In a groundbreaking advancement that promises to revolutionize the way gene mutations are studied and therapeutic compounds are discovered, bioengineers at the University of California San Diego have unveiled a novel method utilizing bacteria as powerful, live biological sensors. Traditional approaches for assessing human gene mutations and screening drug candidates often involve complex, labor-intensive, and expensive biochemical assays conducted in test tubes or cultured human cells. However, this new technique transforms the ordinary gut-dwelling bacterium Escherichia coli (E. coli) into a living diagnostic platform, making the process faster, simpler, and drastically more cost-effective.
At the heart of this innovation lies the newly developed LEICA system — shorthand for live Escherichia coli assay. The ingenious strategy involves substituting a vital enzymatic function within E. coli with its human gene counterpart. Because E. coli’s survival now hinges on the performance of this human enzyme, its growth rate becomes a direct, quantifiable proxy for the enzyme’s functionality. Healthy, fully functional human enzymes support normal bacterial growth rates, whereas mutated enzymes with disease-causing defects result in slower growth or complete growth inhibition. This direct in vivo readout elegantly circumvents many of the complications related to conventional biochemical assays.
Guided by the expertise of Bernhard Palsson, Y.C. Fung Endowed Professor of Bioengineering, and lead postdoctoral researcher Donghui Choe, the UC San Diego team meticulously engineered E. coli strains where an essential bacterial enzyme was replaced with human homologs. Such delicate genetic manipulation ensured that the bacteria’s growth depended solely on the activity of the human enzyme variant present, allowing rapid phenotype assessment without the need for purified proteins or costly cell culture methods. This scientific feat required precision molecular cloning, protein engineering, and cutting-edge gene editing technologies.
Testing the LEICA system’s accuracy and robustness, the researchers introduced multiple human gene variants known from clinical databases. These variants included both benign polymorphisms and harmful mutations implicated in hereditary diseases such as anemia and argininosuccinic aciduria — a metabolic disorder affecting the urea cycle. Remarkably, growth patterns of the engineered bacteria precisely mirrored existing knowledge about the pathogenicity of these mutations. Variants known to be disease-causing impaired bacterial growth significantly, whereas neutral mutations had little to no impact. This correlation affirms LEICA’s utility as a rapid, reliable proxy for human enzyme performance.
Encouraged by these promising findings, the team extended LEICA’s application to drug screening. By exposing the engineered bacteria to hundreds of small molecules one-by-one, they could observe which compounds modulated the human enzyme’s activity in situ, as reflected by shifts in bacterial growth rate. Known activators or inhibitors were readily identified, validating the assay’s sensitivity. Moreover, the system unearthed several previously unknown compounds that selectively slowed bacterial proliferation only when the human enzyme was present. These molecules represent potential new leads for therapeutic drug development, especially for rare genetic diseases lacking effective treatment options.
This microbial-based assay harnesses the speed and ease of bacterial culture, condensing what traditionally takes days or weeks in high-complexity analytical tests into mere hours. Importantly, the live-cell context ensures that enzyme variants are assessed within a biologically relevant environment where folding, post-translational modifications, and cofactor interactions can occur naturally. These factors often prove challenging to replicate accurately in vitro but are critical for enzyme function and drug interaction fidelity.
LEICA’s simplicity and scalability open exciting possibilities beyond single-gene analysis. Its modular framework allows incorporation of diverse human enzymes implicated in a myriad of diseases, enabling large-scale mutational scans enabling conversion of genetic information into functional insights. Additionally, pharmaceutical research can leverage this platform to rapidly triage chemical libraries for candidate molecules capable of rescuing defective enzyme activities or selectively targeting pathological variants.
The impact of LEICA extends to personalized medicine as well. As whole-genome sequencing becomes increasingly common, clinicians often confront the challenge of interpreting the clinical significance of novel or rare gene variants. This assay provides a rapid functional validation tool to classify such variants through phenotypic bacterial growth outcomes, accelerating diagnostic decisions and informing tailored therapeutic strategies.
Despite its transformative potential, the researchers acknowledge challenges remain. Adapting the LEICA system to reflect multifaceted human cellular environments, including complex regulatory networks and compartmentalization, will be an ongoing pursuit. Moreover, further chemical optimization and toxicity profiling of the newly identified compounds will be essential before clinical applications can be envisioned.
Nonetheless, the power of transforming simple gut bacteria into living test tubes for human enzyme function represents a significant leap in biomedical research methodology. It elegantly merges synthetic biology, molecular genetics, and drug discovery into a single streamlined assay. As noted by Donghui Choe, “By turning bacteria into easy, fast test systems, we can rapidly check whether a human gene change is harmful and screen thousands of chemicals to find potential drugs.” This paradigm shift could dramatically accelerate genetic disease research while reducing costs, ultimately facilitating discovery of new treatments for conditions once considered intractable.
The team has published their findings in the prestigious journal Nature Biomedical Engineering, highlighting not only the scientific novelty but also the practical advantages of the LEICA assay. Funded by the Y.C. Fung Endowed Chair in Bioengineering at UC San Diego, this work exemplifies innovative interdisciplinary research with clear translational benefits. The publication serves as a call to the scientific community to explore and expand this live bacterial enzyme assay, unlocking vast potentials hidden within genetic mutations and chemical space alike.
As researchers continue to refine LEICA and explore its many applications, this technology stands as a vibrant example of how synthetic biology and microbiology can synergize to address some of modern medicine’s most urgent challenges. From elucidating the pathogenic mechanisms behind rare genetic disorders to fast-tracking drug discovery pipelines, humble bacteria now bear the potential to serve as indispensable allies in decoding human biology and combating disease.
Subject of Research: Development of a live bacterial enzyme assay for rapid functional analysis of human gene mutations and drug screening.
Article Title: A live bacteria enzyme assay for identification of human disease mutations and drug screening
News Publication Date: April 30, 2025
Web References:
https://www.nature.com/articles/s41551-025-01391-y
http://dx.doi.org/10.1038/s41551-025-01391-y
References:
Choe, D., & Palsson, B. (2025). A live bacteria enzyme assay for identification of human disease mutations and drug screening. Nature Biomedical Engineering. https://doi.org/10.1038/s41551-025-01391-y
Keywords:
LEICA assay, Escherichia coli, human gene mutations, enzyme activity, hereditary diseases, drug screening, synthetic biology, bioengineering, genetic disease diagnostics, personalized medicine, drug discovery, functional genomics
