System-Level Analysis of Phototrophic Metabolism in Rhodopseudomonas Palustris Reveals That Proton Metabolism Affects Metabolic Efficiency and Hydrogen Production

Modern way of life is closely linked to ever increasing consumption of energy.  Given the inevitable exhaustion of fossil fuels, the central challenge facing humanity in the 21^st century is development of renewable alternative sources of energy.  Hydrogen gas (H₂) is an attractive renewable energy source since it burns clean (releasing H₂O) and can be used as a transportation fuel.  To gain a better understanding of the metabolic economy underpinning production of H₂ by purple non-sulfur bacteria, we have developed a curated genome-scale model of metabolism in the metabolically versatile phototrophic bacterium Rhodopseudomonas palustris (RP).  The model was constrained using known metabolic phenotypes and experimentally measured flux values. 

We have used the model to investigate RP’s 1) genetic robustness to various perturbation 2) metabolic capabilities 3) capacity to produce H₂, and 4) carbon metabolism as it pertains to production of H₂.  In case of photoheterotrophic metabolism, results of our analyses agree with previous observations regarding the connection between the oxidizing potential of the imported carbon source and the amount of carbon that is “wasted” by the system as excreted carbon dioxide (CO₂).  Our results show that if the central goal of RP (as assumed in most FBA studies) is maximum rate of growth, then under no conditions except sever nitrogen starvation would the system produce H₂.  Examining the trade-off between productions of H₂, CO₂ and biomass, we find that the production of the first two gasses severely reduces the rate of cellular growth.  On the other hand, production of H₂ and CO₂ is positively linked to one another.  Competition for use of limited quantity of electrons explains these observations.

While there have been a number of studies conducted to examine the role of electron availability on production of H₂ by RP, there has been little attention paid to the role of proton metabolism for production of H₂ and the overall mode of metabolism in this organisms.  Our meticulously mass (including proton) balanced model allowed us to examine the role of protons on efficiency of carbon metabolism as well as production of H₂.  We find that depending on the ratio of carbon to protons and carbon to oxygen atoms in the imported carbon source, RP might import or export small quantities of protons from/to the surrounding system.  Comparing the model predictions with measured metabolic byproducts and rates of growth verifies this finding.  Eliminating these proton transfer processes will reduce the rate of cellular growth.   LLNL-ABS-674338