Scientists rewire bacteria to build ‘designer’ proteins on demand

Researchers have found a way to hijack the natural protein-making facilities of bacteria to manufacture specific proteins of interest. They did this by turning a ‘nutrient gate’ on a bacterial cell into a Trojan horse that could ferry artificial amino acids into cells to make these proteins.

The study, conducted by teams at ETH Zurich in Switzerland and the Technical University of Munich in Germany, was published in Nature. 

All proteins are made of some combination of the 20 natural amino acids. In the lab, chemists can also synthesise thousands of artificial amino acids, many of which have completely new properties. For example, if an amino acid called p-azido-L-phenylalanine can be built into a protein, it would allow scientists to attach drugs to the protein at a precise spot, helping it treat some disease.

The challenge however has been to get cells’ protein-making machines to use these artificial amino acids.

Idea and bottleneck

In the 1980s, Peter Schultz and his colleagues at the University of California, Berkeley, laid the foundations of incorporating artificial amino acids into proteins at specific sites. Over the years, scientists have expanded this toolkit to incorporate artificial amino acids in proteins that cells make. 

Yet one problem has persisted: the struggle to get enough artificial amino acids into the cell. Most lab-made amino acids struggle to cross the cell membrane and enter the cytoplasm, where the ribosomes synthesise proteins. This is because the side chains on artificial amino acids are very water-loving whereas the core of the cell-membrane is water-repelling.

To solve this problem, scientists have used one of three approaches in the past: (i) adding large concentrations of artificial amino acids in the medium so they passively cross the cell membrane; (ii) engineering membrane-binding proteins to smuggle small peptides (short chains of amino acids) across the cell membrane and break them down to amino acids once inside the cell; or (iii) engineering metabolic pathways within the cells to produce artificial amino acids inside the cells.

These methods showed some progress but they were still specific to certain amino acids. They couldn’t be generalised.

In the new study, the researchers pinned down the exact molecule ferrying the peptides into the cell. In the absence of the transporter — the main bacterial system that normally imports small protein fragments as food — the cells almost completely lost the ability to use the artificial amino acids bound to the peptides. That was a sign this specific molecule was the smuggler. Once the peptides were inside, the cell’s own protein-cutting enzymes unpacked them.

The researchers were able to confirm this: when they removed the enzymes that normally cut peptides into individual amino acids, the cell’s protein production dropped. Taken together, the transporter brought the cargo in, then ordinary enzymes freed the artificial amino acid so the cell’s ribosome could use it.

Across the membrane

Kathrin Lang and her colleagues at ETH Zurich started from the same idea: by attaching the artificial amino acid to a short peptide. But this group pushed the idea further in the bacteria Escherichia coli.

Laasya Samhita, assistant professor of biology at Ashoka University in Sonepat, explained that the group engineered an ABC transporter, a specific membrane protein that imports other proteins into the cell, using directed evolution to take up peptides carrying artificial amino acids.

The ABC transporter normally transports tripeptides (i.e. three amino acids) and tetrapeptides (four amino acids) into the cell as sources of nutrients. Dr. Lang and co. designed tripeptides and tetrapeptides in which they hid an artificial amino acid between two natural amino acids, thus causing the transporter to smuggle artificial amino acids into the cell. Once inside, the myriad peptide-cleaving enzymes inside the cell chopped them into individual amino acids, making artificial amino acids available for cells to make new proteins.

Unlike previous reports, this study engineered the transporter to alter a protein located in the space between the inner and the outer membranes of the bacterial cell. The researchers first identified residues that clamped onto the cargo. Then they prepared mutants of the transporter that would take up 10x more amounts of unconventional amino acids than an unmodified counterpart. This is double the efficiency in the uptake of artificial amino acids when compared to previous studies.

Easier to use

The findings matter because in many standard lab broths, there are already lots of natural peptides floating around, and they all compete for the same transporter, reducing how much of the cargo is smuggled inside the cell. So the researchers evolved the transporter step by step to make sure it worked even in these crowded conditions, repeatedly selecting bacterial cells that imported the artificial amino acids’ peptides best. Then they built the improved version into the bacteria’s genomes. The resulting system, they reported, was easier to use to produce proteins in a routine way instead of having to carefully control the media (the broths) first.

As Maximilian Fottner, Senior Scientist in Lang’s group and a lead author of the study, said in a press note, the study makes it “possible to produce designer proteins containing unnatural amino acids just as efficiently as their natural counterparts”. These could be genuinely multifunctional proteins, such as an antibody that carries a drug at one engineered position. 

The team also showed that its approach could deliver two different artificial amino acids, allowing a single protein to carry two engineered features at different positions.

Dr. Lang and colleagues are working on designing a similar system in human cells to produce artificial human-like proteins that could be suited for several therapeutic applications. The idea could extend to import molecules other than amino acids to produce complex chemical compounds, she added.

Joel P. Joseph is a freelance science journalist and researcher.

Published – March 11, 2026 07:15 am IST