Difference between revisions of "Part:BBa K5034214"
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===Basic Description===
 
===Basic Description===
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This composite part includes the PPK1 gene which is initially from Citrobacter freundii and we performed codon optimization on, is expressed in the PYYDT plasmid with the BBa-B0031 RBS, which is a weaker one compared to others. This composite part is designed to facilitate the reversible conversion between inorganic polyphosphate (PolyP) and inorganic phosphate (Pi). The PPK1 enzyme is known for its ability to synthesize PolyP from ATP and to degrade PolyP back to Pi, with a preference for the synthetic reaction, making it a versatile tool for managing phosphate metabolism in engineered systems.In a sentence, this part is activated by a weaker rbs.It can reversibly convert Poly p and Pi. This reversible process favors the generation of Poly P.For the first time, we expressed this element in a strain of Shewanella and conducted codon optimization based on Shewanella.
+
This composite part includes the PPK1 gene which is initially from Citrobacter freundii and we performed codon optimization on, is expressed in the pBBR1MCS-terminator plasmid with the BBa-B0031 RBS, which is a weaker RBS compared to others. This composite part is designed to facilitate the reversible conversion between inorganic polyphosphate (PolyP) and inorganic phosphate (Pi). The PPK1 enzyme is known for its ability to synthesize PolyP from ATP and Pi and to degrade PolyP back to Pi, with a preference for the synthetic reaction, making it a versatile tool for managing phosphate metabolism in engineered systems. In a sentence, this part is activated by a weaker RBS. It can reversibly convert Poly p and Pi. This reversible process favors the generation of Poly P. For the first time, we expressed this element in a strain of Shewanella and conducted codon optimization based on Shewanella.
 
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         <img src="https://static.igem.wiki/teams/5034/engineering/fig3.png" style="width: 500px; height: auto;">
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         <img src="https://static.igem.wiki/teams/5034/engineering/mechanism-of-ppk1.png" style="width: 500px; height: auto;">
 
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===Construct features===
 
===Construct features===
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Promoter: Constitutive promoter for continuous expression. We use tac promoter in our experiment.
+
Promoter: Constitutive promoter for continuous expression. We use Lac promoter in our experiment.
−
RBS: Ribosome binding site for efficient translation. BBa-B0031 here.
+
 
 +
RBS: Ribosome binding site for efficient translation. We use BBa-B0031 here.
 +
 
 
PPK1 Coding Sequence: Encodes the polyphosphate kinase 1 enzyme.
 
PPK1 Coding Sequence: Encodes the polyphosphate kinase 1 enzyme.
−
Terminator: Efficient transcription terminator to ensure proper mRNA processing. We use T7Te terminator in our experiment.
+
 
 +
Terminator: Efficient transcription terminator to ensure proper mRNA processing. We use rrnB T1 terminator and T7Te terminator in our experiment.
 +
 
 +
The basic structure of the part is shown as follows:
 
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Figure 2: Colony PCR indicating plasmid replication in Shewanell
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Figure 2: Basic construction of PPK1 plasmid with BBa-B0031 RBS
 +
 
 +
We transform the plasmids into wild-type Shewanella, express it, and perform colony PCR. The results show that PPK1 is successfully introduced into Shewanella for replication.
 +
<html>
 +
<body>
 +
    <div style="text-align: center;">
 +
        <img src="https://static.igem.wiki/teams/5034/engineering/fig9.png" style="width: 500px; height: auto;">
 +
    </div>
 +
</body>
 +
</html>
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Figure 3: Colony PCR indicating plasmid replication in Shewanell
 +
 
 +
DNA agarose gel electrophoresis results showed that we obtained the plasmid with BBa-B0031 RBS, which is approximately 2.1 kb in size.
 
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Figure 3: Agarose gel electrophoresis indicating the target gene was successfully introduced into Shewanella
+
Figure 4: Agarose gel electrophoresis indicating we got the target gene with the corresponding RBS
 +
 
 +
We performed protein extraction for SDS-PAGE. The results showed that protein expression of the plasmid with BBa-B0031 RBS is the minimum, corresponding to the strength of RBS.
 
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Figure 4: SDS-PAGE results showing that the BBa-B0031 one’s protein expression is the minimum, corresponding to the strength of RBS
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Figure 5: SDS-PAGE results showing that the BBa-B0031 one’s protein expression is the minimum, corresponding to the strength of RBS
  
 
===Origin (Organism)===
 
===Origin (Organism)===
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===Experimental Characterization and results===
 
===Experimental Characterization and results===
−
Alteration of protein expression intensity can regulate the metabolic networks, so we focused on RBS with varying translation strengths to facilitate the regulation of PPK1 concentration in Shewanella thus developing the best ability to produce electricity and polymerize phosphorus.
+
Alteration of protein expression intensity can regulate the metabolic networks, so we focused on RBS with varying translation strengths to facilitate the regulation of PPK1 concentration in Shewanella to develop the best ability to produce electricity and polymerize phosphorus.
−
Conducting molybdate assays to determine Pi concentration and half-cell reaction(electrochemistry) to measure the electricity production ability, we found SPK1(with RBS BBa-B0031) has the worst capacity to polymerize phosphorus but a greatest electroproduction capability.
+
We conduct Pi content detection to determine Pi concentration and half-cell experiment to measure the electricity production ability. We found that SPK1 with RBS BBa-B0031 has the lowest capacity for phosphorus polymerization but the highest electroproduction capability.
 
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Figure 5: statistical data on electricity production capacity of Shewanella with the introduction of PPK1 with different RBS
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Figure 5: Electricity production capacity of Shewanella after the introduction of PPK1 with different RBS
 
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Figure 6: statistical data on phosphorus accumulation capacity of Shewanella with the introduction of PPK1 with different RBS
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Figure 6: Phosphorus accumulation capacity of Shewanella after the introduction of PPK1 with different RBS
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 +
Details of all experiments can be found in the <html><body><a href="https://2024.igem.wiki/nanjing-china/experiments">Experiments section on the Wiki.</a></body></html>
 +
 
 +
==Chassis and genetic==
 +
Chassis：Shewanella onediensis MR-1
 +
 
 +
The gene can be expressed and function properly in Shewanella.
 +
 
 +
==Potential applications==
 +
The PPK1 gene (polyphosphate kinase 1) has potential applications in:
 +
 
 +
Industrial Microbial Engineering: Enhances the production of biofuels, amino acids, or antibiotics by boosting polyphosphate synthesis in microorganisms.
 +
 
 +
Environmental Bioremediation: Assists in the accumulation of heavy metals or radioactive substances for pollution control.
  
 
===References===
 
===References===

Revision as of 15:19, 30 September 2024


PolyP <->Pi

Basic Description

This composite part includes the PPK1 gene which is initially from Citrobacter freundii and we performed codon optimization on, is expressed in the pBBR1MCS-terminator plasmid with the BBa-B0031 RBS, which is a weaker RBS compared to others. This composite part is designed to facilitate the reversible conversion between inorganic polyphosphate (PolyP) and inorganic phosphate (Pi). The PPK1 enzyme is known for its ability to synthesize PolyP from ATP and Pi and to degrade PolyP back to Pi, with a preference for the synthetic reaction, making it a versatile tool for managing phosphate metabolism in engineered systems. In a sentence, this part is activated by a weaker RBS. It can reversibly convert Poly p and Pi. This reversible process favors the generation of Poly P. For the first time, we expressed this element in a strain of Shewanella and conducted codon optimization based on Shewanella.

Figure 1: Basic function of PPK1

Construct features

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

RBS: Ribosome binding site for efficient translation. We use BBa-B0031 here.

PPK1 Coding Sequence: Encodes the polyphosphate kinase 1 enzyme.

Terminator: Efficient transcription terminator to ensure proper mRNA processing. We use rrnB T1 terminator and T7Te terminator in our experiment.

The basic structure of the part is shown as follows:

Figure 2: Basic construction of PPK1 plasmid with BBa-B0031 RBS

We transform the plasmids into wild-type Shewanella, express it, and perform colony PCR. The results show that PPK1 is successfully introduced into Shewanella for replication.

Figure 3: Colony PCR indicating plasmid replication in Shewanell

DNA agarose gel electrophoresis results showed that we obtained the plasmid with BBa-B0031 RBS, which is approximately 2.1 kb in size.

Figure 4: Agarose gel electrophoresis indicating we got the target gene with the corresponding RBS

We performed protein extraction for SDS-PAGE. The results showed that protein expression of the plasmid with BBa-B0031 RBS is the minimum, corresponding to the strength of RBS.

Figure 5: SDS-PAGE results showing that the BBa-B0031 one’s protein expression is the minimum, corresponding to the strength of RBS

Origin (Organism)

The PPK1 gene was sourced from Citrobacter freundii.

Experimental Characterization and results

Alteration of protein expression intensity can regulate the metabolic networks, so we focused on RBS with varying translation strengths to facilitate the regulation of PPK1 concentration in Shewanella to develop the best ability to produce electricity and polymerize phosphorus. We conduct Pi content detection to determine Pi concentration and half-cell experiment to measure the electricity production ability. We found that SPK1 with RBS BBa-B0031 has the lowest capacity for phosphorus polymerization but the highest electroproduction capability.

Figure 5: Electricity production capacity of Shewanella after the introduction of PPK1 with different RBS
Figure 6: Phosphorus accumulation capacity of Shewanella after the introduction of PPK1 with different RBS

Details of all experiments can be found in the Experiments section on the Wiki.

Chassis and genetic

Chassis：Shewanella onediensis MR-1

The gene can be expressed and function properly in Shewanella.

Potential applications

The PPK1 gene (polyphosphate kinase 1) has potential applications in:

Industrial Microbial Engineering: Enhances the production of biofuels, amino acids, or antibiotics by boosting polyphosphate synthesis in microorganisms.

Environmental Bioremediation: Assists in the accumulation of heavy metals or radioactive substances for pollution control.

References

1.Itoh, H., & Shiba, T. (2004). Polyphosphate synthetic activity of polyphosphate:AMP phosphotransferase in Acinetobacter johnsonii 210A. Journal of Bacteriology, 186(15), 5178-5181. 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]