with the introduction of PPK2-NADK
 
</p>
 
</p>
 
</div>
 
</div>
 
</html>
 
</html>
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To explore the possible applications of this component, we conducted a full cell experiment using Shewanella bacteria.Firstly, we use cyclic voltammetry (CV) and linear sweep voltammetry (LSV) techniques for testing. The CV curve shows higher redox activity in the SPPK2-NADK strain.(Fig.5)
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<html>
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<div align="center">
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<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/results/figure19.png">
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<p>
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Figure 5: cyclic voltammetry show higher redox activity in the SPPK2-NADK strain
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</p>
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</div>
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</html>
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the LSV curve indicates lower internal resistance in the MFC cells of the SPPK2-NADK strain.(Fig.6)
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<html>
 +
<div align="center">
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<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/results/figure20.png">
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<p>
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Figure 6: LSV curve indicates lower internal resistance in the MFC cells of the SPPK2-NADK strain
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</p>
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</div>
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</html>
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Next, we measure the relative output power. The power density results show that the SPPK2-NADK strain has a maximum output power of 243.77 ± 25.2 mW/m², which is 2.32 times higher than the WT strain’s output power density (105.06 ± 11.72 mW/m²) (Fig. 7).
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<html>
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<div align="center">
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<img style="width:50%;height:auto;" src="https://static.igem.wiki/teams/5034/results/figure21.png">
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<p>
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Figure 7:  output power of the PPK2-NADK strain
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</p>
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</div>
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</html>
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===chassis and genetic context===
 
===chassis and genetic context===
 
We express this gene on <i>Shawanella oneidensis</i> MR-1
 
We express this gene on <i>Shawanella oneidensis</i> MR-1

Revision as of 09:16, 1 October 2024

PolyP <->Pi, Poly P -> NADP


Basic Description

This composite part includes the PPK2 gene from Pseudomonas aeruginosa and the NADK gene from Mycobacterium tuberculosis H37Rv, both we performed codon optimization on and are expressed in the pBBR1MCS-terminator plasmid together. The PPK2 enzyme facilitates the reversible conversion between inorganic polyphosphate (PolyP) and inorganic phosphate (Pi), while the NADK enzyme converts PolyP to NADP. Importing them separately was successful, thus we intend to proceed with continued optimisation by their combination. This part consists of two enzymes, one is a reversible enzyme that converts Pi and Polyp, and the other is an enzyme that converts Polyp to NADK. The tandem connection of the two enzymes actually promoted the synthesis of NADK, and by maintaining some polyp reserves, it was able to improve the efficiency of electrical production and improve the phosphorus accumulation capacity of Shewanella.


Construct features(only coding sequence included in)

Promoter: Constitutive promoter for continuous expression. We use tac promoter in our experiment.

RBS: Strong ribosome binding site for efficient translation. We use BBa-B0034 which shows the strongest translation in our experiment.

PPK2 Coding Sequence: Encodes the polyphosphate kinase 2 enzyme.

NADK Coding Sequence: Encodes the NAD kinase enzyme.

Terminator: Efficient transcription terminator to ensure proper mRNA processing. We use a double terminator rrnBT1-T7TE(BBa_B0015) in our experiment.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Origin (Organism)

PPK2 Gene: Pseudomonas aeruginosa PAO1 strain. NADK Gene: Mycobacterium tuberculosis H37Rv strain.

Experimental Characterization and results

Students from dry lab group using mathematical modelling to simulate the introduction of the two enzymes and found an enhancement in the polyphosphate and electroproduction capabilities of Shewanella.

Figure 1: Experimental modeling proves that importing PPK2 and NADK simultaneously is better than importing PPK2 or NADK separately

Then, the students in the wet experiment constructed a component that linked two enzymes in series, and the results of colony PCR confirmed the success of our construction. （Fig.2）

Figure 2: Clony PCR to prove that PPK2-NADK plasmid is introduced to S.oneidensis

After successful construction, we transferred it into Shewanella and conducted measurements of its electricity production and phosphorus accumulation effects. We found that after transferring into the Shewanella bacterium, both the electricity production and phosphorus accumulation efficiency were significantly improved compared to the wild type.

Figure 3: statistical data on electricity production capacity and phosphorus accumulation capacity of Shewanella with the introduction of PPK2-NADK

The phosphorus aggregation effect was measured in M9 cultural medium, and the electricity generation effect was measured in LB medium, because M9 medium is the medium used in practical applications and can be better combined with practical applications.

Subsequently, we also investigated the reasons for the improvement in electricity generation and phosphorus aggregation efficiency. We found that the levels of ATP and NADH inside the cell were significantly increased(Fig.4), indicating that the metabolic level of Shewanella increased, leading to an increase in electricity production and phosphorus accumulation levels.

Figure 4: levels of ATP and NADH/NAD+ of S.oneidensis with the introduction of PPK2-NADK

To explore the possible applications of this component, we conducted a full cell experiment using Shewanella bacteria.Firstly, we use cyclic voltammetry (CV) and linear sweep voltammetry (LSV) techniques for testing. The CV curve shows higher redox activity in the SPPK2-NADK strain.(Fig.5)

Figure 5: cyclic voltammetry show higher redox activity in the SPPK2-NADK strain

the LSV curve indicates lower internal resistance in the MFC cells of the SPPK2-NADK strain.(Fig.6)

Figure 6: LSV curve indicates lower internal resistance in the MFC cells of the SPPK2-NADK strain

Next, we measure the relative output power. The power density results show that the SPPK2-NADK strain has a maximum output power of 243.77 ± 25.2 mW/m², which is 2.32 times higher than the WT strain’s output power density (105.06 ± 11.72 mW/m²) (Fig. 7).

Figure 7: output power of the PPK2-NADK strain

chassis and genetic context

We express this gene on Shawanella oneidensis MR-1

Potential Applications

In bioelectrochemical Systems, utilizing PolyP and NADP in microbial fuel cells for further improved electron transfer and energy production.

Figure 3: current and voltage data on full cell experiment of Shewanella with the introduction of PPK2-NADK

References

1.Mori S, Yamasaki M, Maruyama Y, Momma K, Kawai S, Hashimoto W, Mikami B, Murata K. Crystallographic studies of Mycobacterium tuberculosis polyphosphate/ATP-NAD kinase complexed with NAD. J Biosci Bioeng. 2004;98(5):391-3. 2. Zhang, H., Ishige, K., & Kornberg, A. (2002). A polyphosphate kinase (PPK2) widely conserved in bacteria. Proceedings of the National Academy of Sciences, 99(26), 16678-16683. 3. Neville N, Roberge N, Jia Z. Polyphosphate Kinase 2 (PPK2) Enzymes: Structure, Function, and Roles in Bacterial Physiology and Virulence. Int J Mol Sci. 2022 Jan 8;23(2):670.