Fluctuating cellular energy drives microbial bioproduction

Fuzhong Zhang’s lab explores ATP’s role in biomanufacturing

Leah Shaffer 
Professor Fuzhong Zhang and PhD student Xinyue Mu look over microscope images of E. coli used in bioproduction. (Photo: Leah Shaffer/Wash U)
Professor Fuzhong Zhang and PhD student Xinyue Mu look over microscope images of E. coli used in bioproduction. (Photo: Leah Shaffer/Wash U)

In the work of biomanufacturing, tanks of microbes are fine-tuned to produce compounds that can be used as carbon-neutral fuels, chemicals, materials and medicines, but researchers are still learning the basics of how to turbo charge microbes for production. To that end, engineers at Washington University in St. Louis have explored the roles of ATP in microbial metabolism.

Adenosine-5’-triphosphate (ATP) is the primary energy currency that fuels many cellular processes but its levels fluctuate wildly in microbes used in manufacturing, so it is critical to map the connections between ATP levels and microbial growth and nutrient quality and how that affects yields of the microbial products. 

Fuzhong Zhang, the Francis Ahmann Professor in the McKelvey School of Engineering and co-director of the Synthetic Biology Manufacturing of Advanced Materials Research Center (SMARC), led the research to understand ATP dynamics in various fermentation conditions and developed a cost-effective approach to enhance bioproduction through supplementation of ATP-promoting carbon sources. The results were published June 22 in Nature Communications.

“This study has broad implications for understanding microbial energy homeostasis, optimizing bioproduction processes, and identifying sources of metabolic burden,” said Xinyue Mu, a PhD student in Zhang’s lab and first author of the paper. 

This work used a genetically encoded ATP biosensor to explore the rapid changes of ATP concentration in various microbial cells and fermentation conditions.  They found that feeding microbes with different carbon sources results in very different ATP dynamics. Among the tested carbons commonly used for fermentation, acetate induced the highest ATP levels in E. coli while Pseudomonas putida, a microbial strain widely used by the fermentation industry, prefers a fatty acid called oleate. 

“Normally you wouldn’t think acetate is a good carbon source for E. coli,” said Mu, noting that acetate is considered a byproduct of glucose metabolism, something E. coli excretes when eating glucose. “Actually, by feeding it acetate, we see a higher ATP level associated with an enhanced yield of target products,” she adds.

It’s also good news for using acetate as feedstock because researchers at McKelvey are also working on methods that can convert carbon dioxide to acetate.

P. putida produces a bioplastic called polyhydroxyalkanoate (PHA). In this case, feeding P. putida its preferred feedstock — fatty acids —substantially enhanced PHA content, yields and productivity.

In addition to finding the beneficial carbon sources for fermentation, the ATP biosensor also shined light into the cells’ complicated metabolic processes.

Limonene can be microbially produced and used as a renewable solvent or jet fuel, but its bioproduction drastically sucks up ATP and reduces cell growth as well as limonene yield.

Using the ATP biosensor, they start to understand how the expression of limonene biosynthesis enzymes affects ATP balance and how to tune the enzyme expression accordingly to maintain high yields.

indicators of Adenosine-5’-triphosphate

The lit up green areas in this image of E. coli are indicators of Adenosine-5’-triphosphate (ATP), the primary energy currency that fuels many cellular processes. By creating an ATP biosensor, researchers can track ATP levels and how it affects yields of the useful chemicals produced by the microbe.  (Photo: Zhang lab)

“This work not only elucidates the relationship between ATP dynamics and bioproduction but also offers a simple and effective strategy to enhance bioproduction by choosing an ATP-beneficial feedstock. It is useful to various biomanufacturing systems,” Zhang said. 

Mu X, Evans TD, Zhang F. ATP biosensor reveals microbial energetic dynamics and facilitates bioproduction. Nature Communications, June 22, 2024. DOI: https://doi.org/10.1038/s41467-024-49579-1

This work was supported by the National Institute of General Medical Sciences of the National Institutes of Health (R35GM133797) and the Bioenergy Technologies Office (BETO) of U.S. Department of Energy (DE-EE0010301).

The McKelvey School of Engineering at Washington University in St. Louis promotes independent inquiry and education with an emphasis on scientific excellence, innovation and collaboration without boundaries. McKelvey Engineering has top-ranked research and graduate programs across departments, particularly in biomedical engineering, environmental engineering and computing, and has one of the most selective undergraduate programs in the country. With 165 full-time faculty, 1,420 undergraduate students, 1,614 graduate students and 21,000 living alumni, we are working to solve some of society’s greatest challenges; to prepare students to become leaders and innovate throughout their careers; and to be a catalyst of economic development for the St. Louis region and beyond.

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