Designed bacteria can detect specific molecules

Researchers and industry want to be able to detect the presence of various molecules in many settings, including water samples and large fermentation tanks.

This can be achieved in different ways but often requires great investment in materials and devices to perform the analysis. A less expensive alternative may be using biological methods to detect whether a target molecule is present or not.

Bacteria can be useful for this because they can be designed and genetically modified to only grow if a specific molecule is present, and their growth can thereby be correlated to the concentration of this molecule.

Researchers have now developed a method that much more easily transitions from the idea of a bacterium detecting a specific molecule to designing, implementing and testing it in research or industrial production.

“We have described an end-to-end pipeline on how to design, engineer and implement bacteria to detect various molecules in the environment from the initial modelling to the final bacterium. This will accelerate the use and usefulness of biosensors in many applications,” explains a researcher behind the study, Enrico Orsi, Postdoctoral Fellow, Novo Nordisk Foundation Center for Biosustainability. Technical University of Denmark, Kongens Lyngby, Denmark.

The research has been published in Nature Communications.

Researchers from the Technical University of Denmark, the Max Planck Institute for Terrestrial Microbiology and the Max Planck Institute of Molecular Plant Physiology in Germany and the Weizmann Institute of Science in Israel collaborated on developing and validating the method.

Bacteria that grow only when specific molecules are present

Biosensors have many potential applications in detecting the presence of molecules.

Biological fixation of CO₂ is a useful example. Scientists worldwide seek optimum methods of removing CO₂ from the atmosphere so that it does not contribute to global warming.

Researchers are using new bacterial designs to try to develop the consecutive process steps required to enable bacteria (or plants and fungi) to capture CO₂ from the air and fix it.

One of these designs generates the molecule glyoxylate as an intermediate product, which is required to fix CO₂ in some synthetic and energy-efficient metabolic pathways.

To validate their method, the researchers from the Technical University of Denmark designed six engineered strains of Escherichia coli, all of which required glyoxylate to grow.

The researchers used a computer model to identify the required deletions to make the bacteria dependent on glyoxylate to grow. Then they implemented those deletions by genetically engineering the bacteria, demonstrating their dependence on glyoxylate. Furthermore, the researchers investigated two directions for the sensors they had developed.

One approach was to introduce new genes encoding enzymatic activities from alternative metabolic pathways to enable glyoxylate synthesis and thereby restore bacterial growth. Measuring bacterial growth served as an indicator of how effectively the introduced genes restored the ability to synthesise glyoxylate, facilitating enzyme performance comparisons.

The second approach placed the bacteria in an environment where glycolate (a molecule closely related to glyoxylate) was either present or absent. Bacterial growth indicated the presence of glycolate, whereas a lack of growth indicated its absence.

“For the second application, if the molecules are not present in the environment, the bacteria will not grow. The final microbial concentration in the culture correlates with the concentration of glycolate in the environment,” says Enrico Orsi, adding that researchers can use bacterial growth as an inexpensive and high-throughput method to determine the concentration of the target molecule in a sample.

“This is a proof of concept that can be developed to detect the presence of many molecules. Our research is a stepping stone that others can use to make better biosensors,” explains Enrico Orsi.

Many potential applications

Enrico Orsi envisions many settings for using bacteria to detect the presence of specific molecules; using the published method to design them would therefore be useful.

One possible application is the industrial production of molecules in large fermentation tanks with bacteria. For example, much research is focusing on using bacteria to make fuel or bioplastics.

In this setting, designed bacteria can detect the presence of molecules in the production pathways that lead to the production of the fuel or bioplastics. This may shed light on any bottlenecks in production that can be optimised.

Useful for environmental monitoring

Another option is to design bacteria that detect the production of molecules inside a cell.

This can be useful when research is aimed at constructing specific biological pathways to get from a substrate to an industrially useful end product – and whether, based on how well the cells grow, the biological pathway is designed well enough.

Finally, designed bacteria could be used in environmental studies to discover whether specific molecules are present in freshwater or marine environments – for example, to detect microalgae that often create algal blooms, which can be toxic and lead to oxygen depletion.

These microalgae secrete various molecules that can be detected by taking samples and exposing them to bacteria that only grow when these molecules are present.

The method will therefore be useful for environmental monitoring by public authorities.

“Detecting the presence of molecules using bacteria could be useful in many areas. This has long been recognised, but designing a bacterium to detect the presence of a specific molecule is not easy. Our method shows how this can be done from the initial idea to the final validation of a functional bacterial strain,” concludes Enrico Orsi.