Difference between revisions of "Part:BBa K4182006"

 
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<partinfo>BBa_K4182006 parameters</partinfo>
 
<partinfo>BBa_K4182006 parameters</partinfo>
 
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==Profile==
 +
 +
===Base Pairs===
 +
 +
6603
 +
 +
===Design Notes===
 +
 +
The codon of E. coli was optimized
 +
 +
===Source===
 +
 +
E.coli&Neurosparo ceassa
 +
 +
==Usage&Biology==
 +
 +
===Engineer===
 +
 +
We offer an environmentally friendly biofertilizer that attempts to solve the global ecological security and economic problems caused by the widespread use of chemical herbicides through synthetic biology. We constructed an engineered E. coli that produces aspartic acid and extracellular polysaccharide (EPS), a novel herbicide, under blue light and can be released into soil in a controlled manner at high temperatures, avoiding overuse of herbicides and possible residues, and promoting water retention and sand fixation of EPS. Our system consists of a proplasmid that converts glucose into a key precursor, GPP, and multiple functional plasmids that synthesize herbicides and EPS under blue light control. At the same time, our engineered cells would release herbicides and EPS containing lytic genes at a high temperature above 42℃. About 10% of the bacteria will escape the lysis process and recover, facilitating a new round of controlled production and release of herbicides and EPS. The intelligent synthesis and release of our biofertilizers will maximize the effects of herbicides and EPS, contributing to the environment and society.
 +
 +
===Design===
 +
 +
Based on the above hypothesis and the ideas provided by the literature, we designed the upstream control element of the chimeric VVD-AraC fusion structure and the downstream element to verify the effect of the modified operon. We selected sfGFP as the verification protein to efficiently test the expression of the element. The constructed circuit diagram is shown in the following figure.
 +
 +
[[File:XJTU-Design1.png|500px]]
 +
 +
FIG. 1 Verification circuit diagram of blue light-induced regulation system
 +
 +
===Build===
 +
 +
According to our design, the AraC and ParaBAD genes of the Arabinose induction and regulation system from Escherichia coli and the vivid gene from Streptomyces were synthesized respectively. eSD was added as the ribosome binding site. The synthetic genes were amplified by PCR, and the gene fragments were connected by golden gate according to the circuit diagram design.
 +
We selected Native Pc, J23101, and porin as operon gene promoters, and determined the best promoters by synthesizing and detecting the final thallus concentration and the expression yield of the green fluorescent protein.
 +
 +
[[File:XJTU-4.png|300px]]
 +
 +
FIG.2 Electrophoretic diagram of porin-eSD-PCR
 +
 +
[[File:XJTU-7.png|300px]]
 +
 +
FIG.3 PCR electrophoretic diagram of PAVVDH-porin colony
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 +
[[File:XJTU-5.png|300px]]
 +
 +
FIG.3 Blue light induction system using plasmid vector-MCS
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 +
[[File:XJTU-3.png|300px]]
 +
 +
FIG.4 PCR electrophoretic diagram of VVDAraC chimera gene
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 +
[[File:XJTU-6.png|300px]]
 +
 +
FIG.5 PCR electrophoretic diagram of PAVVDH-J23101 colony
 +
 +
==Test==
 +
 +
To explore the expression effect of synthetic plasmids, we independently design and construct a weak blue light induction system, which is mainly composed of a cold light plate and Pulse Width Modulation (PWM) modulation module, powered by USB. The size of the self-cooling plate is 20cm*20cm, the blue wavelength is 470nm, and the power is 5W/㎡.
 +
 +
[[File:XJTU-p1-map.png|400px]]
 +
 +
FIG.6 Plasmid map of blue light induction regulatory system
 +
 +
 +
[[File:XJTU-p1-hard.png|600px]]
 +
 +
FIG. 7 Design drawing of the self-made weak blue light induction system
 +
 +
Through the self-made blue light induction system, we introduced the recombinant plasmid into DH5α thallus, and successfully tested the change of green fluorescent protein yield after 4 hours of induction. Moreover, three PAVVDH promoters were compared and selected effectively.
 +
 +
[[File:XJTU-p1-hard1.png|400px]]
 +
 +
FIG. 8 Circuit diagram of PWM regulating module
 +
 +
[[File:XJTU-p1-hard2.png|400px]]
 +
 +
[[File:XJTU-p1-hard3.png|400px]]
 +
 +
FIG. 9-10 Self-made weak blue light induction system
 +
 +
It can be seen from Figures above that porin has a higher VVD transcription level and sfGFP background expression than the J23101 promoter under non-blue light induction, indicating that the porin promoter can better and more precisely initiate and regulate gene expression. FIG. 17 further proves that porin has a larger dynamic response range and better sensitivity when induced by blue light than the native PC promoter and J23101 promoter. Therefore, the PAVVDH-porin promoter was selected as the follow-up research object.
 +
 +
[[File:XJTU-bl1.png|500px]]
 +
 +
FIG.11 mRNA level of VVD and sfGFP under different promoters without blue light
 +
 +
[[File:XJTU-bl2.png|500px]]
 +
 +
FIG.12 Differential expression of green fluorescent protein of PAVVDH-Pc, PAVVDH-J2301 and PAVVDH-porin
 +
 +
OD600 was used to characterize the cell growth , indicating that blue light irradiation had no inhibitory effect on thallus growth, and the cell growth under induced and uninduced was consistent.
 +
 +
[[File:XJTU-p1-data1.png|500px]]
 +
 +
FIG.13  Line chart of OD600 absorbance value between the induced group and non-induced group
 +
 +
[[File:XJTU-p1-data2.png|500px]]
 +
 +
FIG.14  Line plots of sfGFP absorbance values in induced and non-induced groups
 +
 +
As can be seen from the above figure, compared with the non-induced group, the expression of sfGFP in bacteria undergoing the blue light induction system was significantly increased, which proved the success of our engineering construction of the blue light induction system. At the same time, PAVVD-porin as the promoter of the induction system was detected to be the best expression.
 +
 +
[[File:XJTU-p1-17.png|400px]]
 +
 +
FIG. 15 VVD confocal
 +
 +
The results showed that fluorescent proteins were expressed in large quantities after induction, and the feasibility and efficiency of blue light induction
 +
 +
As shown in the following figure, a more in-depth analysis of bacterial growth and yield was conducted. The production of sfGFP in the blue-induced group was significantly improved compared with that in the blank control group. However, the calculation of the sfGFP fluorescence effect per unit volume of bacteria could more directly illustrate the efficient production capacity of the blue-induced system.
 +
 +
[[File:XJTU-p1-data3.png|500px]]
 +
 +
FIG. 16 Line chart of sfGFP produced per unit volume of bacteria in the induction group
 +
 +
==References==
 +
 +
[1] ROMANO E, BAUMSCHLAGER A, AKMERIÇ E B, et al. Engineering AraC to make it responsive to light instead of arabinose [J]. Nat Chem Biol, 2021, 17(7): 817-27.
 +
 +
[2] RAMAKRISHNAN P, TABOR J J. Repurposing Synechocystis PCC6803 UirS-UirR as a UV-Violet/Green Photoreversible Transcriptional Regulatory Tool in E. coli [J]. ACS Synth Biol, 2016, 5(7): 733-40.
 +
 +
[3] ONG N T, TABOR J J. A Miniaturized Escherichia coli Green Light Sensor with High Dynamic Range [J]. Chembiochem, 2018, 19(12): 1255-8.
 +
 +
[4] OHLENDORF R, VIDAVSKI R R, ELDAR A, et al. From dusk till dawn: one-plasmid systems for light-regulated gene expression [J]. J Mol Biol, 2012, 416(4): 534-42.
 +
 +
[5] LI X, ZHANG C, XU X, et al. A single-component light sensor system allows highly tunable and direct activation of gene expression in bacterial cells [J]. Nucleic Acids Res, 2020, 48(6): e33.
 +
 +
[6] JAYARAMAN P, DEVARAJAN K, CHUA T K, et al. Blue light-mediated transcriptional activation and repression of gene expression in bacteria [J]. Nucleic Acids Res, 2016, 44(14): 6994-7005.
 +
 +
[7] DING Q, MA D, LIU G Q, et al. Light-powered Escherichia coli cell division for chemical production [J]. Nat Commun, 2020, 11(1): 2262.
 +
 +
[8] BAUMSCHLAGER A, AOKI S K, KHAMMASH M. Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control [J]. ACS Synth Biol, 2017, 6(11): 2157-67.

Revision as of 07:13, 12 October 2022


Circuit of blue light induction regulatory system

We designed the upstream control element of the chimeric VVD-AraC fusion structure and the downstream element to verify the effect of the modified operon. We selected sfGFP as the verification protein to efficiently test the expression of the element. The constructed circuit diagram is shown in the following figure.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NotI site found at 3502
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 869
    Illegal BamHI site found at 6543
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 1230
    Illegal AgeI site found at 1070
    Illegal AgeI site found at 6378
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 6151
    Illegal BsaI.rc site found at 3824
    Illegal SapI site found at 6360
    Illegal SapI.rc site found at 39


Profile

Base Pairs

6603

Design Notes

The codon of E. coli was optimized

Source

E.coli&Neurosparo ceassa

Usage&Biology

Engineer

We offer an environmentally friendly biofertilizer that attempts to solve the global ecological security and economic problems caused by the widespread use of chemical herbicides through synthetic biology. We constructed an engineered E. coli that produces aspartic acid and extracellular polysaccharide (EPS), a novel herbicide, under blue light and can be released into soil in a controlled manner at high temperatures, avoiding overuse of herbicides and possible residues, and promoting water retention and sand fixation of EPS. Our system consists of a proplasmid that converts glucose into a key precursor, GPP, and multiple functional plasmids that synthesize herbicides and EPS under blue light control. At the same time, our engineered cells would release herbicides and EPS containing lytic genes at a high temperature above 42℃. About 10% of the bacteria will escape the lysis process and recover, facilitating a new round of controlled production and release of herbicides and EPS. The intelligent synthesis and release of our biofertilizers will maximize the effects of herbicides and EPS, contributing to the environment and society.

Design

Based on the above hypothesis and the ideas provided by the literature, we designed the upstream control element of the chimeric VVD-AraC fusion structure and the downstream element to verify the effect of the modified operon. We selected sfGFP as the verification protein to efficiently test the expression of the element. The constructed circuit diagram is shown in the following figure.

XJTU-Design1.png

FIG. 1 Verification circuit diagram of blue light-induced regulation system

Build

According to our design, the AraC and ParaBAD genes of the Arabinose induction and regulation system from Escherichia coli and the vivid gene from Streptomyces were synthesized respectively. eSD was added as the ribosome binding site. The synthetic genes were amplified by PCR, and the gene fragments were connected by golden gate according to the circuit diagram design. We selected Native Pc, J23101, and porin as operon gene promoters, and determined the best promoters by synthesizing and detecting the final thallus concentration and the expression yield of the green fluorescent protein.

XJTU-4.png

FIG.2 Electrophoretic diagram of porin-eSD-PCR

XJTU-7.png

FIG.3 PCR electrophoretic diagram of PAVVDH-porin colony

XJTU-5.png

FIG.3 Blue light induction system using plasmid vector-MCS

XJTU-3.png

FIG.4 PCR electrophoretic diagram of VVDAraC chimera gene

XJTU-6.png

FIG.5 PCR electrophoretic diagram of PAVVDH-J23101 colony

Test

To explore the expression effect of synthetic plasmids, we independently design and construct a weak blue light induction system, which is mainly composed of a cold light plate and Pulse Width Modulation (PWM) modulation module, powered by USB. The size of the self-cooling plate is 20cm*20cm, the blue wavelength is 470nm, and the power is 5W/㎡.

XJTU-p1-map.png

FIG.6 Plasmid map of blue light induction regulatory system


XJTU-p1-hard.png

FIG. 7 Design drawing of the self-made weak blue light induction system

Through the self-made blue light induction system, we introduced the recombinant plasmid into DH5α thallus, and successfully tested the change of green fluorescent protein yield after 4 hours of induction. Moreover, three PAVVDH promoters were compared and selected effectively.

XJTU-p1-hard1.png

FIG. 8 Circuit diagram of PWM regulating module

XJTU-p1-hard2.png

XJTU-p1-hard3.png

FIG. 9-10 Self-made weak blue light induction system

It can be seen from Figures above that porin has a higher VVD transcription level and sfGFP background expression than the J23101 promoter under non-blue light induction, indicating that the porin promoter can better and more precisely initiate and regulate gene expression. FIG. 17 further proves that porin has a larger dynamic response range and better sensitivity when induced by blue light than the native PC promoter and J23101 promoter. Therefore, the PAVVDH-porin promoter was selected as the follow-up research object.

XJTU-bl1.png

FIG.11 mRNA level of VVD and sfGFP under different promoters without blue light

XJTU-bl2.png

FIG.12 Differential expression of green fluorescent protein of PAVVDH-Pc, PAVVDH-J2301 and PAVVDH-porin

OD600 was used to characterize the cell growth , indicating that blue light irradiation had no inhibitory effect on thallus growth, and the cell growth under induced and uninduced was consistent.

XJTU-p1-data1.png

FIG.13 Line chart of OD600 absorbance value between the induced group and non-induced group

XJTU-p1-data2.png

FIG.14 Line plots of sfGFP absorbance values in induced and non-induced groups

As can be seen from the above figure, compared with the non-induced group, the expression of sfGFP in bacteria undergoing the blue light induction system was significantly increased, which proved the success of our engineering construction of the blue light induction system. At the same time, PAVVD-porin as the promoter of the induction system was detected to be the best expression.

XJTU-p1-17.png

FIG. 15 VVD confocal

The results showed that fluorescent proteins were expressed in large quantities after induction, and the feasibility and efficiency of blue light induction

As shown in the following figure, a more in-depth analysis of bacterial growth and yield was conducted. The production of sfGFP in the blue-induced group was significantly improved compared with that in the blank control group. However, the calculation of the sfGFP fluorescence effect per unit volume of bacteria could more directly illustrate the efficient production capacity of the blue-induced system.

XJTU-p1-data3.png

FIG. 16 Line chart of sfGFP produced per unit volume of bacteria in the induction group

References

[1] ROMANO E, BAUMSCHLAGER A, AKMERIÇ E B, et al. Engineering AraC to make it responsive to light instead of arabinose [J]. Nat Chem Biol, 2021, 17(7): 817-27.

[2] RAMAKRISHNAN P, TABOR J J. Repurposing Synechocystis PCC6803 UirS-UirR as a UV-Violet/Green Photoreversible Transcriptional Regulatory Tool in E. coli [J]. ACS Synth Biol, 2016, 5(7): 733-40.

[3] ONG N T, TABOR J J. A Miniaturized Escherichia coli Green Light Sensor with High Dynamic Range [J]. Chembiochem, 2018, 19(12): 1255-8.

[4] OHLENDORF R, VIDAVSKI R R, ELDAR A, et al. From dusk till dawn: one-plasmid systems for light-regulated gene expression [J]. J Mol Biol, 2012, 416(4): 534-42.

[5] LI X, ZHANG C, XU X, et al. A single-component light sensor system allows highly tunable and direct activation of gene expression in bacterial cells [J]. Nucleic Acids Res, 2020, 48(6): e33.

[6] JAYARAMAN P, DEVARAJAN K, CHUA T K, et al. Blue light-mediated transcriptional activation and repression of gene expression in bacteria [J]. Nucleic Acids Res, 2016, 44(14): 6994-7005.

[7] DING Q, MA D, LIU G Q, et al. Light-powered Escherichia coli cell division for chemical production [J]. Nat Commun, 2020, 11(1): 2262.

[8] BAUMSCHLAGER A, AOKI S K, KHAMMASH M. Dynamic Blue Light-Inducible T7 RNA Polymerases (Opto-T7RNAPs) for Precise Spatiotemporal Gene Expression Control [J]. ACS Synth Biol, 2017, 6(11): 2157-67.