Conversion of Escherichia coli to Generate All Biomass Carbon from CO2

Shmuel Gleizer,Roee Ben-Nissan,Yinon M Bar-On,Niv Antonovsky,Elad Noor,Yehudit Zohar,Ghil Jona,Eyal Krieger,Melina Shamshoum,Arren Bar-Even,Ron Milo

doi:10.1016/j.cell.2019.11.009

Abstract

SummaryThe living world is largely divided into autotrophs that convert CO2 into biomass and heterotrophs that consume organic compounds. In spite of widespread interest in renewable energy storage and more sustainable food production, the engineering of industrially relevant heterotrophic model organisms to use CO2 as their sole carbon source has so far remained an outstanding challenge. Here, we report the achievement of this transformation on laboratory timescales. We constructed and evolved Escherichia coli to produce all its biomass carbon from CO2. Reducing power and energy, but not carbon, are supplied via the one-carbon molecule formate, which can be produced electrochemically. Rubisco and phosphoribulokinase were co-expressed with formate dehydrogenase to enable CO2 fixation and reduction via the Calvin-Benson-Bassham cycle. Autotrophic growth was achieved following several months of continuous laboratory evolution in a chemostat under intensifying organic carbon limitation and confirmed via isotopic labeling.

Highlights

Autotrophic organisms, which generate biomass by fixing inorganic carbon into organic compounds, are the main gateway between the inorganic and living worlds
To enable a complete transition to autotrophy, the host must (1) operate CO2 fixation machinery in a pathway where the carbon input is comprised solely of CO2, while the outputs are organic molecules that enter central carbon metabolism and supply all 12 essential biomass precursors of the cell (Nielsen and Keasling, 2016); (2) express enzymatic machinery to obtain reducing power, either by harvesting non-chemical energy or by oxidizing a reduced chemical compound that does not serve as a carbon source; and (3) regulate and coordinate the energyharvesting and CO2-fixation pathways so that they together support steady-state growth with CO2 as the sole source of carbon (Barenholz et al, 2017)
Previous attempts (Mattozzi et al, 2013; Antonovsky et al, 2016; Schada von Borzyskowski et al, 2018) to establish autocatalytic CO2 fixation cycles in model heterotrophs required the addition of multicarbon organic compounds, which served, at least partially, as a carbon source, in order to achieve stable growth

Summary

Introduction

Autotrophic organisms, which generate biomass by fixing inorganic carbon into organic compounds, are the main gateway between the inorganic and living worlds. They dominate the biomass on Earth (Crowther et al, 2015; Bar-On et al, 2018), supplying all of our food and most of our fuel. A grand challenge in synthetic biology is to engineer autotrophy within a model heterotrophic organism. We can break this formidable task into three essential components. The engineering of a heterotrophic organism to supply all its biomass components from inorganic carbon is still a standing challenge

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Discussion

Conclusion