scholarly journals Viewpoint: Isotopic fractionation by plant nitrate reductase, twenty years later

2006 ◽  
Vol 33 (6) ◽  
pp. 531 ◽  
Author(s):  
Guillaume Tcherkez ◽  
Graham D. Farquhar
Keyword(s):  
Nitrate Reductase ◽  
Isotope Effect ◽  
Nitrate Reduction ◽  
Isotope Effects ◽  
Isotopic Fractionation ◽  
Nitrogen Isotope ◽  
Reaction Rates ◽  
Rate Limiting Step ◽  
18O Isotope ◽  
N Isotopes

Plant nitrate reductase, the enzyme that reduces nitrate (NO3–) to nitrite (NO2–), is known to fractionate N isotopes, depleting nitrite in 15N compared with substrate nitrate. Nearly 20 years ago, the nitrogen isotope effect associated with this reaction was found to be around 1.015. However, the relationships between the isotope effect and the mechanism of the reaction have not yet been examined in the light of recent advances regarding the catalytic cycle and enzyme structure. We thus give here the mathematical bases of the 14N / 15N and also the 16O / 18O isotope effects as a function of reaction rates. Enzymatic nitrate reduction involves steps other than NO3– reduction itself, in which the oxidation number of N changes from +V (nitrate) to +III (nitrite). Using some approximations, we give numerical estimates of the intrinsic N and O isotope effects and this leads us to challenge the assumptions of nitrate reduction itself as being a rate-limiting step within the nitrate reductase reaction, and of the formation of a bridging oxygen as a reaction intermediate.

scholarly journals Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Paul M. Magyar ◽  
Damian Hausherr ◽  
Robert Niederdorfer ◽  
Nicolas Stöcklin ◽  
Jing Wei ◽  
...  
Keyword(s):  
Isotope Effect ◽  
Isotope Composition ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Anammox Bacteria ◽  
Ammonium Oxidation ◽  
Experimental Conditions ◽  
N Transformations ◽  
Natural Systems ◽  
Inverse Isotope Effect

AbstractAnaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (15N/14N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor 15ε for the reduction of nitrite to N2 is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of 15ε for the oxidation of nitrite to nitrate (inverse isotope effect, − 16 to − 43‰) and for the reduction of ammonium to N2 (normal isotope effect, 19–32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.

Isotope Effect Studies on Elimination Reactions. XI. The Nature of the Transition State for the E2 Reaction of 2-Phenylethyldimethylanilinium Salts Containing Substituents in the Aniline Ring with Sodium Ethoxide in Ethanol

1975 ◽  
Vol 53 (23) ◽  
pp. 3513-3525 ◽  
Author(s):  
Peter Schmid ◽  
Arthur Newcombe Bourns
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Structural Changes ◽  
Isotope Effects ◽  
Sodium Ethoxide ◽  
Nitrogen Isotope ◽  
Structural Variations ◽  
Hydrogen Deuterium ◽  
Elimination Reactions ◽  
Pass Through

Kinetic isotope effects have been determined for the E2 reactions of a series of 2-phenylethyldimethylanilinium salts containing substituents in the aniline ring with sodium ethoxide in ethanol at 40 °C. The nitrogen isotope effect, (k14/k15−1)100, is not very sensitive to substituent changes but appears to increase slightly with increasing electron-withdrawing ability of the substituents, i.e., 1.19 ± 0.07, 1.13 ± 0.06, 1.12 ± 0.08, 1.30 ± 0.07, and 1.32 ± 0.06 for p-OCH3, p-CH3, p-H, p-Cl, and, m-CF3, respectively. The hydrogen–deuterium isotope effects pass through a minimum in the region of the unsubstituted compound and increase both with increasing electron-donating as well as with electron-withdrawing power of the substituents, i.e. kH/kD = 4.70 ± 0.06, 4.61 ± 0.04, 4.51 ± 0.04, 4.53 ± 0.09, 5.00 ± 0.07, and 5.39 ± 0.07 for p-OCH3, p-CH3, p-H, p-Cl, m-CF3, and p-CF3, respectively. The results are discussed in terms of recent theoretical treatments of the effect of structural variations in the reactants on the nature of the transition state of E2 elimination reactions. The conclusion is reached that the transition states in the present reaction series can be characterized as 'central with slight carbanion character' and that the effect of a change in the ability of the leaving group on the structure of the transition state manifests itself mainly in the direction perpendicular to the reaction coordinate. A simple novel hypothesis is formulated which emphasizes the importance of the location of the transition state in a More O'Ferrall-type potential energy diagram in determining its sensitivity to structural changes in the reactants.

On the 16O/18O isotope effect associated with photosynthetic O2 production

2007 ◽  
Vol 34 (11) ◽  
pp. 1049 ◽  
Author(s):  
Guillaume Tcherkez ◽  
Graham D. Farquhar
Keyword(s):  
Oxygen Isotope ◽  
Isotope Effect ◽  
Classical Theory ◽  
Isotope Composition ◽  
Isotope Effects ◽  
Oxygen Isotope Composition ◽  
Source Water ◽  
18O Isotope ◽  
O2 Production

While photosynthetically evolved O2 has been repeatedly shown to have nearly the same oxygen isotope composition as source water so that there is no corresponding 16O/18O isotope effect, some recent 18O-enrichment studies suggest that a large isotope effect may occur, thus feeding a debate in the literature. Here, the classical theory of isotope effects was applied to show that a very small isotope effect is indeed expected during O2 production. Explanations of the conflicting results are briefly discussed.

The imprint of anammox on the stable isotope compositions of nitrogen-bearing molecules

2020 ◽  
Author(s):  
Paul Magyar ◽  
Damian Hausherr ◽  
Robert Niederdorfer ◽  
Jing Wei ◽  
Joachim Mohn ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Isotope Effect ◽  
Redox Reactions ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Biological Processes ◽  
Fixed Nitrogen ◽  
Ecological Complexity ◽  
Anammox Process ◽  
Isotope Measurements

<p>Stable isotope measurements of nitrogen and oxygen in nitrogen-containing molecules provide important constraints on the sources, sinks and pools of these molecules in the environment. Anammox is one of two known biological processes for converting fixed nitrogen to N<sub>2</sub>, and through its consumption of ammonium and nitrite and production of nitrate, it impacts the supply of a wide variety of fixed N molecules. Nevertheless, the isotope fractionations associated with the various anammox-associated redox reactions remain poorly constrained. We have measured the isotope effects of anammox in microbial communities enriched for the purpose of nitrogen removal from wastewater by anammox. In this system, we can replicate the ecological complexity exhibited in environmental settings, while also performing controlled experiments. We find that under a variety of conditions, the nitrogen isotope effect for the anaerobic oxidation of ammonium in this system (NH<sub>4</sub><sup>+ </sup>to N<sub>2</sub>) is between 19‰ and 32‰, that for the reduction of nitrite (NO<sub>2</sub><sup>–</sup> to N<sub>2</sub>) is between 7‰ and 18‰, and that for the production of nitrate (NO<sub>2</sub><sup>–</sup> to NO<sub>3</sub><sup>–</sup>) is between -16‰ and -43‰. We propose that these ranges reflect both (1) a mixture of signals from different anammox-performing species and (2) variation of the isotope effect associated with the anammox process within a given microbial community under different conditions. We seek to understand further what factors control this variability to better interpret stable isotope measurements of N-bearing molecules in environmental settings.</p>

Steady-State Nitrogen Isotope Effects of N2 and N2O Production in Paracoccus denitrificans

1999 ◽  
Vol 65 (3) ◽  
pp. 989-994 ◽  
Author(s):  
Carol C. Barford ◽  
Joseph P. Montoya ◽  
Mark A. Altabet ◽  
Ralph Mitchell
Keyword(s):  
Steady State ◽  
Stable Isotope ◽  
Isotope Effect ◽  
Paracoccus Denitrificans ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Dissolved Oxygen Concentration ◽  
Nitrogen Stable Isotope ◽  
N2o Production ◽  
Oxide Substrates

ABSTRACT Nitrogen stable-isotope compositions (δ15N) can help track denitrification and N2O production in the environment, as can knowledge of the isotopic discrimination, or isotope effect, inherent to denitrification. However, the isotope effects associated with denitrification as a function of dissolved-oxygen concentration and their influence on the isotopic composition of N2O are not known. We developed a simple steady-state reactor to allow the measurement of denitrification isotope effects in Paracoccus denitrificans. With [dO2] between 0 and 1.2 μM, the N stable-isotope effects of NO3 − and N2O reduction were constant at 28.6‰ ± 1.9‰ and 12.9‰ ± 2.6‰, respectively (mean ± standard error,n = 5). This estimate of the isotope effect of N2O reduction is the first in an axenic denitrifying culture and places the δ15N of denitrification-produced N2O midway between those of the nitrogenous oxide substrates and the product N2 in steady-state systems. Application of both isotope effects to N2O cycling studies is discussed.

Isotope Effect Studies on Elimination Reactions. IX. The Nature of the Transition State for the E2 Reaction of 2-Arylethylammonium Ions with Ethoxide in Ethanol

1974 ◽  
Vol 52 (5) ◽  
pp. 749-760 ◽  
Author(s):  
P. J. Smith ◽  
A. N. Bourns
Keyword(s):  
Transition State ◽  
Isotope Effect ◽  
Isotope Effects ◽  
Nitrogen Isotope ◽  
Kinetic Isotope Effects ◽  
Ammonium Ions ◽  
Nitrogen Effect ◽  
Kinetic Isotope ◽  
Leaving Group ◽  
Hydrogen Deuterium

Kinetic isotope effects have been determined for the E2 reaction of some 2-arylethyltrimethyl-ammonium ions with ethoxide in ethanol at 40°. The nitrogen effect, (k14/k15 − 1)100, decreased with increasing electron-withdrawing ability of the para substituent; i.e. 1.37, 1.33, 1.14, and 0.88 for p-OCH3, p-H, p-Cl, and p-CF3, respectively. Furthermore, the primary hydrogen–deuterium isotope effects increased for the same substituents, respectively; i.e. kH/kD = 2.64, 3.23, 3.48, and 4.16. A large positive ρ value of 3.66 was found as well as a small secondary α-deuterium effect of 1.02 for p-H. In addition, the nitrogen isotope effect decreased with increasing strength of the abstracting base for the reaction of ethyltrimethylammonium ion; i.e. 1.86 and 1.41 at 60° for reaction with EtO−–EtOH and t-BuO−–t-BuOH, respectively. The results are discussed in terms of recent theoretical treatments of the effect of base, substituents, and nature of the leaving group on the nature of the transition state for an E2 process. The conclusion is reached that any structural change which causes one bond (C—H) to be weakened more at the transition state will have a corresponding effect on the other bond [Formula: see text]

Carbon-13 kinetic isotope effects. V. Substituent effects on k12/k13 for alcoholysis of 1-phenyl-1-bromoethane

1969 ◽  
Vol 47 (13) ◽  
pp. 2506-2509 ◽  
Author(s):  
Jan Bron ◽  
J. B. Stothers
Keyword(s):  
Isotope Effect ◽  
Phenyl Ring ◽  
Kinetic Isotope Effect ◽  
Isotope Effects ◽  
Isotopic Fractionation ◽  
Substituent Effects ◽  
Kinetic Isotope Effects ◽  
Kinetic Isotope ◽  
Factor Governing

As a test of our earlier interpretations of the 13C kinetic isotope effects found for alcoholysis of 1-phenyl-1-bromoethane, we have examined the effect of the p-methyl and p-bromo substituents on the 13C fractionations in ethanol and methanol. Isotopic fractionation at the α-carbon is found to be substituent dependent, and the observed trend is consistent with the proposal that stabilization of the cationic center by the phenyl ring is a major factor governing the isotope effect in these systems. The first example of an inverse primary kinetic isotope effect for carbon (k12/k13 < 1) is described.

scholarly journals Isotope fractionation (δ 13C, δ15N) and microbial community response in degradation of petroleum hydrocarbons by biostimulation in contaminated soil

2021 ◽  
Author(s):  
Heng Liu ◽  
Manli Wu ◽  
Xiqian Guo ◽  
Huan Gao ◽  
Yinrui Xu
Keyword(s):  
Isotope Effect ◽  
Contaminated Soil ◽  
Isotope Fractionation ◽  
Isotope Effects ◽  
Alpha Diversity ◽  
Nitrogen Isotope ◽  
Community Response ◽  
Carbon And Nitrogen ◽  
Stable Isotope Fractionation ◽  
Compost Amendment

Abstract This study investigated the isotope effects of δ13C and δ15N and microbial response during biodegradation of hydrocarbons by biostimulation with nitrate or compost in the petroleum-contaminated soil. Compost and KNO3 amendments promoted the total petroleum hydrocarbon (TPH) removal accompanied by a significant increase of Actinobacteria and Firmicutes phyla. Soil alpha diversity decreased after 90 days of biostimulation. An inverse significant carbon isotope effect (εc = 16.6 ± 0.8‰) and strong significant nitrogen isotope effect (εN = -24.20 ± 9.54‰) were shown by the KNO3 supplementation. For compost amendment, significant carbon and nitrogen isotope effect were εc = 38.8 ± 1.1‰ and εN = -79.49 ± 16.41‰, respectively. A clear difference of the carbon and nitrogen stable isotope fractionation was evident by KNO3 or compost amendment, which indicated the mechanisms of petroleum degradation by adding compost or KNO3 are different.

scholarly journals Sulfur Isotope Effects of Dissimilatory Sulfite Reductase

2015 ◽  
Author(s):  
William D. Leavitt ◽  
Alexander S. Bradley ◽  
André A. Santos ◽  
Inês A.C. Pereira ◽  
David T. Johnston
Keyword(s):  
Sulfate Reduction ◽  
Isotope Effect ◽  
Isotope Fractionation ◽  
Sulfur Isotope ◽  
Isotope Effects ◽  
Isotopic Fractionation ◽  
Sulfite Reductase ◽  
Sulfate Reducers ◽  
Dissimilatory Sulfite Reductase

The precise interpretation of environmental sulfur isotope records requires a quantitative understanding of the biochemical controls on sulfur isotope fractionation by the principle isotope-fractionating process within the S cycle, microbial sulfate reduction (MSR). Here we provide the only direct observation of the major (34S/32S) and minor (33S/32S,36S/32S) sulfur isotope fractionations imparted by a central enzyme in the energy metabolism of sulfate reducers, dissimilatory sulfite reductase (DsrAB). Results from in vitro sulfite reduction experiments allow us to calculate the in vitro DsrAB isotope effect in34S/32S (hereafter,34ϵDsrAB) to be 15.3±2‰, 2σ. The accompanying minor isotope effect in33S, described as33λDsrAB, is calculated to be 0.5150±0.0012, 2σ. These observations facilitate a rigorous evaluation of the isotopic fractionation associated with the dissimilatory MSR pathway, as well as of the environmental variables that govern the overall magnitude of fractionation by natural communities of sulfate reducers. The isotope effect induced by DsrAB upon sulfite reduction is a factor of 0.3 to 0.6 times prior indirect estimates, which have ranged from 25 to 53‰ in34ϵDsrAB. The minor isotope fractionation observed from DsrAB is consistent with a kinetic or equilibrium effect. Our in vitro constraints on the magnitude of34ϵDsrABis similar to the median value of experimental observations compiled from all known published work, where34ϵr-p= 16.1‰ (r – pindicates reactant versus product, n = 648). This value closely matches those of MSR operating at high sulfate reduction rates in both laboratory chemostat experiments (34ϵSO4-H2S= 17.3±1.5‰) and in modern marine sediments (34ϵSO4-H2S= 17.3±3.8‰). Targeting the direct isotopic consequences of a specific enzymatic processes is a fundamental step toward a biochemical foundation for reinterpreting the biogeochemical and geobiological sulfur isotope records in modern and ancient environments.

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