Breath! Breathing microbes generate more energy

How do cells generate and use energy? This question may seem simple, but the answer is far from simple. In addition, it is crucial to know how microbial cells consume energy and how proteins are allocated to do so, during industrial fermentation.

Researchers have now shown that it is possible to evoke a shift from metabolism from fermentation to respiration E. coli and baker's yeast by optimizing the fermentation conditions. This shift means that cells can be pushed to produce more internal energy (ATP).

"This information can be used to design new, improved cell factories," said Jens Nielsen, Corresponding Author, Professor at the Chalmers University of Technology in Sweden, and Scientific Director at the Novo Nordisk Center for Biosecurity in the DTU in Denmark.

In collaboration with the first author, Postdoc Yu Chen, of the Department of Biology and Biological Engineering at Chalmers, Jens Nielsen studied the metabolism of E. coli and baker's yeast through the use of mathematical models and biological experiments. The research has now been published in Proceedings of the National Academy of Sciences (PNAS).

Cells constantly generate high energy molecules called ATP from glucose sugar. ATP is the cellular "food" consumed by workers – the enzymes – in the cells. Enzymes use this energy to build biomass or perform other cell work. The more ATP available, the more microbial work horses perform well in fermentation; at least in principle, many other aspects also play a role.

Using a computer-based approach, the researchers discovered that ATP could be generated by one of two routes: a high-yielding respiratory tract producing 23.5 ATP per molecule of glucose or a fermentative route to low yield generating only 11 ATP per molecule of glucose.

The two pathways complement each other, but researchers have been able to alter the natural balance between the two by altering the fermentation conditions and the amount of sugar and protein available. In addition, they showed that the high-throughput pathway requires more protein mass than the low-yield pathway to consume glucose at the same rate.

They also showed that improving the performance of some key enzymes meant that cells, transformed into low-yielding fermentative metabolism, switched to respiration through high-throughput respiratory metabolism.

This change results in both more intracellular ATP but also avoids the formation of fermentation byproducts; acetate in E. coli and ethanol in baker's yeast.

"These byproducts are unwanted and reduce the yield of the desired molecules you want to produce in your cell factory," says Nielsen.

In addition, researchers have shown that high-performance cells actually use both pathways, not just the high-throughput one, and that more available protein means more efficiency in a given way.

Thus, the solution for improving cell performance in fermentations is not to deactivate the fermentation pathway, but rather to assign more protein to the high throughput pathway.

The researchers only exposed the microbes to different fermentation conditions and did not use genomic engineering to discuss these changes. But at the same time, their studies showed how to modify cell metabolism by genomic engineering to become more efficient in future experiments.