Reduction of Substrates by Nitrogenases

Seefeldt, Lance C.; Yang, Zhi Yong; Lukoyanov, Dmitriy; Harris, Derek F.; Dean, Dennis R.; Raugei, Simone; Hoffman, Brian M.

doi:10.1021/acs.chemrev.9b00556

Cited by 299 publications

(383 citation statements)

References 262 publications

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“…The different hydrogen kinetic isotope effects (KIEs) for H 2 production by Mo-nitrogenase compared to CH 4 production by the V- and Fe-only nitrogenases could be due to different 1 H selectivities by each isoform or due to different contributions by the protonated thiols (orange) compared to the bridging Fe-hydrides (green) for reduction of different substrates (e.g., N 2 versus CO 2 ). For instance, it has been suggested that CO 2 can migrate into the Fe-hydride bond ( 70 , 94 ), although it is not known at which E n state this might occur or whether this is necessarily the only pathway for CO 2 reduction to methane. Modified from reference 73 with permission.…”

Section: Resultsmentioning

confidence: 99%

Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources

Luxem

Leavitt

Zhang

2020

Appl Environ Microbiol

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Biological nitrogen fixation is catalyzed by the enzyme nitrogenase. Two forms of this metalloenzyme, the vanadium (V) and iron (Fe)-only nitrogenases, were recently found to reduce small amounts of carbon dioxide (CO2) into the potent greenhouse gas methane (CH4). Here we report carbon (13C/12C) and hydrogen (2H/1H) stable isotopic compositions and fractionations of methane generated by V- and Fe-only nitrogenases in the metabolically versatile nitrogen fixer Rhodopseudomonas palustris. The stable carbon isotope fractionation imparted by both forms of alternative nitrogenase are within the range observed for hydrogenotrophic methanogenesis (13αCO2/CH4 = 1.051 ± 0.002 for V-nitrogenase and 1.055 ± 0.001 for Fe-only nitrogenase, mean ± SE). In contrast, the hydrogen isotope fractionations (2αH2O/CH4 = 2.071 ± 0.014 for V-nitrogenase and 2.078 ± 0.018 for Fe-only nitrogenase) are the largest of any known biogenic or geogenic pathway. The large 2αH2O/CH4 shows that the reaction pathway nitrogenases use to form methane strongly discriminates against 2H, and that 2αH2O/CH4 distinguishes nitrogenase-derived methane from all other known biotic and abiotic sources. These findings on nitrogenase-derived methane will help constrain carbon and nitrogen flows in microbial communities and the role of the alternative nitrogenases in global biogeochemical cycles. Importance All forms of life require nitrogen for growth. Many different kinds of microbes living in diverse environments make inert nitrogen gas from the atmosphere bioavailable using a special enzyme, nitrogenase. Nitrogenase has a wide substrate range, and in addition to producing bioavailable nitrogen, some forms of nitrogenase also produce small amounts of the greenhouse gas methane. This is different from other microbes that produce methane to generate energy. Until now, there was no good way to determine when microbes with nitrogenases are making methane in nature. Here, we present an isotopic fingerprint that allows scientists to distinguish methane from microbes making it for energy versus those making it as a byproduct of nitrogen acquisition. With this new fingerprint, it will be possible to improve our understanding of the relationship between methane production and nitrogen acquisition in nature.

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Section: Resultsmentioning

confidence: 99%

Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources

Luxem

Leavitt

Zhang

2020

Appl Environ Microbiol

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“…It is even less active than V-nitrogenase and seems to be only expressed in Mo- and V-deficient conditions. 19 , 20 …”

Section: Introductionmentioning

confidence: 99%

Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron–Vanadium Cofactor

Benediktsson

Björnsson

2020

Inorg. Chem.

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The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO 2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron–vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO 3 2– or NO 3 – ligand. Using a quantum mechanics/molecular mechanics model of the VFe protein, starting from the 1.35 Å crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO 3 2– or NO 3 – ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe 7 S 8 C(CO 3 )] 2– model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe–Fe and V–Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe 7 S 8 C(CO 3 )] 2– BS7-235 model is compared to our [MoFe 7 S 9 C] − BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E 1 state of FeMoco. Furthermore, V–Fe interactions in FeVco are not as strong compared to Mo–Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.

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“…Nitrogenases reduce a range of multibond compounds (Hu et al 2011, Yang et al 2011, Lee et al 2010, Zheng et al 2018, and this quality is shared across different nitrogenases (Seefeldt et al 2020). Although DPOR and COR were expressed and present in all metatranscriptomes and metagenomes, expression of both was an order of magnitude higher in the UC4 experiment compared with the LG5, LG6, and L7 experiments (with the exception of COR in LG5).…”

Section: Evidence For Methane Production By Cyanobacteria and Proteobmentioning

confidence: 95%

Biogeochemical and omic evidence for paradoxical methane production via multiple co-occurring mechanisms in aquatic ecosystems

Perez‐Coronel

Beman

2020

Preprint

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Aquatic ecosystems are globally significant sources of the greenhouse gas methane (CH4) to the atmosphere. However, CH4 is produced ‘paradoxically’ in oxygenated water via at least three mechanisms, fundamentally limiting our understanding of overall CH4 production. Here we resolve these CH4 production mechanisms through CH4 measurements, δ13CH4 analyses, 16S rRNA sequencing, and metagenomics/transcriptomics applied to freshwater incubation experiments with multiple time points and treatments (addition of a methanogenesis inhibitor, dark, high-light). We captured significant paradoxical CH4 production, but show that methanogenesis was an unlikely CH4 source. In contrast, abundant freshwater bacteria metabolized methylphosphonate—similar to observations in marine ecosystems. Metatranscriptomics and stable isotopic analyses applied to experimental treatments also identified a potential CH4 production mechanism linked to (bacterio)chlorophyll metabolism by Cyanobacteria and especially Proteobacteria. Variability in these mechanisms across experiments indicates that multiple, widely-distributed bacterial groups and pathways can produce substantial quantities of CH4 in aquatic ecosystems.

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Reduction of Substrates by Nitrogenases

Cited by 299 publications

References 262 publications

Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources

Large Hydrogen Isotope Fractionation Distinguishes Nitrogenase-Derived Methane from Other Methane Sources

Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron–Vanadium Cofactor

Biogeochemical and omic evidence for paradoxical methane production via multiple co-occurring mechanisms in aquatic ecosystems

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