Difference between revisions of "Part:BBa K1682018:Experience"

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how you used this part and how it worked out.
 
how you used this part and how it worked out.
  
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===Background - Lambert_GA 2020===
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===Native Nar Operon - Lambert_GA 2020===
  
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===Background - Lambert_GA 2020===
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[[Image:NativeNar.jpeg|thumb|center|500px|<i>Figure 1. The diagram above shows the native Nar membrane-bound sensor proteins and the corresponding DNA-binding response regulators in E. coli.</i>]]
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Native to <i>E. coli</i>, the Nar Operon regulates anaerobic gene expression in response to two electron acceptors: nitrate and nitrite. This system consists of two homologous membrane-bound sensor proteins (NarX and NarQ) as well as two homologous DNA-binding response regulators (NarL and NarP). NarL’s conjugate is the membrane-bound NarX protein while NarP’s conjugate is the membrane-bound NarQ protein. Lambert iGEM is utilizing this system to test nitrate and nitrite levels, NarL and NarP expression, and downstream GFP expression through mathematical models.
  
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To optimize functionality, Lambert_GA altered the original part designed by HKUST-Rice 2015 by replacing the original terminators with rrNB T1 terminator and T7Te terminator after super folder GFP and a rrnBT1 T1 terminator after TetR.  
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===NarL System - Lambert_GA 2020===
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Nar Operon Background
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Native to E. coli, the Nar Operon regulates anaerobic gene expression in response to two electron acceptors: nitrate and nitrite. This system consists of two homologous membrane-bound sensor proteins (NarX and NarQ) as well as two homologous DNA-binding response regulators (NarL and NarP). NarL’s conjugate is the membrane-bound NarX protein while NarP’s conjugate is the membrane-bound NarQ protein. Our team is utilizing this system to test nitrate and nitrite levels, NarL and NarP expression, and downstream GFP expression through mathematical models.  
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[[Image:NarLConstruct.png|thumb|center|500px|<i>Figure 2: Diagram of the nitrate detection NarL system construct based on HKUST-Rice 2015 Part:BBa_K1682018.</i>]]
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The NarL system is designed based on HKUST-Rice 2015’s part BBa_K1682018, which is modeled after <i>E.coli’s</i> natural nitrate and nitrite sensor. Lambert iGEM’s NarL system is modified to change the original HKUST-Rice 2015 design’s terminators due to problematic DNA synthesis. To optimize functionality, Lambert_GA altered the original part by replacing the original terminators with rrNB T1 terminator and T7Te terminator (BBa_B1002) after super folder GFP and a rrnBT1 T1 terminator (BBa_J61048) after TetR. Both HKUST-Rice’s and Lambert’s NarL biosensors detect nitrate [2].  
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[[Image:_Nardiagram.png|thumb|center|500px|<i>Figure 3: Diagram of the nitrate detection NarL system signalling transduction pathway.</i>]]
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The promoter BBa_J23106, an Anderson Promoter, constitutively produces TetR, which represses the PtetO promoter that produces NarL. By regulating the amount of aTc, the molecule that inhibits TetR, the team can control levels of NarL. NarX, the native membrane-bound protein, senses the amount of nitrate in the cell: in the presence of nitrate, NarX will phosphorylate NarL, activating it; however, if there is no nitrate present, NarX will not phosphorylate NarL [2]. The PdcuS promoter, which naturally produces green fluorescent protein (GFP), is repressed by phosphorylated NarL, causing lower GFP levels in the presence of nitrate [3]. Lambert iGEM plans to correlate the GFP levels to nitrate through mathematical modeling.
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===Applications of BBa_K1682018===
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Lambert_GA 2020 is working on demonstrating that this part can be transformed into competent <i>E.coli</i> cells while retaining functionality. Attempts at ligation both with restriction digest cloning and Gibson Assembly cloning failed. The team is continuing to troubleshoot and clone the NarL part. In 2021, Lambert iGEM plans on utilizing this to model a nitrate biosensor in hydroponic/aquaponic systems.
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===References - Lambert_GA 2020===
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[1] HKUST-Rice iGEM (2015). Potassium, Phosphate and Nitrate Biosensors. Retrieved from http://2015.igem.org/Team:HKUST-Rice/Nitrate_Sensor_PyeaR
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[2] Darwin A.J., & Stewart V. (1996) The NAR Modulon Systems: Nitrate and Nitrite Regulation of Anaerobic Gene Expression. In: Regulation of Gene Expression in Escherichia coli. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-8601-8_17
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[3] Gob E., Bledsoe P., Chen L., Gyaneshwar P., Stewart V., & Igo M. (2005). Hierarchical Control of Anaerobic Gene Expression in Escherichia coli K-12: the Nitrate-Responsive NarX-NarL Regulatory System Represses Synthesis of the Fumarate-Responsive DcuS-DcuR Regulatory System. Journal of Bacteriology, 187(14): 4890–4899. doi: 10.1128/JB.187.14.4890–4899.2005
  
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<img src="https://static.igem.org/mediawiki/parts/b/bc/T--Lambert_GA--_Nardiagram.png"
 
  
 
<!-- DON'T DELETE --><partinfo>BBa_K1682018 StartReviews</partinfo>
 
<!-- DON'T DELETE --><partinfo>BBa_K1682018 StartReviews</partinfo>

Latest revision as of 02:47, 28 October 2020


This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Native Nar Operon - Lambert_GA 2020

Figure 1. The diagram above shows the native Nar membrane-bound sensor proteins and the corresponding DNA-binding response regulators in E. coli.

Native to E. coli, the Nar Operon regulates anaerobic gene expression in response to two electron acceptors: nitrate and nitrite. This system consists of two homologous membrane-bound sensor proteins (NarX and NarQ) as well as two homologous DNA-binding response regulators (NarL and NarP). NarL’s conjugate is the membrane-bound NarX protein while NarP’s conjugate is the membrane-bound NarQ protein. Lambert iGEM is utilizing this system to test nitrate and nitrite levels, NarL and NarP expression, and downstream GFP expression through mathematical models.

NarL System - Lambert_GA 2020

Figure 2: Diagram of the nitrate detection NarL system construct based on HKUST-Rice 2015 Part:BBa_K1682018.

The NarL system is designed based on HKUST-Rice 2015’s part BBa_K1682018, which is modeled after E.coli’s natural nitrate and nitrite sensor. Lambert iGEM’s NarL system is modified to change the original HKUST-Rice 2015 design’s terminators due to problematic DNA synthesis. To optimize functionality, Lambert_GA altered the original part by replacing the original terminators with rrNB T1 terminator and T7Te terminator (BBa_B1002) after super folder GFP and a rrnBT1 T1 terminator (BBa_J61048) after TetR. Both HKUST-Rice’s and Lambert’s NarL biosensors detect nitrate [2].

Figure 3: Diagram of the nitrate detection NarL system signalling transduction pathway.

The promoter BBa_J23106, an Anderson Promoter, constitutively produces TetR, which represses the PtetO promoter that produces NarL. By regulating the amount of aTc, the molecule that inhibits TetR, the team can control levels of NarL. NarX, the native membrane-bound protein, senses the amount of nitrate in the cell: in the presence of nitrate, NarX will phosphorylate NarL, activating it; however, if there is no nitrate present, NarX will not phosphorylate NarL [2]. The PdcuS promoter, which naturally produces green fluorescent protein (GFP), is repressed by phosphorylated NarL, causing lower GFP levels in the presence of nitrate [3]. Lambert iGEM plans to correlate the GFP levels to nitrate through mathematical modeling.

Applications of BBa_K1682018

Lambert_GA 2020 is working on demonstrating that this part can be transformed into competent E.coli cells while retaining functionality. Attempts at ligation both with restriction digest cloning and Gibson Assembly cloning failed. The team is continuing to troubleshoot and clone the NarL part. In 2021, Lambert iGEM plans on utilizing this to model a nitrate biosensor in hydroponic/aquaponic systems.

References - Lambert_GA 2020

[1] HKUST-Rice iGEM (2015). Potassium, Phosphate and Nitrate Biosensors. Retrieved from http://2015.igem.org/Team:HKUST-Rice/Nitrate_Sensor_PyeaR

[2] Darwin A.J., & Stewart V. (1996) The NAR Modulon Systems: Nitrate and Nitrite Regulation of Anaerobic Gene Expression. In: Regulation of Gene Expression in Escherichia coli. Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-8601-8_17

[3] Gob E., Bledsoe P., Chen L., Gyaneshwar P., Stewart V., & Igo M. (2005). Hierarchical Control of Anaerobic Gene Expression in Escherichia coli K-12: the Nitrate-Responsive NarX-NarL Regulatory System Represses Synthesis of the Fumarate-Responsive DcuS-DcuR Regulatory System. Journal of Bacteriology, 187(14): 4890–4899. doi: 10.1128/JB.187.14.4890–4899.2005


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