Quorom Sensing

Overview

Quorum sensing is a process of cell-cell communication that allows bacteria to share information about cell density and adjust gene expression accordingly. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. Here, E.coli uses acylated homoserine lactones (AHL) as autoinducers.

Description

By quorum sensing system, we can adjust the proportion of engineered bacteria in the intestinal microbial community to maintain a balance. Below are the figures depicting our pathway design for quorum sensing module.

Corresponding enzyme express by LuxI to catalyze the formation of AHL. LuxR is the receptor of AHL, which activates bacterial quorum sensing system. AHL passively diffuses across the cell membrane. Extracellular and intracellular AHL molecules denoted as AHL_e and AHL respectively. When the density of the engineered bacteria is low, AHL and LuxR concentrations become low, the combination of the two is weak, glutamate dehydrogenase (GDH) begins to be expressed. Since GDH can make engineered bacteria dominant in competition with natural E.coli, the density of engineered bacteria in the gut microbiome will gradually increase.

As the density of engineered bacteria increases, due to AHL_e concentration gradient distribution, AHL concentration increases. When the engineered bacteria reach a certain proportion, AHL concentration reaches the threshold, and AHL and LuxR concentrations become high, the combination of the two is strong , tetR and β-galactosidase (bga2) begin to be expressed, thus promoting the proliferation of probiotics to slow down the proliferation of engineered bacteria, while GDH will no longer actively be expressed, reducing the competitiveness of engineered bacteria and ensuring that engineered bacteria do not interfere excessively with the intestinal microbiota.

The reactions for the above pathway is as follows.

AHL passively diffuse across the cell membrane

Generation and degradation of LuxR

Generation and degradation of LuxI

Generation and degradation of AHL

Combination of AHL and LuxR

Weak binding initiates P_tetR to generate GDH

Strong binding initiates P_LuxR to generate bga2 and tetR

ODE Model

Assumptions

1. In article [1], we found that when the AHLe concentration is greater than 1.01 g/mL, strong binding initiates P_LuxR to generate bga2 and tetR, and when less than 1.01 g/mL, weak binding initiates P_tetR to generate GDH.
2. Transcription is considered faster than translation, so the mRNA species for genes LuxR, LuxI, GDH, tetR and bga2 are in equilibrium.
3. Using the same assumptions as in [2] for quorum sensing mechanism and cell death. The number of cells N and the AHLe are both extracellular species. The remaining species are intracellular ones.
4. The diffusion coefficient is calculated as D=S·P_n/V_cell min^-1. It depends on the cell surface area S=4πr² (spherical area with r=10 μm), the membrane permeability P_n=3E-3μm⋅min^-1 and the typical E.coli volume V_cell=1.1E-9μL.
 

1. AHLe<1.01g/mL

2. AHLe>1.01g/mL

Parameter

Results

From the results above, we found that the density of engineered bacteria fluctuates between a narrow range, proving the engineered bacteria do oscillate between 0 and 4.

References

1. Li YC, Zhu JR. Role of N-acyl homoserine lactone (AHL)-based quorum sensing (QS) in aerobic sludge granulation. Appl Microbiol Biotechnol. 2014 Sep;98(17):7623-32. doi: 10.1007/s00253-014-5815-3. Epub 2014 May 21. PMID: 24846735.
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2. Yadira Boada, Alejandro Vignoni, and Jesús Picó. Multiobjective identification of a feedback synthetic gene circuit. IEEE Transactions on Control Systems Technology, 28(1):208–223, 2019.
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3. Momar Din, Tal Danino, Arthur Prindle, Matt Skalak, Jangir Selimkhanov, Kaitlin Allen, Ellixis Julio, Eta Atolia, Lev S Tsimring, Sangeeta N Bhatia, et al. Synchronized cycles of bacterial lysis for in vivo delivery. Nature, 536(7614):81–85, 2016.
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