E. Coli cultivated in Lab switches to Carbon Dioxide as source

Researchers have worked for several months to cultivate E. Coli in such a way that it consumes carbon dioxide rather than other organic compounds.

They first converted the E. Coli from heterotrophic consumers to autotrophic consumers by metabolic rewiring and lab evolution. Engineering of the strain to produce non-native enzymes was processed, but it wasn’t enough for the E. Coli to support autotrophy.

So they decided to turn to adaptive laboratory evolution as a metabolic optimization tool. They inactivated central enzymes involved in heterotrophic growth, rendering the bacteria more dependent on autotrophic pathways for growth. They also grew the cells in chemostats with a limited supply of the sugar xylose — a source of organic carbon — to inhibit heterotrophic pathways. The initial supply of xylose for approximately 300 days was necessary to support enough cell proliferation to kick start evolution.

By sequencing the genome and plasmids of the evolved autotrophic cells, the researchers discovered that as few as 11 mutations were acquired through the evolutionary process in the chemostat. One set of mutations affected genes encoding enzymes linked to the carbon fixation cycle. The second category consisted of mutations found in genes commonly observed to be mutated in previous adaptive laboratory evolution experiments, suggesting that they are not necessarily specific to autotrophic pathways. The third category consisted of mutations in genes with no known role.

“The study describes, for the first time, a successful transformation of a bacterium’s mode of growth. Teaching a gut bacterium to do tricks that plants are renowned for was a real long shot,” says first author Shmuel Gleizer (@GleizerShmuel), a Weizmann Institute of Science postdoctoral fellow. “When we started the directed evolutionary process, we had no clue as to our chances of success, and there were no precedents in the literature to guide or suggest the feasibility of such an extreme transformation. In addition, seeing, in the end, the relatively small number of genetic changes required to make this transition was surprising.”

One major study limitation is that the consumption of formate by bacteria releases more CO₂ than is consumed through carbon fixation. In addition, more research is needed before it’s possible to discuss the scalability of the approach for industrial use. In the future, plans to supply energy through renewable electricity to address the problem of CO₂ release, determine whether ambient atmospheric conditions could support autotrophy, and try to narrow down the most relevant mutations for autotrophic growth are being made.

Their work towards this project has appeared in the journal “Cell” on November 27th 2019.