ARC Centre of Excellence in Synthetic Biology

SYNTHETIC BIOLOGY

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1, Mar 2021

Using genes to improve conversion of greenhouse gases

Greenhouse gas waste from factories could be turned into environmentally-friendly chemicals and fuels under an international project seeking to better understand the gene function of bacteria.

Dr Esteban Marcellin, theme leader in the ARC Centre of Excellence in Synthetic Biology, has secured funding for a large-scale study that will improve the efficiency of biofuel and chemical manufacture while recycling waste carbon.

Bringing together the ARC Centre of Excellence in Synthetic Biology, node partner, the University of Queensland,  US Department of Energy Joint Genome Institute (JGI), LanzaTech, the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain), and the University of Tartu, the project will investigate all 4,000 genes of acetogen bacteria to better understand their metabolism.

The team uses anerobic bacteria or acetogens, which use carbon oxides (carbon monoxide (CO) or carbon dioxide (CO2) to grow to convert waste carbon into useful chemicals and biofuels.

As part of this body of work, his team, including the Centre’s PhD student, James Heffernan, and Postdoctoral fellow, Axayacatl Gonzalez-Garcia, have just published a paper with LanzaTech on improving the metabolism of acetogenic bacteria Clostridium autoethanognum using the gene editing tool CRISPRi.

Gas fermentation with Clostridium autoethanognum enables the sustainable biomanufacturing of fuels and valuable chemicals. LanzaTech has successfully been operating a first commercial scale plant since 2018. Up till now, however, the engineering of this microbe has been slow due to limited genetic tools to control gene expression.

“The developed approach streamlines this process and enables precise and dynamic control of genes of interest that was difficult to achieve previously,” says Dr Michael Köpke, Vice-President of Synthetic Biology at LanzaTech.

Dr Marcellin says most chemicals are currently made from fossil fuels.

MAKING CLEANER, GREENER CHEMICALS

“But we’re using recycled carbon to feed the bacteria, producing cleaner, greener chemicals and also using up gases which would usually contribute to climate change,” he says.

The collaborators hope to learn exactly how all these bacteria make energy, with the goal of  improving manufacturing efficiency,  creating a new way to make chemicals and bypassing fossil fuels.

“Understanding what all the genes do is a radical group effort, using cutting-edge automated genetic engineering and generating massive data sets which will need super-computers to analyse,” says Dr Marcellin.

DNA for the project will be synthesised at the Joint Genome Institute in the US, then applied at LanzaTech to knock out each gene individually, using their high throughput cutting-edge robotic technology.

“If we didn’t have this collaboration, it would take hundreds of PhD students and millions of dollars to make this happen,” says Dr Marcellin.

Dr Köpke says making use of integrated robotic systems at LanzaTech’s anaerobic biofoundry allows the process to be automated, reducing the time to complete this project.

Chief Investigator Professor Lars Nielsen’s group from DTU Biosustain, which specialises in analysing big data, will be responsible for making sense of the enormous amount of data the project will produce.

“The sheer volume of data generated in this study enables us to use advanced analytics to explore and explain the complex interaction between bacterial genes and their environment leading to the observed phenotype or behaviour,” says Professor Nielsen.

“Knowing the intricate details about the metabolism of these bacteria will help us improve their ability to transform greenhouse gas waste from factories into chemicals and fuels, and also encourage the bacteria to make an even wider variety of useful products.”

Images courtesy  of University of Queensland.