Difference between revisions of "Part:BBa K2033002"

Revision as of 10:18, 18 October 2016

isovaleryl-HSL, 3-methyl-N-[(3S)-2-oxooxolan-3-yl]butanamide Sender- BjaI

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 294
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE 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 designed to be inserted into a modular sender vector BBa_K2033011 with a constitutive Tet promoter, 2 ribosome binding sites (RBSs), an RFC10 prefix 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:

In addition, this part was sequenced with the help of ASU's Core Laboratory:

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.

@@ Line 30: / Line 30: @@
 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>
+In addition, this part was sequenced with the help of ASU's Core Laboratory:
+<div style="text-align: center;">[[File:T--Arizona State--bjasequence1.png|600px]]</div>
+<div style="text-align: center;">[[File:T--Arizona State--bjasequence2.png|600px]]</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.