Difference between revisions of "Part:BBa K2033004"
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===Short Description=== | ===Short Description=== | ||
| − | This is a synthase enzyme that produces the | + | This is a synthase enzyme that produces the AHL quorum sensing molecule (3S)-3-[(2-oxo-3-phenylpropyl)amino]oxolan-2-one |
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<partinfo>BBa_K2033004 parameters</partinfo> | <partinfo>BBa_K2033004 parameters</partinfo> | ||
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| + | ===Short Description=== | ||
| + | This part produces the AHL quorum sensing molecule isovaleryl-HSL (IV-HSL, also known as 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide. This AHL synthase is paired with a constitutive Tet promoter and mCherry. | ||
| + | |||
| + | ===Bja System=== | ||
| + | AHL quorum sensing functions within two modules. The first module, the "Sender," must be induced by certain environmental conditions, usually population density of surrounding organisms. This will begin production of the AHL by the cell, which is then detected by the second module, the "Receiver." Once a certain threshold of AHLs is breached, the Receiver will cause the expression or silencing of certain genes to achieve the desired purpose of the communication, whether it is the production of GFP or to increase growth rate. | ||
| + | |||
| + | The Bja system originates from the soil bacterium Bradyrhizobium japonicum. It produces an isovaleryl AHL, also known as 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide. The structure is shown below: | ||
| + | |||
| + | <div style="text-align: center;">[[File:T--Arizona State--bjahsl3d.png|250px|]]</div> | ||
| + | |||
| + | This AHL notably has an isovaleryl tail, which will serve as a unique binding domain for the transcription factor. | ||
| + | |||
| + | The BjaI part arises from the soil bacterium Bradyrhizobium japonicum. The designed part by Ryan Muller was cloned into competent DH5AT E. coli cells. These were ligated into the psb1C3 vector and plated, producing the following gel: | ||
| + | <div style="text-align: center;">[[File:T--Arizona State--Gel4.jpg]]</div> | ||
| + | |||
| + | An optical density test was conducted on the produced BjaI construct to determine if the AHL is produced. The plate reader ran an 8-hour read from 580-610nm, indicating the presence of the mCherry fluorescent molecule. The AHL gene lies upstream of the mCherry gene, so successful production of mCherry is a good indicator that the AHL molecule is being produced. A positive growth curve was found for the BjaI construct over the 8-hour read. The initial dip in mCherry levels was likely the result of the transfer of the cells from an aerated, incubated environment to a 96-well plate. However, overall, mCherry production increased over time, suggesting that the BjaI Synthase had been produced in E. coli. | ||
| + | <div style="text-align: center;">[[File:T--Arizona State--BJARFP.png]]</div> | ||
| + | |||
| + | ===Safety=== | ||
| + | This section aims to provide safety information and suggestions about the BjaI part. The greatest concern from this part is the activation of pathogens via crosstalk. According to Integrated DNA Technologies, quorum sensing genes are not considered dangerous by themselves, as they do not directly cause the creation of a new pathogenic strain. They may contribute to pathogenicity, but so do synthetic promoters. So, the actual AHL molecules are the chief concern. | ||
| + | |||
| + | ====Crosstalk Partners==== | ||
| + | BjaI is known to be similar to the Rpa system, according to Lindemann A. (2011). Rpa has been shown to interact with Silicibacter pomeroyi, as well as the well-characterized part Bba_F2620, which was designed for the Lux system. Other crosstalk partners likely exist. | ||
| + | |||
| + | ====Disposal==== | ||
| + | In order to properly dispose of 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide (isovaleryl-HSL), the sample should be autoclaved. This AHL does not possess a beta-ketone group in the acyl tail, and so, bleach is not capable of effectively degrading it. Further details about proper AHL disposal can be found here: http://2016.igem.org/Team:Arizona_State/WhitePaper. | ||
| + | |||
| + | ====Other Considerations==== | ||
| + | No other safety information is available for IV-HSL. | ||
Revision as of 09:49, 17 October 2016
(3S)-3-[(2-oxo-3-phenylpropyl)amino]oxolan-2-one (3-phenyl-HSL) Sender- BraI
Short Description
This is a synthase enzyme that produces the AHL quorum sensing molecule (3S)-3-[(2-oxo-3-phenylpropyl)amino]oxolan-2-one
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 83
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 412
- 1000COMPATIBLE WITH RFC[1000]
Short Description
This part produces the AHL quorum sensing molecule isovaleryl-HSL (IV-HSL, also known as 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide. This AHL synthase is paired with a constitutive Tet promoter and mCherry.
Bja System
AHL quorum sensing functions within two modules. The first module, the "Sender," must be induced by certain environmental conditions, usually population density of surrounding organisms. This will begin production of the AHL by the cell, which is then detected by the second module, the "Receiver." Once a certain threshold of AHLs is breached, the Receiver will cause the expression or silencing of certain genes to achieve the desired purpose of the communication, whether it is the production of GFP or to increase growth rate.
The Bja system originates from the soil bacterium Bradyrhizobium japonicum. It produces an isovaleryl AHL, also known as 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide. The structure is shown below:
This AHL notably has an isovaleryl tail, which will serve as a unique binding domain for the transcription factor.
The BjaI part arises from the soil bacterium Bradyrhizobium japonicum. The designed part by Ryan Muller was cloned into competent DH5AT E. coli cells. These were ligated into the psb1C3 vector and plated, producing the following gel:
An optical density test was conducted on the produced BjaI construct to determine if the AHL is produced. The plate reader ran an 8-hour read from 580-610nm, indicating the presence of the mCherry fluorescent molecule. The AHL gene lies upstream of the mCherry gene, so successful production of mCherry is a good indicator that the AHL molecule is being produced. A positive growth curve was found for the BjaI construct over the 8-hour read. The initial dip in mCherry levels was likely the result of the transfer of the cells from an aerated, incubated environment to a 96-well plate. However, overall, mCherry production increased over time, suggesting that the BjaI Synthase had been produced in E. coli.
Safety
This section aims to provide safety information and suggestions about the BjaI part. The greatest concern from this part is the activation of pathogens via crosstalk. According to Integrated DNA Technologies, quorum sensing genes are not considered dangerous by themselves, as they do not directly cause the creation of a new pathogenic strain. They may contribute to pathogenicity, but so do synthetic promoters. So, the actual AHL molecules are the chief concern.
Crosstalk Partners
BjaI is known to be similar to the Rpa system, according to Lindemann A. (2011). Rpa has been shown to interact with Silicibacter pomeroyi, as well as the well-characterized part Bba_F2620, which was designed for the Lux system. Other crosstalk partners likely exist.
Disposal
In order to properly dispose of 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide (isovaleryl-HSL), the sample should be autoclaved. This AHL does not possess a beta-ketone group in the acyl tail, and so, bleach is not capable of effectively degrading it. Further details about proper AHL disposal can be found here: http://2016.igem.org/Team:Arizona_State/WhitePaper.
Other Considerations
No other safety information is available for IV-HSL.