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Microbial Biosensors

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Microbial biosensors are analytical devices that utilize living microbes to detect specific substances through measurable signals. These devices consist of two main components: biosensing organisms and signal-transducing elements. Biosensing organisms, such as Escherichia coli or Saccharomyces cerevisiae, are typically housed in multiwell plates connected to transducers, enabling rapid, real-time detection of target analytes.Signal Generation MechanismWhen a target analyte—such as...

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Ligify 2.0: a web server for predicted small molecule biosensors.

Simon d'Oelsnitz^1,2,3, Nicole N Zhao^1,3, Pranay Talla^1,3

¹Synthetic Biology HIVE, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States.

Nucleic Acids Research

|May 6, 2026

Summary

This summary is machine-generated.

Ligify 2.0 predicts small molecule biosensors (transcription factors) using genome data. This new web server expands the characterization of these biological sensors for biotechnology applications.

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Area of Science:

Biotechnology
Bioinformatics
Molecular Biology

Background:

Prokaryotic transcription factors (TFs) are valuable small molecule biosensors, but most remain uncharacterized.
Existing methods for TF characterization are limited, hindering their application in biotechnology.

Purpose of the Study:

To introduce Ligify 2.0, an enhanced web server for predicting transcription factor-effector molecule interactions.
To facilitate the systematic characterization of prokaryotic transcription factors as biosensors.

Main Methods:

Leveraged genome context and enzyme reaction databases (Rhea) to predict TF-ligand associations.
Developed an interactive web server featuring TF and ligand visualizations, genome context, and prediction confidence.
Integrated a plasmid builder tool for designing custom biosensor circuits.

Main Results:

Generated 13,435 hypothetical interactions between 1,362 small molecules and 3,164 TFs.
Successfully identified TFs responsive to specific molecules in *Escherichia coli* O157:H7 and *Mycobacterium abscessus*.
The Ligify 2.0 web server provides comprehensive data for TF biosensor exploration.

Conclusions:

Ligify 2.0 significantly expands the predicted TF-ligand interaction landscape.
The web server empowers researchers to discover and design novel biosensors for chemical control of biological systems.
This work advances the development of prokaryotic biosensors for diverse biotechnological applications.