Dataset Information

Respiration and growth of Paracoccus denitrificans R-1 with nitrous oxide as an electron acceptor.

ABSTRACT: In the nitrogen biogeochemical cycle, the reduction of nitrous oxide (N₂O) to N₂ by N₂O reductase, which is encoded by nosZ gene, is the only biological pathway for N₂O consumption. In this study, we successfully isolated a strain of denitrifying Paracoccus denitrificans R-1 from sewage treatment plant sludge. This strain has strong N₂O reduction capability, and the average N₂O reduction rate was 5.10 ± 0.11 × 10^-9 µmol·h^-1·cell^-1 under anaerobic condition in a defined medium. This reduction was accompanied by the stoichiometric consumption of acetate over time when N₂O served as the sole electron acceptor and the reduction can yield energy to support microbial growth, suggesting that microbial N₂O reduction is related to the energy generation process. Genomic analysis showed that the gene cluster encoding N₂O reductase of P. denitrificans R-1 was composed of nosR, nosZ, nosD, nosF, nosY, nosL, and nosZ, which was identified as that in other strains in clade I. Respiratory inhibitors test indicated that the pathway of electron transport for N₂O reduction was different from that of the traditional electron transport chain for aerobic respiration. Cu²⁺, silver nanoparticles, O₂, and acidic conditions can strongly inhibit the reduction, whereas NO₃^- or NH₄⁺ can promote it. These findings suggest that modular N₂O reduction of P. denitrificans R-1 is linked to the electron transport and energy conservation, and dissimilatory N₂O reduction is a form of microbial anaerobic respiration.

Importance

Nitrous oxide (N₂O) is a potent greenhouse gas and contributor to ozone layer destruction, and atmospheric N₂O has increased steadily over the past century due to human activities. The release of N₂O from fixed N is almost entirely controlled by microbial N₂O reductase activities. Here, we investigated the ability to obtain energy for the growth of Paracoccus denitrificans R-1 by coupling the oxidation of various electron donors to N₂O reduction. The modular N₂O reduction process of denitrifying microorganism not only can consume N₂O produced by itself but also can consume the external N₂O generated from biological or abiotic pathways under suitable condition, which should be critical for controlling the release of N₂O from ecosystems into the atmosphere.

SUBMITTER: Zhou J

PROVIDER: S-EPMC11237620 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature

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Respiration and growth of Paracoccus denitrificans R-1 with nitrous oxide as an electron acceptor.

Zhou Jiaxian J Deng Wenfang W Wu Jiapeng J Xiang Hua H Shen Xiaomei X Lin Jih-Gaw J-G Hong Yiguo Y

Microbiology spectrum 20240422 6

In the nitrogen biogeochemical cycle, the reduction of nitrous oxide (N2O) to N2 by N2O reductase, which is encoded by nosZ gene, is the only biological pathway for N2O consumption. In this study, we successfully isolated a strain of denitrifying Paracoccus denitrificans R-1 from sewage treatment plant sludge. This strain has strong N2O reduction capability, and the average N2O reduction rate was 5.10 ± 0.11 × 10<sup ...[more]

PMID: 38647341

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Project description:N2O is generated by denitrifying bacteria as a product of NO reduction. In denitrification, N2O is metabolized further by the enzyme N2O reductase (N2OR), a multicopper protein which converts N2O into dinitrogen and water. The structure of N2OR remained unknown until the recent elucidation of the structure of the enzyme isolated from Pseudomonas nautica. In the present paper, we report the crystal structure of a blue form of the enzyme that was purified under aerobic conditions from Paracoccus denitrificans. N2OR is a head-to-tail homodimer stabilized by a multitude of interactions including two calcium sites located at the intermonomeric surface. Each monomer is composed of two domains: a C-terminal cupredoxin domain that carries the dinuclear electron entry site known as Cu(A), and an N-terminal seven-bladed beta-propeller domain which hosts the active-site centre Cu(Z). The electrons are transferred from Cu(A) to Cu(Z) across the subunit interface. Cu(Z) is a tetranuclear copper cluster in which the four copper ions (Cu1 to Cu4) are ligated by seven histidine imidazoles, a hydroxyl or water oxygen and a bridging inorganic sulphide. A bound chloride ion near the Cu(Z) active site shares one of the ligand imidazoles of Cu1. This arrangement probably influences the redox potential of Cu1 so that this copper is stabilized in the cupric state. The treatment of N2OR with H2O2 or cyanide causes the disappearance of the optical band at 640 nm, attributed to the Cu(Z) centre. The crystal structure of the enzyme soaked with H2O2 or cyanide suggests that an average of one copper of the Cu(Z) cluster has been lost. The lowest occupancy is observed for Cu3 and Cu4. A docking experiment suggests that N(2)O binds between Cu1 and Cu4 so that the oxygen of N2O replaces the oxygen ligand of Cu4. Certain ligand imidazoles of Cu1 and Cu2, as well as of Cu4, are located at the dimer interface. Particularly those of Cu2 and Cu4 are parts of a bonding network which couples these coppers to the Cu(A) centre in the neighbouring monomer. This structure may provide an efficient electron transfer path for reduction of the bound N2O.

Dataset Information

Respiration and growth of Paracoccus denitrificans R-1 with nitrous oxide as an electron acceptor.

Importance

Publications

Respiration and growth of <i>Paracoccus denitrificans</i> R-1 with nitrous oxide as an electron acceptor.

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