『(Abstract)
Carbon fixation is the process by which CO2
is incorporated into organic compounds. In modern agriculture
in which water, light, and nutrients can be abundant, carbon fixation
could become a significant growth-limiting factor. Hence, increasing
the fixation rate is of major importance in the road toward sustainability
in food and energy production. There have been recent attempts
to improve the rate and specificity of Rubisco, the carboxylating
enzyme operating in the Calvin-Benson cycle; however, they have
achieved only limited success. nature employs several alternative
carbon fixation pathways, which prompted us to ask whether more
efficient novel synthetic cycles could be devised. Using the entire
repertoire of approximately 5,000 metabolic enzymes known to occur
in nature, we computationally identified alternative carbon fixation
pathways that combine existing metabolic building blocks from
various organisms. We compared the natural and synthetic pathways
based on physicochemical criteria that include kinetics, energetics,
and topology. Our study suggests that some of the proposed synthetic
pathways could have significant quantitative advantages over their
natural counterparts, such as the overall kinetic rate. One such
cycle, which is predicted to be two to three times faster than
the Calvin-Benson cycle, employs the most effective carboxylating
enzyme, phosphoenolpyruvate carboxylase, using the core of the
naturally evolved C4 cycle. Although implementing such alternative
cycles presents daunting challenges related to expression levels,
activity, stability, localization, and regulation, we believe
our findings suggest exciting avenues of exploration in the grand
challenge of enhancing food and renewable fuel production via
metabolic engineering and synthetic biology.
(Keywords:) metabolic engineering; synthetic biology; photosynthesis;
carboxylation; biological optimization』
(Introduction)
Results
Pathway analysis metrics enable a comprehensive comparison between
pathways
NADPH cost
ATP cost
Number of enzymes
Metabolic compatibility of the synthetic pathways
A systematic method to locate synthetic carbon fixation pathways
reveals the simplest carbon fixation cycles
Kinetically efficient carbon fixing pathways using the most attractive
carboxylating enzymes
Discussion
Analysis and optimization of carbon fixation pathways
Implementing the synthetic carbon fixation pathways
Materials and methods
Algorithm for finding carbon fixation cycles
Calculating pathway specific activity
Pathway evaluation and comparison
Acknowledgments
(References)