Engineering the cell factory

To stay competitive, industries need to increase their productivity. Typically this is done by improving the process of manufacturing, the factory efficiency. Synthetic biology is no different. Natalia Kakko, a doctoral student at the Center for Young Synbio Scientists, is working on the vital task of streamlining the productivity of cells. By improving “cellular factories,” her work could enable some (or all) synthetic biology-based companies to be more productive and more profitable, as well as support several UN sustainable development goals.

More than ever before, we need innovative ways to shift from traditional industrial production towards a more sustainable economy. One possibility is to apply nature’s own means of making things. New advances in synthetic biology now allow using living cells to produce products ranging from pharmaceuticals to biofuels, even making cellulose without trees.

Due to this growing potential, the synthetic biology industry has raised over $12 billion in investments in the past 10 years, with a predicted market of several trillions in the next decade. However, high level production of valuable compounds is still limited and the growing pressure to scale-up demands more and more from the tiny units of life.

In order to produce something specific for us, a cell’s internal chemistry must be directed as much as possible towards the product. If the cell stops making proteins for its own growth and redirects these resources into producing our compound, its productivity will increase and the whole process becomes more efficient. Researchers are thus working hard on the problem: how to optimally engineer the metabolism, aka the functional capabilities, of living cells?

Re-focusing cells with metabolic engineering

Engineering cell metabolism allows synthetic biologists to re-imagine the future of production. One such synthetic biologist is Natalia Kakko, a doctoral student at the Centre for Young Synbio Scientists working on focusing and honig the behavior of cell factories.

Her project aims to alter yeast cells’ productivity by introducing an inducible protein degradation system – a platform that allows selected proteins within the cell to be erased at will. Ideally, the system would limit competition for essential resources, cease cell growth, and focus these metabolic efforts towards producing a desired product, all without causing harmful toxicity to the cell.

Kakko’s strategy was to use genome engineering to create the protein degradation system. By applying CRISPR/Cas, a genome editing tool, she attached selected protein encoding genes with specific tags that would mark them up for elimination. Once expressed in the cell, a protein degradation system (the ClpXP proteasome), would identify these proteins and shred them into bits.

Kakko then added another level of fine-tuning to the protein shredder. The degradation system’s gene expression was placed under a controller, a synthetic promoter, that kept the gene “off” until bound by a synthetic activator. This activator in turn was dependent on a chemical agent doxycycline, making the system inducible. This means that Kakko could adjust the levels of doxycycline and see an increase in the presence of the protein degradation system. This, in turn, caused the tagged proteins to be dismantled accordingly.

Kakko’s research demonstrated that accumulating levels of the degradation system drove down the levels of the tagged proteins. The yeast cells had also stopped growing while maintaining metabolic activity. Further analysis is still underway to reveal the full effect of the degradation system on the yeast cells’ metabolic activities.

From metabolic optimization to living cell factories

In addition to modifying cell metabolism, Kakko can introduce new genetic constructs into a cell to produce useful compounds. CRISPR technology can be used to insert genes of metabolic pathways for making a specific compound, or to eliminate genes that interfere with its synthesis. Part of Kakko’s research centres on adding production pathways from other organisms into yeast, such as the glycolic acid and muconic acid synthesis pathways.

Similar strategies have already produced industrially useful compounds in yeast, including bioplastic polymers, chemicals such as terpenoids and β-carotene, and products naturally made by plants. Manipulation of genetic pathways opens up ways to exploit yeast as a cell factory, optimized for more sustainable production of desired molecules for fuel, chemical, medical and materials industries.

Challenges in predictability

However, several questions remain in the predictability of the built genetic constructs and their effects on cell activity. Although widely used in laboratories, the chemical doxycycline is too expensive as an inducing agent for industrial use and alternatives may have unpredictable effects. Creating desired metabolic outcomes requires vast amounts of data on the genes, enzymes, pathways, and host organism involved. Rigorous genome sequencing, protein characterization and metabolic studies are still required for reliable predictive modelling.

In the future, machine learning could advance metabolic engineering and pathway prediction. Inspired by computational genomics, Kakko notes that digital metabolic modelling tools are readily available and applying them for a systems driven approach is now a mere question of more interdisciplinary learning.

Coupled with predictive tools, metabolic engineering could help produce essentially any product more efficiently. Overall, Kakko’s work shows that using cell factories is one powerful path towards a circular economy.

Laura Turpeinen



The Center for Young Synbio Scientists promotes synthetic biology research in Finland by supporting young researchers, PhD students and post-docs.