Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy

PLoS One. 2016 Jun 23;11(6):e0157851. doi: 10.1371/journal.pone.0157851. eCollection 2016.

Abstract

The strong advances in synthetic biology enable the engineering of novel functions and complex biological features in unprecedented ways, such as implementing synthetic autotrophic metabolism into heterotrophic hosts. A key challenge for the sustainable production of fuels and chemicals entails the engineering of synthetic autotrophic organisms that can effectively and efficiently fix carbon dioxide by using sustainable energy sources. This challenge involves the integration of carbon fixation and energy uptake systems. A variety of carbon fixation pathways and several types of photosystems and other energy uptake systems can be chosen and, potentially, modularly combined to design synthetic autotrophic metabolism. Prior to implementation, these designs can be evaluated by the combination of several computational pathway analysis techniques. Here we present a systematic, integrated in silico analysis of photo-electro-autotrophic pathway designs, consisting of natural and synthetic carbon fixation pathways, a proton-pumping rhodopsin photosystem for ATP regeneration and an electron uptake pathway. We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force). The photo-electro-autotrophic designs are predicted to have a limited potential for anaerobic, autotrophic growth of E. coli, given the relatively low ATP regenerating capacity of the proton pumping rhodopsin photosystems and the high ATP maintenance of E. coli. If these factors can be tackled, our analysis indicates the highest growth potential for the natural reductive tricarboxylic acid cycle and the synthetic pyruvate synthase-pyruvate carboxylate -glyoxylate bicycle. Both carbon fixation cycles are very ATP efficient, while maintaining fast kinetics, which also results in relatively low estimated protein costs for these pathways. Furthermore, the synthetic bicycles are highly thermodynamic favorable under conditions analysed. However, the most important challenge identified for improving photo-electro-autotrophic growth is increasing the proton-pumping rate of the rhodopsin photosystems, allowing for higher ATP regeneration. Alternatively, other designs of autotrophy may be considered, therefore the herein presented integrated modeling approach allows synthetic biologists to evaluate and compare complex pathway designs before experimental implementation.

MeSH terms

  • Adenosine Triphosphate / metabolism
  • Algorithms
  • Autotrophic Processes*
  • Carbon Cycle
  • Carbon Dioxide / metabolism
  • Computer Simulation*
  • Heterotrophic Processes
  • Kinetics
  • Metabolic Networks and Pathways*
  • Photosynthesis
  • Proton Pumps / metabolism
  • Rhodopsin / metabolism
  • Synthetic Biology / methods*
  • Thermodynamics

Substances

  • Proton Pumps
  • Carbon Dioxide
  • Adenosine Triphosphate
  • Rhodopsin

Grants and funding

LifeGlimmer GmbH provided support in the form of salaries for authors MV and VAPMdS, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. N.J.C is supported by Wageningen University by the IP/OP program Systems Biology (KB-17003.02-024), www.wageningenur.nl. E.N. is funded by an European Molecular Biology Organisation Long-Term Fellowship (ALTF 510-2014), www.embo.org. W.M.d.V. acknowledges financial support by the Netherlands Organization for Scientific Research through a Spinoza grant, www.nwo.nl. None of these funders had a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.