Nitrite oxidoreductase

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Nitrite oxidoreductase (NOR or NXR) is an enzyme involved in nitrification. It is the last step in the process of aerobic ammonia oxidation, which is carried out by two groups of nitrifying bacteria: ammonia oxidizers such as Nitrosospira , Nitrosomonas, and Nitrosococcus convert ammonia to nitrite, while nitrite oxidizers such as Nitrobacter and Nitrospira oxidize nitrite to nitrate. NXR is responsible for producing almost all nitrate found in nature. [1]

Contents

NXR belongs to the class of EC numbers 1.7.2- [2] [3] where 1 describes an oxidoreductase, 1.7 describes nitrogen compounds as donors, and 1.7.2- describes cytochromes as acceptors. [3]

Structure

NXR is composed of 2 mainly known subunits; nitrite oxidoreductase α (NxrA), and nitrite oxidoreductase β (NxrB) (sometimes written as NorA and NorB). [3]   However, recent studies describe a third and fourth subunit, NxrC and NxrT [3] [4] The enzyme's known active site is on the NxrA subunit. [4] There are two types of NXR; one where the NxrA subunit is located in the periplasmic space of a cell, and the other where NxrA is located in the cytoplasm [5]

The enzyme is bound to the inner cytoplasmic surface of the bacterial membrane and contains iron-sulfur centers and a molybdenum cofactor. [6] [7] The enzyme is relatively abundant, making up 10-30% of the total protein in these bacteria and forms densely packed structures on the membrane surface. [8] To date, little is known about the exact structure of NXR, but has been discovered to form tubule structures that are hundreds of nanometers long. [5]

Pathway

Reaction

NXR oxidizes nitrite into nitrate in aerobic nitrogen oxidizing bacteria as well as ammonia to nitrite in ammonia oxidizing bacteria or archaea.  When it oxidizes nitrite to nitrate, two electrons are shuttled into the respiratory chain. Electrons flow through the subunits of the enzyme through cytochrome c toward the terminal oxidase. [4] This reaction can be reversed to reduce nitrate to nitrite in anaerobic conditions, though the driving force of this reversal is poorly understood. [9]

Metabolism

In periplasmic NXR types, protons are derived from water and contribute to proton motive force, which then contributes to the cell's energy budget. However, cytoplasmic NXR does not contribute to proton motive force. [4]   The two electrons that are generated from the nitrite oxidation are then donated to molecular oxygen, which yields energy. [5]   The NXR pathway for nitrite oxidation generally has a low energy yield (ΔG’ = -74 kJ/mol NO2). [4]

See also

Related Research Articles

<span class="mw-page-title-main">Oxidative phosphorylation</span> Metabolic pathway

Oxidative phosphorylation or electron transport-linked phosphorylation or terminal oxidation is the metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine triphosphate (ATP). In eukaryotes, this takes place inside mitochondria. Almost all aerobic organisms carry out oxidative phosphorylation. This pathway is so pervasive because it releases more energy than alternative fermentation processes such as anaerobic glycolysis.

<span class="mw-page-title-main">Electron transport chain</span> Energy-producing metabolic pathway

An electron transport chain (ETC) is a series of protein complexes and other molecules that transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples this electron transfer with the transfer of protons (H+ ions) across a membrane. The electrons that are transferred from NADH and FADH2 to the ETC involves four multi-subunit large enzymes complexes and two mobile electron carriers. Many of the enzymes in the electron transport chain are embedded within the membrane.

<span class="mw-page-title-main">Nitrification</span> Biological oxidation of ammonia/ammonium to nitrate

Nitrification is the biological oxidation of ammonia to nitrate via the intermediary nitrite. Nitrification is an important step in the nitrogen cycle in soil. The process of complete nitrification may occur through separate organisms or entirely within one organism, as in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.

Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.

<span class="mw-page-title-main">Anammox</span> Anaerobic ammonium oxidation, a microbial process of the nitrogen cycle

Anammox, an abbreviation for "anaerobic ammonium oxidation", is a globally important microbial process of the nitrogen cycle that takes place in many natural environments. The bacteria mediating this process were identified in 1999, and were a great surprise for the scientific community. In the anammox reaction, nitrite and ammonium ions are converted directly into diatomic nitrogen and water.

Methanotrophs are prokaryotes that metabolize methane as their source of carbon and chemical energy. They are bacteria or archaea, can grow aerobically or anaerobically, and require single-carbon compounds to survive.

<i>Nitrosomonas</i> Genus of bacteria

Nitrosomonas is a genus of Gram-negative bacteria, belonging to the Betaproteobacteria. It is one of the five genera of ammonia-oxidizing bacteria and, as an obligate chemolithoautotroph, uses ammonia as an energy source and carbon dioxide as a carbon source in presence of oxygen. Nitrosomonas are important in the global biogeochemical nitrogen cycle, since they increase the bioavailability of nitrogen to plants and in the denitrification, which is important for the release of nitrous oxide, a powerful greenhouse gas. This microbe is photophobic, and usually generate a biofilm matrix, or form clumps with other microbes, to avoid light. Nitrosomonas can be divided into six lineages: the first one includes the species Nitrosomonas europea, Nitrosomonas eutropha, Nitrosomonas halophila, and Nitrosomonas mobilis. The second lineage presents the species Nitrosomonas communis, N. sp. I and N. sp. II, meanwhile the third lineage includes only Nitrosomonas nitrosa. The fourth lineage includes the species Nitrosomonas ureae and Nitrosomonas oligotropha and the fifth and sixth lineages include the species Nitrosomonas marina, N. sp. III, Nitrosomonas estuarii and Nitrosomonas cryotolerans.

<i>Nitrobacter</i> Genus of bacteria

Nitrobacter is a genus comprising rod-shaped, gram-negative, and chemoautotrophic bacteria. The name Nitrobacter derives from the Latin neuter gender noun nitrum, nitri, alkalis; the Ancient Greek noun βακτηρία, βακτηρίᾱς, rod. They are non-motile and reproduce via budding or binary fission. Nitrobacter cells are obligate aerobes and have a doubling time of about 13 hours.

Nitrite reductase refers to any of several classes of enzymes that catalyze the reduction of nitrite. There are two classes of NIR's. A multi haem enzyme reduces NO2− to a variety of products. Copper containing enzymes carry out a single electron transfer to produce nitric oxide.

Microbial metabolism is the means by which a microbe obtains the energy and nutrients it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.

<span class="mw-page-title-main">Nitrate reductase</span> Class of enzymes

Nitrate reductases are molybdoenzymes that reduce nitrate to nitrite. This reaction is critical for the production of protein in most crop plants, as nitrate is the predominant source of nitrogen in fertilized soils.

Nitrifying bacteria are chemolithotrophic organisms that include species of genera such as Nitrosomonas, Nitrosococcus, Nitrobacter, Nitrospina, Nitrospira and Nitrococcus. These bacteria get their energy from the oxidation of inorganic nitrogen compounds. Types include ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB). Many species of nitrifying bacteria have complex internal membrane systems that are the location for key enzymes in nitrification: ammonia monooxygenase, hydroxylamine oxidoreductase, and nitrite oxidoreductase.

Nitrospira translate into “a nitrate spiral” is a genus of bacteria within the monophyletic clade of the Nitrospirota phylum. The first member of this genus was described 1986 by Watson et al. isolated from the Gulf of Maine. The bacterium was named Nitrospira marina. Populations were initially thought to be limited to marine ecosystems, but it was later discovered to be well-suited for numerous habitats, including activated sludge of wastewater treatment systems, natural biological marine settings, water circulation biofilters in aquarium tanks, terrestrial systems, fresh and salt water ecosystems, and hot springs. Nitrospira is a ubiquitous bacterium that plays a role in the nitrogen cycle by performing nitrite oxidation in the second step of nitrification. Nitrospira live in a wide array of environments including but not limited to, drinking water systems, waste treatment plants, rice paddies, forest soils, geothermal springs, and sponge tissue. Despite being abundant in many natural and engineered ecosystems Nitrospira are difficult to culture, so most knowledge of them is from molecular and genomic data. However, due to their difficulty to be cultivated in laboratory settings, the entire genome was only sequenced in one species, Nitrospira defluvii. In addition, Nitrospira bacteria's 16S rRNA sequences are too dissimilar to use for PCR primers, thus some members go unnoticed. In addition, members of Nitrospira with the capabilities to perform complete nitrification has also been discovered and cultivated.

<i>Nitrosopumilus</i> Genus of archaea

Nitrosopumilus maritimus is an extremely common archaeon living in seawater. It is the first member of the Group 1a Nitrososphaerota to be isolated in pure culture. Gene sequences suggest that the Group 1a Nitrososphaerota are ubiquitous with the oligotrophic surface ocean and can be found in most non-coastal marine waters around the planet. It is one of the smallest living organisms at 0.2 micrometers in diameter. Cells in the species N. maritimus are shaped like peanuts and can be found both as individuals and in loose aggregates. They oxidize ammonia to nitrite and members of N. maritimus can oxidize ammonia at levels as low as 10 nanomolar, near the limit to sustain its life. Archaea in the species N. maritimus live in oxygen-depleted habitats. Oxygen needed for ammonia oxidation might be produced by novel pathway which generates oxygen and dinitrogen. N. maritimus is thus among organisms which are able to produce oxygen in dark.

<span class="mw-page-title-main">Cytochrome c nitrite reductase</span> Class of enzymes

Cytochrome c nitrite reductase (ccNiR) is a bacterial enzyme that catalyzes the six electron reduction of nitrite to ammonia; an important step in the biological nitrogen cycle. The enzyme catalyses the second step in the two step conversion of nitrate to ammonia, which allows certain bacteria to use nitrite as a terminal electron acceptor, rather than oxygen, during anaerobic conditions. During this process, ccNiR draws electrons from the quinol pool, which are ultimately provided by a dehydrogenase such as formate dehydrogenase or hydrogenase. These dehydrogenases are responsible for generating a proton motive force.

<span class="mw-page-title-main">SHARON Wastewater Treatment</span>

SHARON is a sewage treatment process. A partial nitrification process of sewage treatment used for the removal of ammonia and organic nitrogen components from wastewater flow streams. The process results in stable nitrite formation, rather than complete oxidation to nitrate. Nitrate formation by nitrite oxidising bacteria (NOB) is prevented by adjusting temperature, pH, and retention time to select for nitrifying ammonia oxidising bacteria (AOB). Denitrification of waste streams utilizing SHARON reactors can proceed with an anoxic reduction, such as anammox.

Nitrososphaera is a mesophilic genus of ammonia-oxidizing Crenarchaeota. The first Nitrososphaera organism was discovered in garden soils at the University of Vienna leading to the categorization of a new genus, family, order and class of Archaea. This genus is contains three distinct species: N. viennensis, Ca. N. gargensis, and Ca N. evergladensis. Nitrososphaera are chemolithoautotrophs and have important biogeochemical roles as nitrifying organisms.

Nitrospira moscoviensis was the second bacterium classified under the most diverse nitrite-oxidizing bacteria phylum, Nitrospirae. It is a gram-negative, non-motile, facultative lithoauthotropic bacterium that was discovered in Moscow, Russia in 1995. The genus name, Nitrospira, originates from the prefix “nitro” derived from nitrite, the microbe’s electron donor and “spira” meaning coil or spiral derived from the microbe’s shape. The species name, moscoviensis, is derived from Moscow, where the species was first discovered. N. moscoviensis could potentially be used in the production of bio-degradable polymers.

Comammox is the name attributed to an organism that can convert ammonia into nitrite and then into nitrate through the process of nitrification. Nitrification has traditionally thought to be a two-step process, where ammonia-oxidizing bacteria and archaea oxidize ammonia to nitrite and then nitrite-oxidizing bacteria convert to nitrate. Complete conversion of ammonia into nitrate by a single microorganism was first predicted in 2006. In 2015 the presence of microorganisms that could carry out both conversion processes was discovered within the genus Nitrospira, and the nitrogen cycle was updated. Within the genus Nitrospira, the major ecosystems comammox are primarily found in natural aquifers and engineered ecosystems.

Dissimilatory nitrate reduction to ammonium (DNRA), also known as nitrate/nitrite ammonification, is the result of anaerobic respiration by chemoorganoheterotrophic microbes using nitrate (NO3−) as an electron acceptor for respiration. In anaerobic conditions microbes which undertake DNRA oxidise organic matter and use nitrate (rather than oxygen) as an electron acceptor, reducing it to nitrite, then ammonium (NO3−→NO2−→NH4+).

References

  1. ↑ Chicano, Tadeo Moreno; Dietrich, Lea; de Almeida, Naomi M.; Akram, Mohd.; Hartmann, Elisabeth; Leidreiter, Franziska; Leopoldus, Daniel; Mueller, Melanie; Sánchez, Ricardo; Nuijten, Guylaine H. L.; Reimann, Joachim; Seifert, Kerstin-Anikó; Schlichting, Ilme; van Niftrik, Laura; Jetten, Mike S. M. (2021-07-15). "Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex". Nature Microbiology. 6 (9): 1129–1139. doi:10.1038/s41564-021-00934-8. ISSN   2058-5276. PMC   8387239 . PMID   34267357.
  2. ↑ Caspi, Ron; Billington, Richard; Fulcher, Carol A; Keseler, Ingrid M; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Midford, Peter E; Ong, Quang; Ong, Wai Kit; Paley, Suzanne; Subhraveti, Pallavi; Karp, Peter D (2017-10-20). "The MetaCyc database of metabolic pathways and enzymes". Nucleic Acids Research. 46 (D1): D633–D639. doi: 10.1093/nar/gkx935 . ISSN   0305-1048. PMC   5753197 . PMID   29059334.
  3. 1 2 3 4 "ENZYME: 1.7.2.-". enzyme.expasy.org. Retrieved 2023-10-19.
  4. 1 2 3 4 5 Daims, Holger; Lücker, Sebastian; Wagner, Michael (September 2016). "A New Perspective on Microbes Formerly Known as Nitrite-Oxidizing Bacteria". Trends in Microbiology. 24 (9): 699–712. doi:10.1016/j.tim.2016.05.004. PMC   6884419 . PMID   27283264.
  5. 1 2 3 Holmes, Dawn E.; Dang, Yan; Smith, Jessica A. (2019), "Nitrogen cycling during wastewater treatment", Advances in Applied Microbiology, Elsevier, vol. 106, pp. 113–192, doi:10.1016/bs.aambs.2018.10.003, ISBN   978-0-12-816975-9, S2CID   73468296 , retrieved 2023-10-19
  6. ↑ Spieck E, Ehrich S, Aamand J, Bock E (1998). "Isolation and immunocytochemical location of the nitrite-oxidizing system in nitrospira moscoviensis". Arch. Microbiol. 169 (3): 225–30. Bibcode:1998ArMic.169..225S. doi:10.1007/s002030050565. PMID   9477257. S2CID   21868756.
  7. ↑ Meincke M, Bock E, Kastrau D, Kroneck PMH (1992). "Nitrite oxidoreductase from Nitrobacter hamburgensis: redox centers and their catalytic role". Arch. Microbiol. 158 (2): 127–31. Bibcode:1992ArMic.158..127M. doi:10.1007/BF00245215. S2CID   6903429.
  8. ↑ Spieck E, Muller S, Engel A, Mandelkow E, Patel H (1996). "Two-dimensional structure of membrane-bound nitrite oxidoreductase from Nitrobacter hamburgensis" (PDF). J. Struct. Biol. 117 (2): 117–123. doi:10.1006/jsbi.1996.0076.
  9. ↑ Ward, B.B. (2011), "Measurement and Distribution of Nitrification Rates in the Oceans", Research on Nitrification and Related Processes, Part A, Methods in Enzymology, Elsevier, vol. 486, pp. 307–323, doi:10.1016/b978-0-12-381294-0.00013-4, ISBN   9780123812940, PMID   21185441 , retrieved 2023-10-19


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