1. Biochemistry and Chemical Biology
  2. Microbiology and Infectious Disease

Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli

  1. Avi I Flamholz
  2. Eli Dugan
  3. Cecilia Blikstad
  4. Shmuel Gleizer
  5. Roee Ben-Nissan
  6. Shira Amram
  7. Niv Antonovsky
  8. Sumedha Ravishankar
  9. Elad Noor
  10. Arren Bar-Even
  11. Ron Milo  Is a corresponding author
  12. David Savage  Is a corresponding author
  1. University of California, Berkeley, United States
  2. Weizmann Institute of Science, Israel
  3. University of California, San Diego, United States
  4. ETH Zurich, Switzerland
  5. Max Planck Institute of Molecular Plant Physiology, Germany
https://doi.org/10.7554/eLife.59882
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Cite this article
  1. Avi I Flamholz
  2. Eli Dugan
  3. Cecilia Blikstad
  4. Shmuel Gleizer
  5. Roee Ben-Nissan
  6. Shira Amram
  7. Niv Antonovsky
  8. Sumedha Ravishankar
  9. Elad Noor
  10. Arren Bar-Even
  11. Ron Milo
  12. David Savage
(2020)
Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli
eLife 9:e59882.
https://doi.org/10.7554/eLife.59882
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Abstract

Many photosynthetic organisms employ a CO2 concentrating mechanism (CCM) to increase the rate of CO2 fixation via the Calvin cycle. CCMs catalyze ≈50% of global photosynthesis, yet it remains unclear which genes and proteins are required to produce this complex adaptation. We describe the construction of a functional CCM in a non-native host, achieved by expressing genes from an autotrophic bacterium in an E. coli strain engineered to depend on rubisco carboxylation for growth. Expression of 20 CCM genes enabled E. coli to grow by fixing CO2 from ambient air into biomass, with growth in ambient air depending on the components of the CCM. Bacterial CCMs are therefore genetically compact and readily transplanted, rationalizing their presence in diverse bacteria. Reconstitution enabled genetic experiments refining our understanding of the CCM, thereby laying the groundwork for deeper study and engineering of the cell biology supporting CO2 assimilation in diverse organisms.

Data availability

All source data for all figures is available in the linked github repository along with accompanying Jupyter notebooks generating the data-driven portions of all figures.

Article and author information

Author details

  1. Avi I Flamholz

    Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9278-5479

  2. Eli Dugan

    Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2400-5511

  3. Cecilia Blikstad

    Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5740-926X

  4. Shmuel Gleizer

    Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.

  5. Roee Ben-Nissan

    Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.

  6. Shira Amram

    Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.

  7. Niv Antonovsky

    Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
    Competing interests
    No competing interests declared.

  8. Sumedha Ravishankar

    Division of Biological Sciences, University of California, San Diego, San Diego, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4026-0742

  9. Elad Noor

    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8776-4799

  10. Arren Bar-Even

    Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
    Competing interests
    Arren Bar-Even, A.B.-E. is co-founder of b.fab, a company aiming to commercialize engineered C1-assimilation in microorganisms. The company was not involved in this work in any way..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1039-4328

  11. Ron Milo

    Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
    For correspondence
    ron.milo@weizmann.ac.il
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1641-2299

  12. David Savage

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    For correspondence
    savage@berkeley.edu
    Competing interests
    David Savage, D.F.S. is a co-founder of Scribe Therapeutics and a scientific advisory board member of Scribe Therapeutics and Mammoth Biosciences. These companies were not involved in this work in any way..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0042-2257

Funding

Energy Biosciences Institute (CW163755)

  • David Savage

US Department of Energy (DE-SC00016240)

  • David Savage

European Research Council (NOVCARBFIX 646827)

  • Ron Milo

National Science Foundation (MCB-1818377)

  • David Savage

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2020, Flamholz et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Avi I Flamholz
  2. Eli Dugan
  3. Cecilia Blikstad
  4. Shmuel Gleizer
  5. Roee Ben-Nissan
  6. Shira Amram
  7. Niv Antonovsky
  8. Sumedha Ravishankar
  9. Elad Noor
  10. Arren Bar-Even
  11. Ron Milo
  12. David Savage
(2020)
Functional reconstitution of a bacterial CO2 concentrating mechanism in E. coli
eLife 9:e59882.
https://doi.org/10.7554/eLife.59882

Share this article

https://doi.org/10.7554/eLife.59882

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Further reading

    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Genetic Engineering: Increasing the uptake of carbon dioxide

    Eric Franklin, Martin Jonikas
    Insight

    A mechanism for concentrating carbon dioxide has for the first time been successfully transferred into a species that lacks such a process.