Difference between revisions of "Part:BBa K5034220"
Line 3: Line 3:
 
<partinfo>BBa_K5034220 short</partinfo>
 
<partinfo>BBa_K5034220 short</partinfo>
 
__TOC__
 
__TOC__
 +
 
===Basic Description===
 
===Basic Description===
−
This composite part includes the PPK1 gene which is initially from <i>Citrobacter freundii</i> and we performed codon optimization on, is expressed in the pBBR1MCS-terminator 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.
+
This composite part includes the <i>PPK1</i> gene which is initially from <i>Citrobacter freundii</i> and we performed codon optimization on, is expressed in the pBBR1MCS-terminator 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.
 
<html>
 
<html>
 
<body>
 
<body>
Line 13: Line 14:
 
</html>
 
</html>
 
Figure 1: Basic function of PPK1
 
Figure 1: Basic function of PPK1
−
<span class='h3bb'>Sequence and Features</span>
+
 
−
<partinfo>BBa_K5034220 SequenceAndFeatures</partinfo>
+
 
===Construct features===
 
===Construct features===
−
Promoter: Constitutive promoter for continuous expression. We use tac promoter in our experiment.
+
 
−
RBS: Ribosome binding site for efficient translation. BBa-B0031 here.
+
<partinfo>BBa_K5034220 SequenceAndFeatures</partinfo>
 +
 
 +
 
 +
Plasmid Backbone: pBBR1MCS-terminator plasmid
 +
 
 +
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.
 
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.
 +
 
 
<html>
 
<html>
 
<body>
 
<body>
 
     <div style="text-align: center;">
 
     <div style="text-align: center;">
−
         <img src="https://static.igem.wiki/teams/5034/engineering/fig3.png" style="width: 500px; height: auto;">
+
         <img src="https://static.igem.wiki/teams/5034/results/new/basic-structure-of-spk3.png" style="width: 500px; height: auto;">
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
−
Figure 2: Basic construction of PPK1 with B0031-RBS plasmid
+
Figure 2: Basic construction of <i>PPK1</i> with BBa-B0031 RBS plasmid
 
<html>
 
<html>
 
<body>
 
<body>
 
     <div style="text-align: center;">
 
     <div style="text-align: center;">
−
         <img src="https://static.igem.wiki/teams/5034/engineering/b0031-p-y-y-dt.png" style="width: 500px; height: auto;">
+
         <img src="https://static.igem.wiki/teams/5034/engineering/pbbr1mcs-terminator-31-ppk1.png" style="width: 500px; height: auto;">
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
−
Figure 3: Construction of PPK1 with B0031 RBS plasmid
+
Figure 3: Construction of <i>PPK1</i> with BBa-B0031 RBS plasmid
 +
 
 +
 
 +
We transformed the plasmids into wild-type <i>S. oneidensis.</i>, expressed it, and performed colony PCR. The results showed that <i>PPK1</i> was successfully introduced into <i>Shewanella</i> for replication.
 
<html>
 
<html>
 
<body>
 
<body>
Line 43: Line 56:
 
</body>
 
</body>
 
</html>
 
</html>
−
Figure 4: Colony PCR indicating plasmid replication in Shewanella
+
Figure 4: Colony PCR indicating plasmid replication in <i>S. oneidensis.</i>
 +
 
 +
 
 +
DNA agarose gel electrophoresis results showed that we obtained the plasmid with BBa-B0031 RBS, which is approximately 2.1 kb in size.
 
<html>
 
<html>
 
<body>
 
<body>
Line 51: Line 67:
 
</body>
 
</body>
 
</html>
 
</html>
−
Figure 5: Agarose gel electrophoresis indicating the target gene was successfully introduced into Shewanella
+
Figure 5: Agarose gel electrophoresis indicating we got the target gene with the corresponding RBS
 +
 
 +
 
 +
We performed protein extraction for SDS-PAGE. SDS-PAGE results showed that protein expression of the plasmid with BBa-B0031 RBS is the minimum, corresponding to the strength of RBS.
 
<html>
 
<html>
 
<body>
 
<body>
Line 60: Line 79:
 
</html>
 
</html>
 
Figure 6: SDS-PAGE results showing that the BBa-B0031 one’s protein expression is the minimum, corresponding to the strength of RBS.
 
Figure 6: 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)===
−
The PPK1 gene was sourced from Citrobacter freundii. The PYYDT plasmid backbone is a standard vector used for gene expression in synthetic biology applications.
+
The <i>PPK1</i> gene was sourced from <i>Citrobacter freundii</i>. The pBBR1MCS-terminator plasmid backbone is a standard vector used for gene expression in synthetic biology applications.
  
 
===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 <i>S. oneidensis.</i> 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 conducted Pi content detection to determine Pi concentration and half-cell experiment to measure the electricity production ability, we found SPK3 with RBS BBa-B0031 has the worst capacity to polymerize phosphorus but a greatest electroproduction capability.
 +
 
 
<html>
 
<html>
 
<body>
 
<body>
Line 74: Line 96:
 
</body>
 
</body>
 
</html>
 
</html>
−
Figure 7: statistical data on electricity production capacity of Shewanella with the introduction of PPK1 with different RBS
+
Figure 7: Electricity production capacity of <i>S. oneidensis.</i> with the introduction of <i>PPK1</i> with different RBS
 
<html>
 
<html>
 
<body>
 
<body>
Line 82: Line 104:
 
</body>
 
</body>
 
</html>
 
</html>
−
Figure 8: statistical data on phosphorus accumulation capacity of Shewanella with the introduction of PPK1 with different RBS
+
Figure 8: Phosphorus accumulation capacity of <i>S. oneidensis.</i> with the introduction of <i>PPK1</i> with different RBS
  
−
===References===
+
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>
−
1.Itoh, H., & Shiba, T. (2004). Polyphosphate synthetic activity of polyphosphate:AMP phosphotransferase in Acinetobacter johnsonii 210A. Journal of Bacteriology, 186(15), 5178-5181.
+
  
−
<!-- Add more about the biology of this part here
+
===Chassis and genetic===
−
===Usage and Biology===
+
Chassis：<i>Shewanella onediensis</i> MR-1
  
−
<!-- -->
+
The gene can be expressed and function properly in <i>S. oneidensis.</i>.
  
 +
===Potential applications===
 +
The <i>PPK1</i> 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.
  
−
<!-- Uncomment this to enable Functional Parameter display
+
Environmental Bioremediation: Assists in the accumulation of heavy metals or radioactive substances for pollution control.
−
===Functional Parameters===
+
 
−
<partinfo>BBa_K5034220 parameters</partinfo>
+
===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.

Revision as of 07:00, 1 October 2024


Pi <-> Poly P

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 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.

Figure 1: Basic function of PPK1

Construct features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal prefix found in sequence at 4981
    Illegal suffix found in sequence at 1
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 4981
    Illegal SpeI site found at 2
    Illegal PstI site found at 16
    Illegal NotI site found at 9
    Illegal NotI site found at 2834
    Illegal NotI site found at 4987
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 4981
    Illegal BglII site found at 3580
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal prefix found in sequence at 4981
    Illegal suffix found in sequence at 2
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal prefix found in sequence at 4981
    Illegal XbaI site found at 4996
    Illegal SpeI site found at 2
    Illegal PstI site found at 16
    Illegal NgoMIV site found at 562
    Illegal NgoMIV site found at 4244
    Illegal NgoMIV site found at 4527
    Illegal AgeI site found at 402
  • 1000
    COMPATIBLE WITH RFC[1000]


Plasmid Backbone: pBBR1MCS-terminator plasmid

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.

Figure 2: Basic construction of PPK1 with BBa-B0031 RBS plasmid
Figure 3: Construction of PPK1 with BBa-B0031 RBS plasmid


We transformed the plasmids into wild-type S. oneidensis., expressed it, and performed colony PCR. The results showed that PPK1 was successfully introduced into Shewanella for replication.

Figure 4: Colony PCR indicating plasmid replication in S. oneidensis.


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

Figure 5: Agarose gel electrophoresis indicating we got the target gene with the corresponding RBS


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

Figure 6: 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. The pBBR1MCS-terminator plasmid backbone is a standard vector used for gene expression in synthetic biology applications.

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 S. oneidensis. to develop the best ability to produce electricity and polymerize phosphorus.

We conducted Pi content detection to determine Pi concentration and half-cell experiment to measure the electricity production ability, we found SPK3 with RBS BBa-B0031 has the worst capacity to polymerize phosphorus but a greatest electroproduction capability.

Figure 7: Electricity production capacity of S. oneidensis. with the introduction of PPK1 with different RBS
Figure 8: Phosphorus accumulation capacity of S. oneidensis. with 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 S. oneidensis..

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.