Autotrophic growth of E. coli is achieved by a small number of genetic changes

Ben Nissan, R.; Milshtein, E.; Pahl, V.; de Pins, B.; Jona, G.; Levi, D.; Yung, H.; Nir, N.; Ezra, D.; Gleizer, S.; Link, H.; Noor, E.; Milo, R.

doi:10.1101/2023.06.03.543535

bioRxiv · 10.1101/2023.06.03.543535

Autotrophic growth of E. coli is achieved by a small number of genetic changes

Ben Nissan, R.·Milshtein, E.·Pahl, V.·de Pins, B.·Jona, G.·Levi, D.·Yung, H.·Nir, N.·Ezra, D.·Gleizer, S.·Link, H.·Noor, E.·Milo, R.

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Abstract

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for E. coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzymes activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycles electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs.

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Ben Nissan, R., Milshtein, E., Pahl, V., de Pins, B., Jona, G., Levi, D., Yung, H., Nir, N., Ezra, D., Gleizer, S., Link, H., Noor, E., Milo, R.. 2023-06-03. Autotrophic growth of E. coli is achieved by a small number of genetic changes. https://doi.org/10.1101/2023.06.03.543535

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