ENTRY       sly00910                    Pathway
NAME        Nitrogen metabolism - Solanum lycopersicum (tomato)
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 sly00910  Nitrogen metabolism
MODULE      sly_M00531  Assimilatory nitrate reduction, nitrate => ammonia [PATH:sly00910]
DBLINKS     GO: 0006807
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101258424  uncharacterized protein LOC101258424 isoform X1 [KO:K01455] [EC:3.5.1.49]
            101257730  high affinity nitrate transporter 2.7 isoform X1 [KO:K02575]
            543827  LeNRT2.3; nitrate transporter NRT2.3 [KO:K02575]
            101265831  NRT2.2; putative high-affinity nitrate transporter [KO:K02575]
            101247028  high affinity nitrate transporter 2.4-like [KO:K02575]
            101250864  high affinity nitrate transporter 2.4-like [KO:K02575]
            100736473  NR; nitrate reductase [NADH] [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            778326  ferredoxin--nitrite reductase, chloroplastic [KO:K00366] [EC:1.7.7.1]
            778325  nii1; nitrite reductase [KO:K00366] [EC:1.7.7.1]
            544015  gdh1; glutamate dehydrogenase [KO:K00261] [EC:1.4.1.3]
            101246116  glutamate dehydrogenase [KO:K00261] [EC:1.4.1.3]
            101252088  glutamate dehydrogenase A-like [KO:K00261] [EC:1.4.1.3]
            101257803  NADP-specific glutamate dehydrogenase isoform X2 [KO:K00262] [EC:1.4.1.4]
            101261030  glutamine synthetase-like isoform X1 [KO:K01915] [EC:6.3.1.2]
            544275  GS1; glutamine synthetase [KO:K01915] [EC:6.3.1.2]
            101248274  glutamine synthetase cytosolic isozyme-like isoform X1 [KO:K01915] [EC:6.3.1.2]
            543998  GS2; glutamine synthetase [KO:K01915] [EC:6.3.1.2]
            543756  gts1; glutamine synthetase cytosolic isozyme 1-1 [KO:K01915] [EC:6.3.1.2]
            101254281  glutamate synthase 1 [NADH], chloroplastic isoform X1 [KO:K00264] [EC:1.4.1.14]
            101246028  ferredoxin-dependent glutamate synthase, chloroplastic [KO:K00284] [EC:1.4.7.1]
            101259288  cyanate hydratase [KO:K01725] [EC:4.2.1.104]
            543803  ca2; carbonic anhydrase isoform 1 [KO:K01673] [EC:4.2.1.1]
            101257401  beta carbonic anhydrase 5, chloroplastic isoform X2 [KO:K01673] [EC:4.2.1.1]
            100147727  ca3; carbonic anhydrase [KO:K01673] [EC:4.2.1.1]
            543802  carbonic anh isoform 2 [KO:K01673] [EC:4.2.1.1]
            101247478  alpha carbonic anhydrase 4 [KO:K01674] [EC:4.2.1.1]
            101254722  alpha carbonic anhydrase 1, chloroplastic isoform X1 [KO:K01674] [EC:4.2.1.1]
            101268239  alpha carbonic anhydrase 7-like [KO:K01674] [EC:4.2.1.1]
            101258967  bifunctional monodehydroascorbate reductase and carbonic anhydrase nectarin-3-like [KO:K01674] [EC:4.2.1.1]
            101259260  bifunctional monodehydroascorbate reductase and carbonic anhydrase nectarin-3-like [KO:K01674] [EC:4.2.1.1]
            101264130  bifunctional monodehydroascorbate reductase and carbonic anhydrase nectarin-3-like isoform X1 [KO:K01674] [EC:4.2.1.1]
            101267926  alpha carbonic anhydrase 7-like isoform X1 [KO:K01674] [EC:4.2.1.1]
            101264399  alpha carbonic anhydrase 7 [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   PMID:14702404
  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   PMID:17408485
  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   PMID:11004450
  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   PMID:15528644
  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   PMID:11921398
  AUTHORS   Stolz JF, Basu P
  TITLE     Evolution of nitrate reductase: molecular and structural variations on a common function.
  JOURNAL   Chembiochem 3:198-206 (2002)
            DOI:10.1002/1439-7633(20020301)3:2/3<198::AID-CBIC198>3.0.CO;2-C
REFERENCE   PMID:18021072
  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   PMID:19247843
  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   PMID:22221911
  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   PMID:26610024
  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   PMID:26610025
  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
REL_PATHWAY sly00220  Arginine biosynthesis
            sly00250  Alanine, aspartate and glutamate metabolism
            sly00460  Cyanoamino acid metabolism
            sly00630  Glyoxylate and dicarboxylate metabolism
KO_PATHWAY  ko00910
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