Engineering New Metabolic Pathways that Function Across Microbial Kingdoms

Scientists discover unexploited biosynthetic pathways and redesign them to produce useful bioproducts in a wide range of microbes.

Image courtesy of Michael Helfenbein and Jaymin Patel
Artist’s representation of the treasure trove of microbial diversity and the metabolic capacity they have acquired through billions of years of evolution.

The Science

The huge range of microbes in environments around the Earth possess an enormous potential to produce all kinds of metabolites. Metabolites are substances that microbes use or create when they break down food or other material. These metabolites have many potential applications in industry. Microbes make these metabolites using groups of genes that code for the sets of necessary natural catalysts called enzymes. Within microbial genomes, those gene sets are found in groups called biosynthetic gene clusters (BGCs). Scientists have computationally predicted the products of hundreds of thousands of BGCs. However, they have experimentally confirmed fewer than 2,000 of them. Now researchers have developed a computational and experimental strategy to redesign BGCs and determine the natural chemical products they create. The approach can be applied to diverse types of microbes.

The Impact

Microbes have numerous BGCs that have the potential to create many different metabolites. However, scientists can produce only a fraction of these metabolites using a handful of microbes in the laboratory. To test a BGC’s ability to create metabolites, scientists must often introduce its genes into a different microbe. But this is complicated because each organism has different mechanisms for regulating genes, and organisms tend to eliminate introduced genes. A new strategy allows scientists to computationally redesign BCGs to function and persist across diverse microbial hosts. This allows researchers to easily analyze the products of BGCs in a broad range of microbes.


Through diverse biosynthetic pathways, microbes produce countless small molecules to fulfill a variety of functions, from cross-species communication to building cellular structures. These molecules have an untapped biotechnological potential as renewable fuels, chemicals, and materials. However, biosynthetic gene clusters (BGCs) often do not function in their native hosts and scientists currently have a limited set of model organisms to try heterologous expression.

In this study, scientists from Yale University developed a computer-aided design strategy to redesign BGCs with hybrid eukaryotic and prokaryotic regulatory elements and optimized coding sequences. These redesigned sequences can be expressed in different microbial hosts. The researchers then tackled the problem of the silencing of heterologous gene expression using a combination of conjugation techniques and mobile DNA elements. With this approach, they guaranteed that the introduced BGC would land on a safe genomic location in diverse hosts. As a proof of concept, the researchers introduced a computationally predicted but uncharacterized bacterial BGC into multiple other bacterial hosts simultaneously. Expressing the optimized BGC in different hosts led the scientists to experimentally biosynthesize the predicted metabolic product. This new approach establishes a general strategy for the redesign, expression, mobilization, and characterization of biosynthetic genes in diverse microbes and microbial communities.


Farren J. Isaacs
Yale University


Funding was provided by the Department of Energy Office of Science, Biological and Environmental Research program, the Sandia National Laboratories Secure Biosystems Design project; the National Institutes of Health; the Burroughs Wellcome Fund; the Camille & Henry Dreyfus Foundation; and Yale University.


Patel, J.R., et al., Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell 185, 1487–1505 (2022). [DOI: 10.1016/j.cell.2022.03.008]

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