In-depth computational analysis of natural and artificial carbon fixation pathways

Abstract

In the recent years, engineering new-to-nature CO2 and C1 fixing metabolic pathways made a leap forward. These new, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway “better” than another.In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their ATP-efficiency and specific activity considering the kinetics and thermodynamics of the reactions. Beside natural pathways, this included the artificial Reductive Glycine Pathway, the CETCH cycle and two completely new cycles with superior stoichiometry: The Reductive Citramalyl-CoA cycle and the 2-Hydroxyglutarate-Reverse Tricarboxylic Acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways and missing kinetic data was sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway specific activities.We found that the Reductive Glycine Pathway, the CETCH cycle and the new Reductive Citramalyl-CoA cycle were predicted to have higher ATP-efficiencies and specific activities than the natural cycles. The Calvin Cycle performed better than previously thought, however. It can be concluded that the weaker overall characteristics in the design of the Calvin Cycle might be compensated by other benefits like robustness, low nutrient demand and a good compatibility with the host’s physiological requirements. Nevertheless, the artificial carbon fixation cycles hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.

Topological Analysis of the Carbon-Concentrating CETCH Cycle and a Photorespiratory Bypass Reveals Boosted CO2-Sequestration by Plants

“…The higher affinity of the enzyme for oxygen leads to the energetically wasteful process of photorespiration. Many attempts have been made so far to engineer Rubisco to have a higher carboxylase activity, exchanging it with more efficient CO₂-fixing enzymes and/or full synthetic pathways, as well as implementing bypasses in photorespiration to avoid energy loss ( Löwe and Kremling, 2021 ). Our topological analysis addresses these issues with the aim of finding optimal pathways with better efficiency and low fitness cost.…”

“…In vitro analysis of the CETCH proved that these enzymes are more energy efficient than those of the CBB cycle, ( Löwe and Kremling, 2021 ). Our analyses are unique in studying the impact of various artificial cycles and even their combinatorial possibilities that are assessed with due pros and cons.…”

Thermodynamic limitations of metabolic strategies for PHB production from formate and fructose in Cupriavidus necator

“…The energy of three formate molecules is required to fix one molecule of CO 2 via the CBB cycle (Grunwald et al, 2015). Synthetic formate assimilation pathways provide the potential to increase biomass yield on formate (Claassens et al, 2020), (Löwe & Kremling, 2021), though these were not considered here. All enumerated EFMs fell within the biomass-PHB production envelope (Figure 2A-B, shaded area), which contains every possible flux distribution to these products that can be obtained by flux balance analysis (FBA).…”

Choice of Microbial System for In-Situ Resource Utilization on Mars

“…While chemical carbon capture and utilization technologies are rapidly advancing (Ho et al, 2019), biology still offers the highest flexibility to fix inorganic carbon in order to make it available as a means of life-support and for further conversion into chemical products (Lee et al, 2019;Chen et al, 2020b;Löwe and Kremling, 2021). For a differentiation on process-level, it is most meaningful to distinguish autotrophic systems into phototrophs and chemotrophs.…”