Enzyme level N and O isotope effects of assimilatory and dissimilatory nitrate reduction

Abstract

To provide mechanistic constraints to interpret nitrogen (N) and oxygen (O) isotope ratios of nitrate (NO3−), 15N/14N and 18O/16O, in the environment, we measured the enzymatic NO3− N and O isotope effects (15ε and 18ε) during its reduction by NO3− reductase enzymes, including (1) a prokaryotic respiratory NO3− reductase, Nar, from the heterotrophic denitrifier Paracoccus denitrificans, (2) eukaryotic assimilatory NO3− reductases, eukNR, from Pichia angusta and from Arabidopsis thaliana, and (3) a prokaryotic periplasmic NO3− reductase, Nap, from the photoheterotroph Rhodobacter sphaeroides. Enzymatic Nar and eukNR assays with artificial viologen electron donors yielded identical 18ε and 15ε of ∼28‰, regardless of [NO3−] or assay temperature, suggesting analogous kinetic mechanisms with viologen reductants. Nar assays fuelled with the physiological reductant hydroquinone (HQ) also yielded 18ε ≈ 15ε, but variable amplitudes from 21‰ to 33.0‰ in association with [NO3−], suggesting analogous substrate sensitivity in vivo. Nap assays fuelled by viologen revealed 18ε:15ε of 0.50, where 18ε ≈ 19‰ and 15ε ≈ 38‰, indicating a distinct catalytic mechanism than Nar and eukNR. Nap isotope effects measured in vivo showed a similar 18ε:15ε of 0.57, but reduced 18ε ≈ 11‰ and 15ε ≈ 19‰. Together, the results confirm identical enzymatic 18ε and 15ε during NO3− assimilation and denitrification, reinforcing the reliability of this benchmark to identify NO3− consumption in the environment. However, the amplitude of enzymatic isotope effects is apt to vary in vivo. The distinctive signature of Nap is of interest for deciphering catalytic mechanisms but may be negligible in most environments given its physiological role.