KEGG   PATHWAY: osa00910
osa00910                    Pathway                                
Nitrogen metabolism - Oryza sativa japonica (Japanese rice) (RefSeq)
The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. The core nitrogen cycle involves four reduction pathways and two oxidation pathways. Nitrogen fixation [MD:M00175] is the process of reducing atmospheric molecular nitrogen to ammonia, a biologically useful reduced form incorporated into amino acids and other vital compounds. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction [MD:M00531] and dissimilatory nitrate reduction [MD:M00530] both for conversion to ammonia, and denitrification [MD:M00529]. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions, producing gaseous nitrogen compounds (N2, NO and N2O) to the atmosphere. The two oxidation pathways are nitrification [MD:M00528] and anaerobic ammonium oxidation (anammox). Nitrification is the oxidation of ammonia (NH3) with oxygen into nitrite followed by the oxidation of nitrite into nitrate. The first step is performed by ammonia-oxidizing microorganisms (e.g., Nitrosomonas and Nitrosococcus) and the second step by nitrite-oxidizing microorganisms (e.g., Nitrobacter). Anammox is a biochemical process of oxidizing ammonium (NH4+) into dinitrogen gas (N2) using nitrite as an electron acceptor. It occurs in the anammoxosome, a membrane bound compartment inside the cytoplasm, of anammox bacteria (e.g., Planctomycetes).
Metabolism; Energy metabolism
Pathway map
osa00910  Nitrogen metabolism

osa_M00531  Assimilatory nitrate reduction, nitrate => ammonia [PATH:osa00910]
Other DBs
GO: 0006807
Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
4326894  uncharacterized protein LOC4326894 [KO:K01455] [EC:]
4328051  high-affinity nitrate transporter 2.1 [KO:K02575]
4328052  high-affinity nitrate transporter 2.1 [KO:K02575]
4324249  high-affinity nitrate transporter 2.3 [KO:K02575]
107277478  probable high-affinity nitrate transporter 2.4 [KO:K02575]
4330867  nitrate reductase [NAD(P)H] [KO:K10534] [EC:]
4345795  nitrate reductase [NADH] 1 [KO:K10534] [EC:]
4345798  nitrate reductase [NADH] 1-like [KO:K10534] [EC:]
4330835  ferredoxin--nitrite reductase, chloroplastic-like [KO:K00366] [EC:]
4326014  ferredoxin--nitrite reductase, chloroplastic [KO:K00366] [EC:]
4334405  glutamate dehydrogenase [KO:K00261] [EC:]
4330164  glutamate dehydrogenase A [KO:K00261] [EC:]
4336554  glutamate dehydrogenase 2 [KO:K00261] [EC:]
4324672  NADP-specific glutamate dehydrogenase isoform X1 [KO:K00262] [EC:]
4337272  glutamine synthetase, chloroplastic [KO:K01915] [EC:]
4333896  glutamine synthetase cytosolic isozyme 1-3 [KO:K01915] [EC:]
4330649  glutamine synthetase cytosolic isozyme 1-1 [KO:K01915] [EC:]
4332108  glutamine synthetase cytosolic isozyme 1-2 [KO:K01915] [EC:]
4339561  glutamate synthase 2 [NADH], chloroplastic [KO:K00264] [EC:]
4324398  glutamate synthase 1 [NADH], chloroplastic isoform X1 [KO:K00264] [EC:]
4344164  ferredoxin-dependent glutamate synthase, chloroplastic [KO:K00284] [EC:]
4348870  cyanate hydratase [KO:K01725] [EC:]
4326583  carbonic anhydrase, chloroplastic isoform X1 [KO:K01673] [EC:]
4347305  beta carbonic anhydrase 5, chloroplastic isoform X1 [KO:K01673] [EC:]
4329556  alpha carbonic anhydrase 1, chloroplastic [KO:K01674] [EC:]
4345604  alpha carbonic anhydrase 7 [KO:K01674] [EC:]
4351529  alpha carbonic anhydrase 7 [KO:K01674] [EC:]
9267362  alpha carbonic anhydrase 7 [KO:K01674] [EC:]
4349804  alpha carbonic anhydrase 7 [KO:K01674] [EC:]
4335782  alpha carbonic anhydrase 1, chloroplastic [KO:K01674] [EC:]
4347247  alpha carbonic anhydrase 7 isoform X1 [KO:K01674] [EC:]
9268297  alpha carbonic anhydrase 7 [KO:K01674] [EC:]
9270004  alpha carbonic anhydrase 5 [KO:K01674] [EC:]
107276201  alpha carbonic anhydrase 7-like [KO:K01674] [EC:]
C00011  CO2
C00014  Ammonia
C00025  L-Glutamate
C00058  Formate
C00064  L-Glutamine
C00088  Nitrite
C00169  Carbamoyl phosphate
C00192  Hydroxylamine
C00244  Nitrate
C00288  HCO3-
C00488  Formamide
C00533  Nitric oxide
C00697  Nitrogen
C00726  Nitrile
C00887  Nitrous oxide
C01417  Cyanate
C01563  Carbamate
C05361  Hydrazine
C06058  Nitroalkane
Scott JD, Ludwig RA
Azorhizobium caulinodans electron-transferring flavoprotein N electrochemically couples pyruvate dehydrogenase complex activity to N2 fixation.
Microbiology 150:117-26 (2004)
Kneip C, Lockhart P, Voss C, Maier UG
Nitrogen fixation in eukaryotes--new models for symbiosis.
BMC Evol Biol 7:55 (2007)
Whittaker M, Bergmann D, Arciero D, Hooper AB
Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea.
Biochim Biophys Acta 1459:346-55 (2000)
Cabello P, Roldan MD, Moreno-Vivian C
Nitrate reduction and the nitrogen cycle in archaea.
Microbiology 150:3527-46 (2004)
Stolz JF, Basu P
Evolution of nitrate reductase: molecular and structural variations on a common function.
Morozkina EV, Zvyagilskaya RA
Nitrate reductases: structure, functions, and effect of stress factors.
Biochemistry (Mosc) 72:1151-60 (2007)
Jetten MS, Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ
Biochemistry and molecular biology of anammox bacteria.
Crit Rev Biochem Mol Biol 44:65-84 (2009)
Luesken FA, Wu ML, Op den Camp HJ, Keltjens JT, Stunnenberg H, Francoijs KJ, Strous M, Jetten MS
Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis.
Environ Microbiol 14:1024-34 (2012)
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M
Complete nitrification by Nitrospira bacteria.
Nature 528:504-9 (2015)
van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lucker S
Complete nitrification by a single microorganism.
Nature 528:555-9 (2015)
osa00220  Arginine biosynthesis
osa00250  Alanine, aspartate and glutamate metabolism
osa00460  Cyanoamino acid metabolism
osa00630  Glyoxylate and dicarboxylate metabolism
KO pathway

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