Enzymatic Mechanism, Efficiency, and Environmental Activity of Biological Nitrogen Fixation Revealed by the Natural Abundance of Stable Isotopes

Abstract

Nitrogenase is the only natural enzyme capable of supplying new nitrogen (N) to the biosphere. It converts inert atmospheric N2 into bioavailable NH3 using a metal cofactor containing molybdenum (Mo) most prevalently, or vanadium or only iron alternatively. The 15N/14N fractionation during N2 fixation is a key parameter for studying environmental N cycling. In vivo fractionation varies by cofactor type, but the mechanism determining fractionation at the nitrogenase active site and in a N2-fixing cell remains unidentified. Additionally, Mo as a cofactor component limits environmental N2 fixation rates in some regions, and the activity of Mo-free alternative nitrogenases has been studied in land ecosystems. This dissertation investigates the fractionation mechanism and environmental activity of nitrogenase isozymes. Chapter 2 examines an isotopic mechanism of fractionation using Azotobacter vinelandii. In vivo fractionation values of natural and mutant nitrogenase (2.5‰ to 7‰) were smaller than the kinetic isotope effect of N≡N bond-break (27‰), and a mutant Mo-nitrogenase with altered N2 access to the active site showed higher in vivo fractionation than a natural Mo-nitrogenase (6.8‰ vs. 2.5‰). This reveals that (i) the nitrogenase reaction is highly committed to NH3 production, and (ii) enzymatic N2 diffusion limits cellular N2 fixation rate, indicating high catalytic efficiency (high kcat/Km) of in vivo nitrogenase reaction. Diffusion limitation may have evolved to protect the cofactor from O2 driven inactivation during the oxygenation of Earth's atmosphere. Chapter 3 demonstrates that asymbiotic N2 fixation occurs, albeit slowly, in leaf litter and soils of temperate forests. Stable carbon isotopic variability in ethylene produced from acetylene confirmed alternative nitrogenase activity to varying degrees. The N2 fixation rate and alternative nitrogenase contribution showed no clear correlation with the content of Mo, vanadium, and carbon-to-nitrogen ratio, and did not change with Mo amendment, although both in soils changed by adding carbon. Previous studies showed Mo increases N2 fixation and reduces alternative nitrogenase activity. However, this study's results contradict this, suggesting quantity of elemental Mo is not equivalent to bioavailability in environmental settings. These two research projects highlight the catalytic efficiency and environmental activity of nitrogenase isozymes, featuring the technical implication of the natural abundance of stable isotopes in studying microbial N2 fixation.