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

Roee Ben Nissan; Eliya Milshtein; Vanessa Pahl; Benoit de Pins; Ghil Jona; Dikla Levi; Hadas Yung; Noga Nir; Dolev Ezra; Shmuel Gleizer; Hannes Link; Elad Noor; Ron Milo

doi:10.7554/eLife.88793

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

Roee Ben Nissan, Eliya Milshtein, Vanessa Pahl, Benoit de Pins, Ghil Jona, Dikla Levi, Hadas Yung, Noga Nir, Dolev Ezra, Shmuel Gleizer, Hannes Link, Elad Noor, Ron Milo^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

2 Citations (Scopus)

Abstract

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO₂. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Util-ising this genetic diversity, we identify that just three mutations are sufficient for Escherichia 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 enzyme’s 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 cycle’s 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 hetero-trophic organisms into autotrophs.

Original language	English
Article number	RP88793
Number of pages	22
Journal	eLife
Volume	13
DOIs	https://doi.org/10.7554/eLife.88793
Publication status	Published - Feb 2024

Bibliographical note

We thank Alon Barshap, Alon Savidor, Aliza Fedorenko, Avi Flamholz, Avihu Yona, Daria Fedorova, Emanuel Avrahami, Ifat, Goldstein, Ilana Rogachev, Ido Cohen, Lior Greenspoon, Lior Shachar, Margarita Gortikov, Merav Hagag, Niv Antonovsky, Ofir Shechter, Ron Sender, Samuel Lovat, Tasneem Bareia, Tali Wiesel, Yafit Sugas, Yinon Bar-on, Yotam David, Yuval Kushmaro and Yuval Rosenberg for their support of this project. We acknowledge the De Botton Protein Profiling institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science for their services and contribution to this project. This research was generously supported by the Mary and Tom Beck Canadian Center for Alternative Energy Research, the Schwartz-Reisman Collaborative Science Program, the Ullmann Family Foundation and the Yotam Project. Prof. Ron Milo is the Head of the Mary and Tom Beck Canadian Center for Alternative Energy Research and the incumbent of the Charles and Louise Gartner Professorial Chair. RBN is a Weizmann SAERI fellow. EM is a fellow of the Ariane de Rothschild Women Doctoral Program. HL and VP acknowledge funding from the Cluster of Excellence EXC 2124 from the Deutsche Forschungsgemeinschaft. Funding: Mary and Tom Beck Canadian Center for Alternative Energy Research (RM), Schwartz-Reisman Collaborative Science Program (RM), Ullmann Family Foundation and the Yotam Project (RM), Sustainability and Energy Weizmann Doctoral Fellowship (RBN), Ariane de Rothschild Women Doctoral Program (EM), Cluster of Excellence EXC 2124 from the Deutsche Forschungsgemeinschaft (HL, VP)

Publisher Copyright:
© 2023, Ben Nissan, Milshtein et al.

All Science Journal Classification (ASJC) codes

General Neuroscience
General Biochemistry,Genetics and Molecular Biology
General Immunology and Microbiology

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10.7554/eLife.88793Licence: CC BY

Cite this

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title = "Autotrophic growth of Escherichia coli is achieved by a small number of genetic changes",

abstract = "Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Util-ising this genetic diversity, we identify that just three mutations are sufficient for Escherichia 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 enzyme{\textquoteright}s 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 cycle{\textquoteright}s 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 hetero-trophic organisms into autotrophs.",

author = "{Ben Nissan}, Roee and Eliya Milshtein and Vanessa Pahl and {de Pins}, Benoit and Ghil Jona and Dikla Levi and Hadas Yung and Noga Nir and Dolev Ezra and Shmuel Gleizer and Hannes Link and Elad Noor and Ron Milo",

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AU - Milshtein, Eliya

AU - Pahl, Vanessa

AU - de Pins, Benoit

AU - Jona, Ghil

AU - Levi, Dikla

AU - Yung, Hadas

AU - Nir, Noga

AU - Ezra, Dolev

AU - Gleizer, Shmuel

AU - Link, Hannes

AU - Noor, Elad

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

Abstract

Bibliographical note

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