Stepping on the gas to a circular economy: accelerating development of carbon-negative chemical production from gas fermentation

N Fackler, BD Heijstra, BJ Rasor… - Annual review of …, 2021 - annualreviews.org
Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change
poses significant environmental, economic, and social challenges globally. Technologies …

NADPH-generating systems in bacteria and archaea

SK Spaans, RA Weusthuis, J Van Der Oost… - Frontiers in …, 2015 - frontiersin.org
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron
donor in all organisms. It provides the reducing power that drives numerous anabolic …

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0

L Heirendt, S Arreckx, T Pfau, SN Mendoza… - Nature protocols, 2019 - nature.com
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …

eQuilibrator 3.0: a database solution for thermodynamic constant estimation

ME Beber, MG Gollub, D Mozaffari… - Nucleic acids …, 2022 - academic.oup.com
Abstract eQuilibrator (equilibrator. weizmann. ac. il) is a database of biochemical equilibrium
constants and Gibbs free energies, originally designed as a web-based interface. While the …

Recon3D enables a three-dimensional view of gene variation in human metabolism

E Brunk, S Sahoo, DC Zielinski, A Altunkaya… - Nature …, 2018 - nature.com
Genome-scale network reconstructions have helped uncover the molecular basis of
metabolism. Here we present Recon3D, a computational resource that includes three …

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

D Machado, S Andrejev, M Tramontano… - Nucleic acids …, 2018 - academic.oup.com
Genome-scale metabolic models are instrumental in uncovering operating principles of
cellular metabolism, for model-guided re-engineering, and unraveling cross-feeding in …

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

S Magnúsdóttir, A Heinken, L Kutt, DA Ravcheev… - Nature …, 2017 - nature.com
Genome-scale metabolic models derived from human gut metagenomic data can be used
as a framework to elucidate how microbial communities modulate human metabolism and …

The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease

A Noronha, J Modamio, Y Jarosz… - Nucleic acids …, 2019 - academic.oup.com
A multitude of factors contribute to complex diseases and can be measured with 'omics'
methods. Databases facilitate data interpretation for underlying mechanisms. Here, we …

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

M Scheffen, DG Marchal, T Beneyton, SK Schuller… - Nature Catalysis, 2021 - nature.com
The capture of CO2 by carboxylases is key to sustainable biocatalysis and a carbon-neutral
bio-economy, yet currently limited to few naturally existing enzymes. Here, we developed …

Construction and modular implementation of the THETA cycle for synthetic CO2 fixation

S Luo, C Diehl, H He, YJ Bae, M Klose, P Claus… - Nature Catalysis, 2023 - nature.com
Synthetic biology offers the opportunity to build solutions for improved capture and
conversion of carbon dioxide (CO2) that outcompete those evolved by nature. Here we …