Engineering Yeast Cells to Facilitate Information Exchange

TL;DR

This work addresses the gap between molecular communications theory and practical microscale validation by introducing the first MC testbed built with engineered yeast cells. It develops an end-to-end (E2E) model comprising a GAL-driven transmitter, a diffusion channel, and a MAPK-based receiver that reports via Fus1-driven GFP, validated against experimental data. Key contributions include detailed transmitter/receiver modeling, an analytically tractable diffusion impulse response, and comprehensive experimental validation with Bar1+ and bar1Δ yeast receivers, revealing rapid RNA responses but slower protein reporting, and the potential for higher rates with alternative reporting. The study demonstrates the feasibility of yeast-based MC testbeds and lays the groundwork for optimized yeast biosensors and IoBNT integration, with future work aimed at faster reporting, noise modeling, and advanced modulation strategies.

Abstract

Although continuous advances in theoretical modelling of Molecular Communications (MC) are observed, there is still an insuperable gap between theory and experimental testbeds, especially at the microscale. In this paper, the development of the first testbed incorporating engineered yeast cells is reported. Different from the existing literature, eukaryotic yeast cells are considered for both the sender and the receiver, with α-factor molecules facilitating the information transfer. The use of such cells is motivated mainly by the well understood biological mechanism of yeast mating, together with their genetic amenability. In addition, recent advances in yeast biosensing establish yeast as a suitable detector and a neat interface to in-body sensor networks. The system under consideration is presented first, and the mathematical models of the underlying biological processes leading to an end-to-end (E2E) system are given. The experimental setup is then described and used to obtain experimental results which validate the developed mathematical models. Beyond that, the ability of the system to effectively generate output pulses in response to repeated stimuli is demonstrated, reporting one event per two hours. However, fast RNA fluctuations indicate cell responses in less than three minutes, demonstrating the potential for much higher rates in the future.

Figures (9)

• Figure 1: Schematic diagram of the yeast mating signaling pathway coupled to the heterologous expression of a mammalian GPCR. The GPCR occupancy by the stimulating ligand on the cell surface triggers the splitting of the receptor-bound heterotrimeric G-protein into the G$\alpha$ subunit, and the G$\beta$$\gamma$ dimer. Replacement of the endogenous G$\alpha$ subunit by a chimeric yeast/mammalian G$\alpha$ protein couples the heterologous receptor to the endogenous MAPK signaling pathway and the downstream expression of the mating-responsive GFP reporter gene. The engineered elements of the pathway are outlined in red color.
• Figure 2: End-to-End system.
• Figure 3: Fundamental point-to-point yeast communication system.
• Figure 4: Bar1 protease degrading pheromone particles.
• Figure 5: Stimulation of MATa cells with 10 $\mu$M synthetic $\alpha$-factor and assessment of GFP RNA levels. GFP transcript levels were determined by quantitative PCR following the induction of Bar1p+ (Bar1 present) and bar1$\Delta$ (Bar1 Knockout) cells with 10 $\mu$M of exogenously provided $\alpha$-factor. RNA levels were monitored for 120’ following initial induction, at the indicated timepoints. The values were normalized to the expression of $\beta$-actin and presented as a fold change over non-induced cells. Values from two independent experiments in both Fig.\ref{['single Bar1 RNA']} and Fig.\ref{['single no Bar1 RNA']}, are presented as mean $\pm$ standard error of the mean (SEM).