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Weizmann Institute team engineers E. coli to eat carbon dioxide

Researchers at the Weizmann Institute of Science in Rehovot, Israel have created a strain of the bacterium Escherichia coli that grows by consuming carbon dioxide instead of sugars or other organic molecules.

The findings point to means of developing, in the future, carbon-neutral fuels. An open-access paper on the work is published in the journal Cell.

Milo_press release autotrophic E. coli final version_0

Researchers converted the common lab, sugar-eating (heterotrophic) E. coli bacterium (left) to producing all of its biomass from CO2 (autotrophic), using metabolic engineering combined with lab evolution. The new bacterium (center) uses the compound formate as a form of chemical energy to drive CO2 fixation by a synthetic metabolic pathway. The bacterium may provide the infrastructure for the future renewable production of food and green fuels (right).


The achievement involved nearly a decade of rational design, genetic engineering and a sped-up version of evolution in the lab of Prof. Ron Milo of the Weizmann Institute.

The study began by identifying crucial genes for the process of carbon fixation—the way plants take carbon from CO2 for the purpose of turning it into such biological molecules as protein, DNA, etc. The research team added and rewired the needed genes.

They found that many of the “parts” for the machinery that were already present in the bacterial genome could be used as is. They also inserted a gene that allowed the bacteria to get energy from a readily available substance called formate that can be produced directly from electricity and air and which is apt to “give up” electrons to the bacteria.

Just giving the bacteria the “means of production” was not enough, it turned out, for them to make the switch. There was still a need for another trick to get the bacteria to use this machinery properly, and this involved a delicate balancing act.

Together with Roee Ben-Nissan, Yinon Bar-On and other members of Milo’s team in the Institute’s Plant and Environmental Sciences Department, Gleizer used lab evolution; in essence, the bacteria were gradually weaned off the sugar they were used to eating. At each stage, cultured bacteria were given just enough sugar to keep them from complete starvation, as well as plenty of CO2 and formate.

As some “learned” to develop a taste for CO2 (giving them an evolutionary edge over those that stuck to sugar), their descendants were given less and less sugar until after about a year of adapting to the new diet some of them eventually made the complete switch, living and multiplying in an environment that served up pure CO2.

To check whether the bacteria were not somehow “snacking” on other nutrients, some of the evolved E. coli were fed CO2 containing a heavy isotope: 13C. Then the bacterial body parts were weighed, and the weight they had gained checked against the mass that would be added from eating the heavier version of carbon. The analysis showed the carbon atoms in the body of the bacteria were all extracted directly from CO2 alone.

The research team then set out to characterize the newly-evolved bacteria. What changes were essential to adapting to this new diet? While some of the genetic changes they identified may have been tied to surviving hunger, others appeared to regulate the synchronization of the steps of making building blocks through accumulation from CO2.

Yet other changes the team noted had to do with transcription—regulating how existing genes are turned on and off.

Milo notes that today, biotech companies use cell cultures to produce commodity chemicals. Such cells—yeast or bacteria—could be induced to live on a diet of CO2 and renewable electricity, and thus be weaned from the large amounts of corn syrup they live on today. Bacteria could be further adapted so that rather than taking their energy from a substance such as formate, they might be able to get it straight up—say electrons from a solar collector—and then store that energy for later use as fuel in the form of carbon fixed in their cells. Such fuel would be carbon-neutral if the source of its carbon was atmospheric CO2.

Our lab was the first to pursue the idea of changing the diet of a normal heterotroph (one that eats organic substances) to convert it to autotrophism (‘living on air’). It sounded impossible at first, but it has taught us numerous lessons along the way, and in the end we showed it indeed can be done. Our findings are a significant milestone toward our goal of efficient, green scientific applications.

—Ron Milo

Prof. Ron Milo is the Head of the Mary and Tom Beck - Canadian Center for Alternative Energy Research. His research is supported by the Zuckerman STEM Leadership Program; the Larson Charitable Foundation New Scientist Fund; the Ullmann Family Foundation; Dana and Yossie Hollander; and the European Research Council. Prof. Milo is the incumbent of the Charles and Louise Gartner Professorial Chair.

Resources

  • Shmuel Gleizer, Roee Ben-Nissan, Yinon M. Bar-On, Niv Antonovsky, Elad Noor, Yehudit Zohar, Ghil Jona, Eyal Krieger, Melina Shamshoum, Arren Bar-Even, Ron Milo (2019) “Conversion of Escherichia coli to Generate All Biomass Carbon from CO2Cell doi: 10.1016/j.cell.2019.11.009

Comments

mahonj

OK, imagine it works and works well.
Should we put it in the exhaust outflow from a gas fired power station (or cement plant) or work directly from the atmosphere ?

sd

OK, but why is this better than algae that already take in C02 and sunlight to create biomass or for that matter, all of the other green plants that exist.

mahonj

@sd: Algal fuel just doesn't seem to be working out.
Look at the wiki article.
https://en.wikipedia.org/wiki/Algae_fuel

In particular, they are up against the farmers corn lobby in the USA, which doesn't help.
They've been at it for 30 years, in particular after the oil price spike in 2005 - 2014.

I think fracking + palm oil killed it.
+ it was just very expensive, especially capital intensive (compared to open field farming).

Engineer-Poet

This is very clever, I admit.  The use of selection pressure to drive the evolution of a new metabolic pathway from sideline to main food source is classic; much like making a new breed of dogs, but in just 1 year.

However, I don't see it being useful in the near term.  The efficiency is going to be low and sugar will probably be a more economic substrate for producing custom bacterial chemicals.  One of the few uses I can see for this is as the base of a food chain powered directly by electricity, such as something on a space station.  CO2 and water go in, formate and O2 come out, formate becomes biomass which can be harvested.  Perhaps a couple steps up the food chain you can get something humans find tasty.

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