Research at the SSM Lab
Microorganisms have evolved to survive in environments as diverse as deep-sea hydrothermal vents and the human gut. To thrive in these settings, they rely on enzymes: tiny molecular machines that carry out the chemical reactions needed for life. These enzymes enable microbes to grow on different substrates present in their environment and to produce chemicals with applications in the chemical and pharmaceutical industries.
Together, these enzymes form the metabolic network of the cell. While nature has created a wide range of metabolic pathways, advances in genetic engineering and synthetic biology allow us to go further: to design entirely new enzymes and pathways that don’t exist in nature.
At the SSM Lab, we create and optimize these new-to-nature metabolic pathways to develop sustainable biotechnology solutions of the future. We implement them in both model and non-model microbes, build customized biosensors to monitor enzyme activity, and we apply rational design and directed evolution to improve enzyme function.
Engineering new- to- nature C1 assimilation pathways
Atmospheric CO₂ poses both a challenge and an opportunity: while elevated levels drive global warming and climate change, CO₂ also represents an abundant feedstock for a circular carbon economy. Accordingly, technologies to capture and convert CO₂ into reduced one-carbon (C1) compounds such as methanol or formic acid are advancing rapidly.
Driven by the goal of sustainable bioproduction, we design and implement both natural and synthetic C1-assimilation pathways in industrially relevant microbes. Examples include the reductive glycine pathway, the serine-threonine cycle, and the formyl-phosphate route for assimilation of CO₂-derived formate, as well as the ribulose-monophosphate and xylulose-monophosphate cycles for CO₂-derived methanol.
To select for pathway activity, we use a methodology called growth-coupled design (see below). This approach lets us select directly for enzyme activity in vivo, so we can iteratively assemble and optimize new-to-nature pathways within living cells.
Growth coupled selection
Growth-coupled selection (GCS) has emerged as a powerful method for establishing new-to-nature enzymes — and even entire metabolic pathways — inside living cells. Traditional in vitro assays measure enzyme activity in isolation, under conditions that rarely reflect the crowded, dynamic environment of a living cell. GCS takes the opposite approach: it evaluates enzymes directly within cellular metabolism, providing a quantitative, in vivo readout under conditions that actually matter for application.
The principle is simple: we engineer a direct link between enzyme activity and cell growth, so that survival becomes the assay. If the strain grows, the enzyme works. This makes GCS especially well-suited to pathway engineering, where multiple enzymes must function together — GCS reports on the whole system at once, including substrate availability, cofactor balance, and metabolic context. We have used this approach to establish new-to-nature C1-assimilation pathways such as the reductive glycine pathway and the serine-threonine cycle in living cells.
Because growth rate reflects enzymatic performance, GCS also integrates naturally with directed and adaptive laboratory evolution: improved variants gain a fitness advantage and are spontaneously enriched during continuous cultivation, letting the cell do much of the screening itself.
Development of bacterial biosensors for enzyme engineering
Cell-based biosensors have emerged as versatile, cost-effective tools for applications spanning environmental monitoring to clinical diagnostics. Unlike chemical sensors, they self-assemble, are straightforward to handle, and have a low environmental footprint. An ideal biosensor combines high specificity with a broad dynamic range for detecting its target.
We build our biosensors on the principle of growth-coupled selection, using Escherichia coli as a chassis. E. coli is among the most extensively characterized microorganisms, with a well-mapped metabolism and a versatile toolbox for genome engineering, making it especially well suited for the kind of metabolic rewiring our sensors require. By strategically interrupting native metabolic routes, we create synthetic auxotrophies that can be rescued by the activity of an introduced enzyme or pathway — turning cell growth itself into a direct, in vivo readout of enzyme function.
A key strength of our approach is the ability to tune selection stringency by design. By engineering biosensors with different biomass dependencies — auxotrophic for one, two, or three essential metabolites — we can apply progressively stronger selection pressures and screen for enzymes of correspondingly higher activity. Our lab has developed a suite of such strains targeting enzymes involved in both biomass formation and energy metabolism. Because the sensor circuits are integrated into the genome rather than carried on plasmids, these strains function as robust, "plug-and-play" platforms for the high-throughput screening of large enzyme libraries.
