European research grant facilitates production of valuable fuels and chemicals using microbial cell factories
IMAGE:
KASPAR VALGEPEA, ASSOCIATE PROFESSOR OF GAS FERMENTATION TECHNOLOGIES AT THE UNIVERSITY OF TARTU
view moreCREDIT: CREDIT TO THE AUTHOR ANDRES TENNUS
Kaspar Valgepea, Associate Professor of Gas Fermentation Technologies at the University of Tartu, will advance understanding of gas-consuming bacteria, supported by European Research Council grant funding. The project will pioneer a novel method for creating a large number of genetically engineered strains and compile a knowledgebase that will accelerate engineering of cell factories and research in the field of biotechnology, as well as knowledge transfer supporting a circular economy.
Acetogen bacteria are microorganisms capable of consuming both exhaust gases and gasified organic waste, including the most common household waste. While bacterial strains present in nature can produce a handful of useful compounds, bioengineering their metabolism would allow gas-fermenting acetogens to produce the necessary compounds for fuels and chemicals more efficiently and in a notably larger range. This process is called gas fermentation. It is a technology that is already in industrial use in the world, but so far mainly for the production of ethanol.
The unsolved mystery of the bacterium
One of the reasons for the current restricted use of acetogens is the lack of knowledge about which genes exactly influence which processes. As these bacteria live in environments without oxygen and consume toxic and explosive gases, studying them is challenging. So far, genetically modified strains have essentially been handmade one-by-one that is very time-consuming. Therefore, it is still unclear what exactly are the functions of the majority of the roughly 4,000 genes in the studied acetogen bacterium (Clostridium autoethanogenum).
For the same reason, there is also a lack of a comprehensive dataset describing how modifications in different genes affect bacterial phenotypes at systems-level. According to Valgepea, such datasets have only been compiled for a few of the most studied microorganisms, such as the bacterium Escherichia coli or baker's yeast. Even for them, around 160 strains are characterised in the datasets.
Impact on the future of biotechnology
The novelty of Valgepea's project is that, within five years, it will create nearly 750 modified bacterial strains and consolidate the collected data as well as existing similar information about acetogens in a public knowledgebase (A-BASE). As the method for creating genetically modified strains would also be applicable to other microorganisms, the expected impact of the project is significant for the fields of microbiology, synthetic biology, and biotechnology, both for research and industrial applications.
The distinctiveness of the method being developed by Valgepea is that in addition to creating a large-scale library of strains, it also aims to find a way how to grow and study the strains individually. In selecting the genes for modification, the researchers will focus on three aspects, the exploration of which has had a great impact on other bacterial strains. Thus, they will be exploring genes essential for growth, factors that influence DNA transcription, and proteome "dark matter" that play an important role in engineering of bacterial metabolism. Applying data mining and machine learning on the data collected while focusing on the three aspects will enable to find the best target mutations faster than before, so that acetogen cell factories could more efficiently produce a greater number of compounds, which production would otherwise have a significant environmental footprint in the traditional chemical industry.
"The key issue in reducing the environmental impact of the global economy is how to move from carbon mining to carbon recycling. According to the McKinsey Institute, nearly 60% of the physical inputs to the global economy can be produced via biological systems. My project has a significant impact on the development of one technology contributing to the latter – gas fermentation“, explained Valgepea, who at the Institute of Bioengineering, University of Tartu is the leader of one of the few laboratories in the world that could execute such a project. The amount of the Consolidator Grant from the European Research Council is slightly above two million euros. The project lasts five years.
Microbial division of labor produces higher biofuel yields
IMAGE:
A RESEARCH TEAM CO-LED BY FOOD SCIENCE AND HUMAN NUTRITION PROFESSOR YONG-SU JIN, PICTURED HERE, WITH BIOENGINEERING PROFESSOR TING LU, NOT PICTURED, FOUND A WAY TO INCREASE ETHANOL PRODUCTION FROM A MIXTURE OF SUGARS USING A MICROBIAL DIVISION-OF-LABOR APPROACH AND MATHEMATICAL MODELING.
view more
CREDIT: PHOTO BY FRED ZWICKY
CHAMPAIGN, Ill. — Scientists have found a way to boost ethanol production via yeast fermentation, a standard method for converting plant sugars into biofuels. Their approach, detailed in the journal Nature Communications, relies on careful timing and a tight division of labor among synthetic yeast strains to yield more ethanol per unit of plant sugars than previous approaches have achieved.
“We constructed an artificial microbial community consisting of two engineered yeast strains: a glucose specialist and a xylose specialist,” said Yong-Su Jin, a professor of food science and human nutrition at the University of Illinois Urbana-Champaign, who co-led the new research with U. of I. bioengineering professor Ting Lu. “We investigated how the timing of mixing the two yeast populations and the ratios in which the two populations were mixed affected the production of cellulosic ethanol.”
Postdoctoral researcher Jonghyeok Shin and Siqi Lao, a Ph.D. student in the Center for Biophysics and Quantitative Biology at the U. of I., carried out the work.
Glucose and xylose are the two most abundant sugars obtained from the breakdown of plant biomass such as agricultural wastes. The team was trying to overcome a common problem that occurs when using yeast to convert these plant sugars into ethanol. In the wild, the yeast strain of interest, Saccharomyces cerevisiae, prefers glucose and lacks the ability to metabolize xylose. Other scientists have used genetic engineering to alter the yeast so that it also consumes xylose, but these engineered strains still prefer glucose, reducing their overall efficiency in ethanol production.
Some scientists have pursued the idea that communities of microbes, each with its own special function, can operate more efficiently than a single, highly engineered strain.
“My group is dedicated to the design, analysis and engineering of synthetic microbial communities. Jin’s lab specializes in yeast metabolic engineering and biofuel production,” Lu said.
“Our complementary expertise enabled us to test whether a division-of-labor approach among yeast might work well in biofuels production.”
The researchers conducted a series of experiments testing the use of their two specialist yeast strains. They altered the order in which the different strains were added to the sugar mixture and the timing of each addition.
“We also investigated the ratios at which the two populations were mixed to determine their effects on the rapid and efficient production of cellulosic ethanol,” Jin said.
The team also developed a mathematical model that accurately predicts their yeasts’ performance and ethanol yields.
“We used the data from the experiments to train our mathematical model so that it captures the characteristic ecosystem behaviors,” Lu said. “The model was then used to predict optimal fermentation conditions, which were later validated by corresponding experiments.”
The researchers discovered that adding the xylose-fermenting yeast specialist to the mixture first, followed 14 to 29 hours later by the glucose specialist, dramatically boosted ethanol production, more than doubling the yield.
“This study demonstrates the functional potential of division of labor in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications,” the authors wrote.
Yong-Su Jin and Ting Lu also are professors in the Biosystems Design theme in the Carl R. Woese Institute for Genomic Biology at the U. of I. Jonghyeok Shin is now a scientist at the Korea Research Institute of Bioscience and Biotechnology.
The Department of Energy and the Korea Research Institute of Bioscience and Biotechnology supported this research.
Editor’s notes:
To reach Yong-Su Jin, email ysjin@illinois.edu.
To reach Ting Lu, email luting@illinois.edu.
The paper “Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium” is available online or from the U. of I. News Bureau.
DOI: 10.1038/s41467-024-45011-w
JOURNAL
Nature Communications
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium
ARTICLE PUBLICATION DATE
26-Feb-2024
No comments:
Post a Comment