All life on planet Earth relies on a process known as carbon fixation. This is the ability of plants, algae and various forms of bacteria to pump carbon dioxide from the environment, add solar or other energy and turn it into the sugars that are required starting point needed for life processes.
The top of the food chain is made up of different organisms that use the opposite means of survival. They actually eat sugars and then release carbon dioxide into the atmosphere. The process is known as heterotrophism. Humans are, for example, heterotrphs in the biological sense because the food we consume originates from the carbon fixation processes of nonhuman producers.
Scientists have long wondered if it were possible to reprogram an organism that is found higher in the food chain (one that consumes sugar and releases carbon dioxide) in order to make them consume carbon dioxide from the environment and produce the sugars needed to build their own body mass. A group of Weizmann Institute of Science researchers may have found the answer to this question, the answer being: yes.
Dr. Niv Antonovsky led the research in Professor Ron Milo’s lab at the Institute’s Plant and Environmental Sciences Department. He says that the ability to improve carbon fixation is crucial for our ability to cope with future challenges including the need to supply food to a growing population on shrinking land resources while using less fossil fuel.
Institute scientists inserted the metabolic pathway for carbon fixation and sugar production (the Calvin cycle) into the bacterium E. coli, which is a known consumer organism that eats sugar and in turn, releases carbon dioxide. Milo and his group believed that with proper planning, they would be able to attach the genes containing the information for building it into the bacterium’s genome. The main enzyme used in plants to fix carbon, RuBisCO, utilizes as a substrate for the CO2 fixation reaction a metabolite which is toxic for the bacterial cells. This meant the design had to include precisely regulating the expression levels of the various genes across the multistep pathway.
In part, the team’s plan was a success. The bacteria did produce the carbon fixation enzymes, which were also functional. However, the machinery as a whole did not deliver what it was supposed to. Even though the carbon fixation machinery was expressed, the bacteria failed to use CO2 for sugar synthesis. It ended up relying on an external supply of sugar. Antonovsky says since the team was working with an organism that has evolved over millions of years to eat sugar, not CO2, they turned to evolution to help build the system they required.
The team of researchers designed tanks known as “chemostats” which they grew inside bacteria that over time pushed them into wanting to eat CO2. At first, the bacterium in the tanks was offered a large amount of pyruvate (an energy source), bubbles of CO2 and barely enough sugar to survive. By changing the environment over time and placing stress on the bacteria, the bacteria were forced to learn to use the more abundant materials in the environment; at around month and a half, some of the bacteria showed signs of doing much more than just surviving.
By month three, scientists were able to completely wean the evolved bacteria off of sugar and raise them on CO2 and pyruvate alone. Isotope labeling of the carbon dioxide molecules showed that the bacteria were using CO2 to create a significant portion of their body mass, as well as all the sugars needed to make the cell.
When scientists sequenced the genomes of the evolved bacteria, they discovered that there had been many changes scattered throughout the bacterial chromosomes. Milo says the changes were completely different than what had been predicted. It took the team two years of intense work to come to an understanding of which of these were essential and to unravel the logic involved in the evolution. Upon repeating the experiment, scientists were given clues that helped them to identify the mutations required to change E. coli diet from one based on sugar to one using carbon dioxide.
Milo says the ability to program and reengineer E. coli to fix carbon could give researchers a new toolbox for studying and improving this basic process. The bacteria currently release CO2 into the atmosphere but the team may be able to apply their insights into creating microorganisms that soak up atmospheric CO2 and convert it into stored energy or to achieving crops with carbon fixing pathways, resulting in higher yields and better adaption to feeding humanity.