Millions of tonnes of plastic waste accumulate in landfills and oceans every year. One promising response is to engineer microbes to break the plastic down into useful chemical building blocks. However, teaching a bacterium to digest plastic efficiently demands fine-tuning not just one gene, but entire clusters of genes working in concert, like upgrading every machine on a factory assembly line rather than swapping out a single part.
A new platform developed by researchers from the National University of Singapore (NUS) could make that possible. Called Lytic Selection and Evolution (LySE), the system harnesses a modified bacteriophage — a virus that infects bacteria — to rapidly create and test many small genetic changes. It can improve long stretches of DNA (up to about 40,000 DNA letters), big enough to include most sets of genes needed for important chemical processes in cells.
A crash course in plastic-eating
To “teach” bacteria to break down new chemicals (such as ingredients in plastic), scientists give them a set of genes – called a gene pathway – that work together like an assembly line. After each round (called an “evolution”), scientists keep the bacteria that perform best (for example, the ones that grow better using the target chemical) and repeat the process. LySE is designed to speed up this “training” process.
In a proof-of-concept demonstration, LySE improved a set of five genes that let E. coli bacteria feed on ethylene glycol, a chemical used in making PET plastics. After only five cycles, the best-performing bacteria grew more than 50 per cent better on ethylene glycol. Because LySE changes only the chosen genes and uses fresh bacteria each round, scientists can move the improved genes into new bacteria easily, a critical step toward deploying plastic degrading microbes at scale.
Researchers led by Assistant Professor Julius Fredens from the Department of Biochemistry and the NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI) programme at the NUS Yong Loo Lin School of Medicine, describe the platform in a paper published in Nature Microbiology on 1st May 2026.
“Traditionally, scientists had to choose between slow but highly controlled evolution methods, or super-fast but uncontrollable continuous methods,” said Asst Prof Fredens. “Our goal was to create a best-of-both-worlds system: a tool that rapidly evolves large biological pathways while still letting us hit the pause button to control the process and prevent unwanted genetic errors.”
“Sloppy” by design
Directed evolution is a method scientists use to “speed up” natural selection in the lab. They make random changes (mutations) to a gene, then test and keep the versions that work best, repeating this process many times.
Another method, continuous evolution, such as phage-assisted continuous evolution (PACE), can do these mutation-and-selection cycles very quickly, but they have two main problems: they can only handle small pieces of DNA (about 8,000 DNA letters long), and they can get “cheaters” where the bacteria mutate their own DNA in a way that tricks the test and helps them survive, without actually improving the target gene.
“LySE sidesteps those two problems by exploiting bacteriophage T7, a virus that infects E. coli bacteria,” explained PhD candidate, Shujian Ong, who conducted much of the research. “T7 replicates rapidly and breaks the bacterial cell open within minutes. We have engineered the virus so that, when it makes new virus particles, it also packs in an extra small ring of DNA called a phagemid which carries the group of genes they want to improve.”
To make a lot of the new versions of those genes, the phagemid is copied by a specially engineered DNA-copying enzyme (T7 DNA polymerase) that is intentionally error-prone. Think of a normal DNA polymerase as a precise photocopier: this engineered variant is deliberately sloppy, making many “typos” (mutations), — about 160,000 times more than the bacterium’s own DNA copying system.
Paradoxically, the high error rate is what makes the system controllable. Because the polymerase is so “sloppy”, it also messes up the virus’s own DNA. As a result, the phage becomes weaker, losing the ability to spread uncontrollably; it can only destroy the bacteria when added in large numbers.
By adjusting the ratio of phage to bacteria, the researchers toggle between a mutation phase in which the target genes get a lot of new mutations and these mutated genes are packed into new phage particles, and a selection phase, in which mutated genes are put into fresh, normal bacteria and tested for improved function.
From antibiotic resistance to plastic digestion
The NUS team validated the LySE method in two ways. In an antibiotic-resistance check, the improved trait persisted after the genes were moved into new bacteria, confirming the changes were built into the target gene cluster.
Second, the researchers tried improving a whole “mini-factory” in cells: a five-gene pathway that lets bacteria use ethylene glycol for growth and energy. After five rounds with less glucose each time, the best-performing strain produced 50.9 per cent more biomass using ethylene glycol as its sole food source.
Sequencing showed LySE changed both regulatory regions (switches that control how much a gene is turned on or off) and protein-coding genes, and each helpful mutation was confirmed by adding it back one at a time into a fresh host.
“Without LySE, a bacterium’s instinct is to mutate its own entire genome to find ways to eat more plastic, but it struggles to find optimal solutions that way,” added Asst Prof Fredens. “LySE improves the target gene cluster tremendously without accumulating unwanted mutations in the rest of the bacterium’s DNA. Because all the improvements are strictly contained within our specific gene cluster, we can easily transfer this highly optimised pathway into entirely different bacteria.”
Engineering new-to-nature biology
The platform’s capacity to handle gene clusters of up to 40 kilobases in length — five times the limit of the most commonly used phage-based evolution method — opens the door to applications that were previously impractical. These include optimising biosynthetic pathways for pharmaceuticals, engineering microbes that break down environmental pollutants and evolving entirely synthetic metabolic routes for carbon capture. The workflow requires only standard laboratory equipment and the mixing of phage lysates with cell cultures, making the technology accessible to laboratories without specialist phage biology expertise.
A patent has been filed for the LySE technology. Looking ahead, the team plans to apply LySE to systems that are entirely synthetic and new to nature.
“A key target is engineering synthetic CO2-fixing metabolic pathways, taking computationally designed routes that have never existed in the real world and optimising them so they actually function efficiently inside living cells,” said Asst Prof Fredens. “With LySE, we can take AI-designed enzymes and metabolic pathways and rapidly optimise them to work in practice. That is where massive potential lies.”