Algorithmic Programming of Sequential Logic and Genetic Circuits for Recording Biochemical Concentration in a...

Area of Science:

• Synthetic Biology
• Microbial Engineering
• Genetic Circuit Design

Background:

• Engineered probiotics offer noninvasive gastrointestinal diagnostics by reporting detected biomarkers.
• Genetic circuits require memory functions for signal recording in probiotic microorganisms.
• Understanding circuit component performance in clinically relevant strains like Escherichia coli Nissle 1917 (EcN) is crucial.

Purpose of the Study:

• To develop a scalable computational approach for designing robust sequential logic circuits in Escherichia coli Nissle 1917 (EcN).
• To enable engineered probiotics to record and report detected signals within the gastrointestinal tract.
• To create multiplexed diagnostic tools for the gut environment.

Main Methods:

• Utilized TetR-family transcriptional repressors to construct genetic logic gates for sequential logic circuits.
• Experimentally characterized 16 genetic NOT gates and nine sensors in EcN.
• Employed a theory-based, scalable computational design approach for genetic circuits.

Main Results:

• Successfully designed and predicted the performance of sequential logic circuits in EcN.
• Demonstrated genetic circuits encoding both combinational and sequential logic with outputs matching predictions.
• Developed an analog-like concentration recording circuit detecting three input signal ranges.

Conclusions:

• The developed computational approach enables the design of robust sequential logic circuits in the probiotic strain EcN.
• This work advances the use of engineered probiotics as diagnostic tools with genetically encoded memory.
• The findings support multiplexed biomarker interrogation and analog signal recording in the gut.