Biosensor characterization: formal methods from the perspective of proteome fractions

Area of Science:

• Synthetic Biology
• Systems Biology
• Molecular Systems Engineering

Background:

• Characterizing regulatory elements in gene expression is crucial for recombinant systems.
• Existing methods often lack a formal approach to analyze variations in regulatory components.
• A formal framework is needed to precisely quantify these variations in biological circuits.

Purpose of the Study:

• To establish a formal framework for analyzing regulatory circuits in bacterial systems.
• To develop convenient methods for characterizing expression fractions and dose-response parameters.
• To link biosensor outputs to fundamental bacterial physiology.

Main Methods:

• Modeled the bacterial cell as a collection of proteome fractions.
• Derived a general theorem for time-dependent proteome fraction changes based on expression fraction.
• Utilized direct protein quantification and analyzed growth rate versus proteome fraction production rate.

Main Results:

• A method was established to reliably measure expression fraction through protein quantification.
• Demonstrated a linear correlation between protein production rate and specific growth rate, indicating a constant expression fraction.
• Expression fractions determined by novel methods yielded consistent dose-response parameters for Isopropyl β- d-1-thiogalactopyranoside (IPTG), mercury, and cumate biosensors.

Conclusions:

• The presented framework provides convenient methods for obtaining valid dose-response parameters.
• The methods enable a clear definition of the time interval for parameter validity.
• Offers a robust framework for interpreting biosensor outputs in the context of bacterial physiology.