Revision as of 01:24, 12 October 2023

PobR-Threshold Guard Switch

Sequence and Features

Description

This composite part consists of four main components: the pobR, the pobR RBS, the pobR operator, the pobA/R dual-directional promoter, and the digitizer.

pobR

The gene pobR creates a transcriptional activator that attaches to the pobR operator on the dsDNA before combining with 4-HBA. Once 4-HBA is introduced to the solution, PobR binds with it and triggers the transcription of the dual pobA/R promoter on the side of pobA.

One of the advantages of this protein is its sensitivity and low leakage properties. Even tiny amounts of 4-HBA, at the micromolar level, can trigger transcription. This characteristic is crucial in creating a high-quality digitizer with a sharp response between two stable states^[1].

Additionally, research indicates that most analogs of 4-HBA, such as p-aminobenzoate, can impede the activation of PobR, ensuring precise detection of 4-HBA.

Moreover, the combination of the non-activated PobR and pobR operator will inhibit the transcription of pobR when there is no 4-HBA stimulus, reducing the pressure on our bacteria.

Threshold Guard Switch

The promoters we utilize are controlled by signal-sensitive receptors, which typically demonstrate different relationships between inputs and outputs when exposed to specific inducers.

However, it's important to highlight that a more thorough transcription halt allows for tighter signaling control, which is undoubtedly vital for trace chemical detection. Therefore, We placed the original threshold guard switch (first developed by Ángel & Víctor^[2]) downstream of our detection fragment. Here are the critical components of this post-transcriptional control circuit:

Given PobR's excellent properties, we create a chimeric switch by combining it with a portion of the original threshold guard switch.

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Experiment & Result

The Threshold Guard Switch

As described by Ángel and Víctor, the “Digitalizer module” they built has a clearly defined on-and-off status. As mentioned in Design, we used it as a threshold guard switch that only allowed a specific inducer of a specific concentration to open our promoter. To verify the functionality and the minimum threshold of this switch, we conducted a series of gradient concentration tests using classical inducers of the Xyls/Pm system: Benzoic acid and 3MBz.

Inducer: Benzoic acid

Initially, a wide range of 2000µM to 0µM benzoic acid was added to E. coli BL21(DE3) (initial OD value = 0.688) that had the switch sequence (BBa_K3202045). msfGFP fluorescence was measured by a synergy HTX microplate reader with excitation at 485 nm (±20 nm) and emission at 520 nm (±20 nm). Fluorescence was normalized to the OD after the background fluorescence value was subtracted from all RFU data. Continually Measuring every 2 minutes for 12 hours, we surprisingly found that the turning-on threshold of this lay at a low level—between 150 μM and 100 μM.(shown in the figure below)

Besides, the time that this switch needed to turn on was collected when the relative fluorescent units (RFU) reached above 200, providing strong evidence that when the concentration of benzoic acid was above 150μM can be regarded as a line separating the on-and-off status of this switch. However, the response time might not be as promising as we thought. The minimum time our switch cost to reach the on-status was 74.33 minutes at 2000μM Benz. Acid.(shown in the figure below)

Being curious about what happened when benzoic acid concentration changed from 100μM to 150μM, we performed a detailed threshold test around this range (80μM~150μM). Using the same bacteria (initial OD value = 0.480) and following the same protocol, we obtained the detailed situation shown in the figure below. Although the absolute value of RFU might be different from the previous test due to the initial growth status, we still found it distinguishable between the on (above 100 μM) and off (below 100 μM) models of this switch. (shown in the figure below)

Inducer: 3MBz

In order to ensure the on-and-off status that happened on our threshold guard switch is non-specific to benzoic acid, we used 3MBz as another inducer. The result shown below also provided an on-and-off threshold line at 10μM and aligned with the work done by Ángel and Víctor^[2].

pobr

References

1. ^[1]Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotech 31: 170 – 174
2. ^[2]Calles B , Goni-Moreno A , Lorenzo V D .Digitalizing heterologous gene expression in Gram-negative bacteria with a portable on/off module[J]. 2019.DOI:10.1101/783506.