A framework and model system to investigate linear system behavior in Escherichia coli

Area of Science:

• Synthetic biology
• Systems biology
• Genetic engineering

Background:

• Engineering biological systems is challenged by nonlinear responses of genetic devices.
• Genetic devices often interact due to shared cellular machinery, leading to emergent properties.
• Linear behavior in biological systems, analogous to physical systems, could enable predictable engineering.

Purpose of the Study:

• To investigate the potential for linear system behavior in Escherichia coli (E. coli).
• To develop a framework for characterizing device linearity and nonlinearity.
• To assess the independence of genetic devices when co-expressed.

Main Methods:

• Developed a model system with three genetic devices in E. coli.
• Utilized transfer curve concepts and device transfer curves (DTCs) for quantitative characterization.
• Employed real-time quantitative PCR to measure gene expression levels.

Main Results:

• Identified that E. coli transcriptional system can exhibit linear behavior under small perturbation conditions.
• The green fluorescent protein (gfp) device showed nonlinearity, while neomycin phosphotransferase II (nptII) and chloramphenicol acetyl transferase (cat) devices exhibited linear responses.
• Device independence was lost when gfp was present at higher copy numbers, confirming nonlinear interactions.

Conclusions:

• Linear system behavior is achievable in E. coli.
• Understanding the nonlinearity of devices like gfp can lead to design rules for predictable biological systems.
• Principles from physical systems, such as DTCs, can aid in the characterization and design of biological systems.