KEGG   PATHWAY: osa00910
Entry
osa00910                    Pathway                                
Name
Nitrogen metabolism - Oryza sativa japonica (Japanese rice) (RefSeq)
Description
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).
Class
Metabolism; Energy metabolism
Pathway map
osa00910  Nitrogen metabolism
osa00910

Module
osa_M00531  Assimilatory nitrate reduction, nitrate => ammonia [PATH:osa00910]
Other DBs
GO: 0006807
Organism
Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
Gene
4326894  uncharacterized protein LOC4326894 [KO:K01455] [EC:3.5.1.49]
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:1.7.1.1 1.7.1.2 1.7.1.3]
4345795  nitrate reductase [NADH] 1 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
4345798  nitrate reductase [NADH] 1-like [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
4330835  ferredoxin--nitrite reductase, chloroplastic-like [KO:K00366] [EC:1.7.7.1]
4326014  ferredoxin--nitrite reductase, chloroplastic [KO:K00366] [EC:1.7.7.1]
4334405  glutamate dehydrogenase [KO:K00261] [EC:1.4.1.3]
4330164  glutamate dehydrogenase A [KO:K00261] [EC:1.4.1.3]
4336554  glutamate dehydrogenase 2 [KO:K00261] [EC:1.4.1.3]
4324672  NADP-specific glutamate dehydrogenase isoform X1 [KO:K00262] [EC:1.4.1.4]
4337272  glutamine synthetase, chloroplastic [KO:K01915] [EC:6.3.1.2]
4333896  glutamine synthetase cytosolic isozyme 1-3 [KO:K01915] [EC:6.3.1.2]
4330649  glutamine synthetase cytosolic isozyme 1-1 [KO:K01915] [EC:6.3.1.2]
4332108  glutamine synthetase cytosolic isozyme 1-2 [KO:K01915] [EC:6.3.1.2]
4339561  glutamate synthase 2 [NADH], chloroplastic [KO:K00264] [EC:1.4.1.14]
4324398  glutamate synthase 1 [NADH], chloroplastic isoform X1 [KO:K00264] [EC:1.4.1.14]
4344164  ferredoxin-dependent glutamate synthase, chloroplastic [KO:K00284] [EC:1.4.7.1]
4348870  cyanate hydratase [KO:K01725] [EC:4.2.1.104]
4326583  carbonic anhydrase, chloroplastic isoform X1 [KO:K01673] [EC:4.2.1.1]
4347305  beta carbonic anhydrase 5, chloroplastic isoform X1 [KO:K01673] [EC:4.2.1.1]
4329556  alpha carbonic anhydrase 1, chloroplastic [KO:K01674] [EC:4.2.1.1]
4345604  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
4351529  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
9267362  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
4349804  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
4335782  alpha carbonic anhydrase 1, chloroplastic [KO:K01674] [EC:4.2.1.1]
4347247  alpha carbonic anhydrase 7 isoform X1 [KO:K01674] [EC:4.2.1.1]
9268297  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
9270004  alpha carbonic anhydrase 5 [KO:K01674] [EC:4.2.1.1]
107276201  alpha carbonic anhydrase 7-like [KO:K01674] [EC:4.2.1.1]
Compound
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
Reference
  Authors
Scott JD, Ludwig RA
  Title
Azorhizobium caulinodans electron-transferring flavoprotein N electrochemically couples pyruvate dehydrogenase complex activity to N2 fixation.
  Journal
Microbiology 150:117-26 (2004)
DOI:10.1099/mic.0.26603-0
Reference
  Authors
Kneip C, Lockhart P, Voss C, Maier UG
  Title
Nitrogen fixation in eukaryotes--new models for symbiosis.
  Journal
BMC Evol Biol 7:55 (2007)
DOI:10.1186/1471-2148-7-55
Reference
  Authors
Whittaker M, Bergmann D, Arciero D, Hooper AB
  Title
Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea.
  Journal
Biochim Biophys Acta 1459:346-55 (2000)
DOI:10.1016/S0005-2728(00)00171-7
Reference
  Authors
Cabello P, Roldan MD, Moreno-Vivian C
  Title
Nitrate reduction and the nitrogen cycle in archaea.
  Journal
Microbiology 150:3527-46 (2004)
DOI:10.1099/mic.0.27303-0
Reference
  Authors
Stolz JF, Basu P
  Title
Evolution of nitrate reductase: molecular and structural variations on a common function.
  Journal
Reference
  Authors
Morozkina EV, Zvyagilskaya RA
  Title
Nitrate reductases: structure, functions, and effect of stress factors.
  Journal
Biochemistry (Mosc) 72:1151-60 (2007)
DOI:10.1134/S0006297907100124
Reference
  Authors
Jetten MS, Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ
  Title
Biochemistry and molecular biology of anammox bacteria.
  Journal
Crit Rev Biochem Mol Biol 44:65-84 (2009)
DOI:10.1080/10409230902722783
Reference
  Authors
Luesken FA, Wu ML, Op den Camp HJ, Keltjens JT, Stunnenberg H, Francoijs KJ, Strous M, Jetten MS
  Title
Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis.
  Journal
Environ Microbiol 14:1024-34 (2012)
DOI:10.1111/j.1462-2920.2011.02682.x
Reference
  Authors
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
  Title
Complete nitrification by Nitrospira bacteria.
  Journal
Nature 528:504-9 (2015)
DOI:10.1038/nature16461
Reference
  Authors
van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lucker S
  Title
Complete nitrification by a single microorganism.
  Journal
Nature 528:555-9 (2015)
DOI:10.1038/nature16459
Related
pathway
osa00220  Arginine biosynthesis
osa00250  Alanine, aspartate and glutamate metabolism
osa00460  Cyanoamino acid metabolism
osa00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00910   
LinkDB

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