Nature Search

Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection

Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for sensing glyoxylate and glycolate, with applications in pathway engineering and environmental monitoring.

Enrico Orsi
Helena Schulz-Mirbach
Pablo I. Nikel
ResearchOpen Access04 Mar 2025
Nature Communications

Volume: 16, P: 1-16
Design and implementation of aerobic and ambient CO₂-reduction as an entry-point for enhanced carbon fixation

Available enzymatic CO2 reduction strategies are not suitable for aerobic microorganisms and many industrial settings. Here, the authors design a new metabolic pathway that can operate under fully aerobic conditions, ambient CO2 levels, and seamlessly integrate with well-established C1-assimilation pathways.

Ari Satanowski
Daniel G. Marchal
Tobias J. Erb
ResearchOpen Access01 Apr 2025
Nature Communications

Volume: 16, P: 1-18
New-to-nature CO₂-dependent acetyl-CoA assimilation enabled by an engineered B₁₂-dependent acyl-CoA mutase

Acetyl-CoA assimilation pathways are usually associated with the loss of carbon in the form of CO₂. Here, the authors report a new metabolic pathway enabled by an engineered B₁₂-dependent acyl-CoA mutase, in which CO₂ is fixed during acetyl-CoA assimilation.

Helena Schulz-Mirbach
Philipp Wichmann
Tobias J. Erb
ResearchOpen Access26 Nov 2024
Nature Communications

Volume: 15, P: 1-13
Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules

The need for redox balancing limits the array of fermentable substrate-product combinations in anaerobic microbe-based bioproduction. Here, the authors design and engineer an E. coli strain with new-to-nature aerobic fermentative metabolism that allows tightly controlled re-balanced fermentations.

Helena Schulz-Mirbach
Jan Lukas Krüsemann
Steffen N. Lindner
ResearchOpen Access07 Aug 2024
Nature Communications

Volume: 15, P: 1-15
A new-to-nature carboxylation module to improve natural and synthetic CO₂ fixation

Biological CO₂ fixation is restricted to few enzymes and pathways, limiting its value in environmental protection and agricultural productivity. Now, a new-to-nature CO₂-fixing enzyme allows CO₂-dependent assimilation of glycolate in a designed pathway, and its use for different applications is demonstrated.

Marieke Scheffen
Daniel G. Marchal
Tobias J. Erb
ResearchOpen Access04 Jan 2021
Nature Catalysis

Volume: 4, P: 105-115
The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

There are several pathways for CO₂ fixation in photoautotrophic and chemoautotrophic microorganisms. Here, the authors provide experimental demonstration for the operation of the reductive glycine pathway in a natural microorganism, Desulfovibrio desulfuricans.

Irene Sánchez-Andrea
Iame Alves Guedes
Alfons J. M. Stams
ResearchOpen Access09 Oct 2020
Nature Communications

Volume: 11, P: 1-12
Transcription control reprogramming in genetic backup circuits

Ran Kafri
Arren Bar-Even
Yitzhak Pilpel
Research20 Feb 2005
Nature Genetics

Volume: 37, P: 295-299
Growth of E. coli on formate and methanol via the reductive glycine pathway

Redesigning the central carbon metabolism of Escherichia coli with the reductive glycine pathway enables growth on the one-carbon compounds formate and CO₂, and the addition of methanol dehydrogenase further enables growth on methanol and CO₂.

Seohyoung Kim
Steffen N. Lindner
Arren Bar-Even
Research10 Feb 2020
Nature Chemical Biology

Volume: 16, P: 538-545
One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle

An engineered one-carbon-fixation pathway increases biomass yields of Cupriavidus necator compared with the Calvin cycle and can support future, sustainable bio-based production.

Beau Dronsella
Enrico Orsi
Nico J. Claassens
ResearchOpen Access27 Feb 2025
Nature Microbiology

Volume: 10, P: 646-653
Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli

One-carbon substrates are attractive feedstocks for circular bioeconomy. Here, the authors design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, demonstrate the activity of the core reactions in E. coli, and show its integration with pathway reactions existed in pentose phosphate pathway and glycolysis.

Tong Wu
Paul A. Gómez-Coronado
Hai He
ResearchOpen Access20 Dec 2023
Nature Communications

Volume: 14, P: 1-12
Making quantitative sense of electromicrobial production

Electromicrobial production can replace fossil carbon with CO₂ and electricity as feedstocks for chemical production. This work analyses and compares different electromicrobial production approaches, providing a data-driven roadmap for the sustainable and efficient implementation of this technology.

Nico J. Claassens
Charles A. R. Cotton
Arren Bar-Even
Research13 May 2019
Nature Catalysis

Volume: 2, P: 437-447
Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

The diurnal cycle exerts influences on various aspects of plant biology. Here, the authors generate and compare diurnal transcriptomics data from nine members of Archaeplastida representing major clades.

Camilla Ferrari
Sebastian Proost
Marek Mutwil
ResearchOpen Access13 Feb 2019
Nature Communications

Volume: 10, P: 1-13
Awakening a latent carbon fixation cycle in Escherichia coli

Current efforts to establish synthetic carbon fixation in model heterotrophs rely on expression of heterologous enzymes. Here, the authors explore the presence and activity of a latent CO₂-assimilation pathway in E. coli based only on endogenous enzymes and a reversible decarboxylase.

Ari Satanowski
Beau Dronsella
Arren Bar-Even
ResearchOpen Access16 Nov 2020
Nature Communications

Volume: 11, P: 1-14
Noise in protein expression scales with natural protein abundance

Arren Bar-Even
Johan Paulsson
Naama Barkai
Research21 May 2006
Nature Genetics

Volume: 38, P: 636-643
Rethinking glycolysis: on the biochemical logic of metabolic pathways

Arren Bar-Even
Avi Flamholz
Ron Milo
Reviews17 May 2012
Nature Chemical Biology

Volume: 8, P: 509-517
Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

Adrian Jinich
Dmitrij Rappoport
Alán Aspuru-Guzik
ResearchOpen Access12 Nov 2014
Scientific Reports

Volume: 4, P: 1-6

Search

Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection

Design and implementation of aerobic and ambient CO₂-reduction as an entry-point for enhanced carbon fixation

New-to-nature CO₂-dependent acetyl-CoA assimilation enabled by an engineered B₁₂-dependent acyl-CoA mutase

Engineering new-to-nature biochemical conversions by combining fermentative metabolism with respiratory modules

A new-to-nature carboxylation module to improve natural and synthetic CO₂ fixation

The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans

Transcription control reprogramming in genetic backup circuits

Growth of E. coli on formate and methanol via the reductive glycine pathway

One-carbon fixation via the synthetic reductive glycine pathway exceeds yield of the Calvin cycle

Engineering a synthetic energy-efficient formaldehyde assimilation cycle in Escherichia coli

Making quantitative sense of electromicrobial production

Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida

Awakening a latent carbon fixation cycle in Escherichia coli

Noise in protein expression scales with natural protein abundance

Rethinking glycolysis: on the biochemical logic of metabolic pathways

Quantum Chemical Approach to Estimating the Thermodynamics of Metabolic Reactions

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