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Pathway Description
Lysine Metabolism
Arabidopsis thaliana
Metabolic Pathway
The biosynthesis of lysine starts with oxoglutaric acid interacting with acetyl-coa through a homocitrate synthase resulting in the release of homocitric acid. This reaction may happen in the cytosol or in the mitochondria. The homocitric acid spontaneously releases water an is transformed into cis-homoaconitate, The cis-homoaconitate reacts with homoaconitase resulting in the release of water and a homoisocitrate. Homoisocitrate reacts with a NAD dependent homoisocitrate dehydrogenase resulting in the release of a carbon dioxide, a NADH and a oxoadipic acid. These set of reactions happen in the mitochondria. Oxoadipic acid reacts with a glutamic acid resulting in the release of oxoglutaric acid and aminoadipic acid. The aminoadipic acid reacts with a holo-[LYS2 peptidyl-carrier-protein] through an ATP driven L-2-aminoadipate reductase resulting in the release of AMP, pyrophosphate and L-2-aminoadipyl-[lys2 peptidyl-carrier-protein]. This resulting element reacts with a NADPH dependent L-2-aminoadipate reductase resulting in the release of allysine. Allysine reacts with a glutamic acid through a NADPH dependent saccharopine dehydrogenase resulting in the release of water, NADP and saccharopine. Saccharopine reacts with a water molecule and a NAD dependent saccharopine dehydrogenase resulting in the release of oxoglutaric acid and L-lysine. This last reaction is reversible and leads to the degradation of lysine
References
Lysine Metabolism References
Hudson AO, Bless C, Macedo P, Chatterjee SP, Singh BK, Gilvarg C, Leustek T: Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways. Biochim Biophys Acta. 2005 Jan 18;1721(1-3):27-36. doi: 10.1016/j.bbagen.2004.09.008. Epub 2004 Nov 4.
Pubmed: 15652176
Jander G, Joshi V: Aspartate-Derived Amino Acid Biosynthesis in Arabidopsis thaliana. Arabidopsis Book. 2009;7:e0121. doi: 10.1199/tab.0121. Epub 2009 Jun 10.
Pubmed: 22303247
Frankard V, Vauterin M, Jacobs M: Molecular characterization of an Arabidopsis thaliana cDNA coding for a monofunctional aspartate kinase. Plant Mol Biol. 1997 May;34(2):233-42.
Pubmed: 9207839
Paris S, Wessel PM, Dumas R: Overproduction, purification, and characterization of recombinant aspartate semialdehyde dehydrogenase from Arabidopsis thaliana. Protein Expr Purif. 2002 Feb;24(1):99-104. doi: 10.1006/prep.2001.1538.
Pubmed: 11812229
Rognes SE, Dewaele E, Aas SF, Jacobs M, Frankard V: Transcriptional and biochemical regulation of a novel Arabidopsis thaliana bifunctional aspartate kinase-homoserine dehydrogenase gene isolated by functional complementation of a yeast hom6 mutant. Plant Mol Biol. 2003 Jan;51(2):281-94.
Pubmed: 12602885
Sarrobert C, Thibaud MC, Contard-David P, Gineste S, Bechtold N, Robaglia C, Nussaume L: Identification of an Arabidopsis thaliana mutant accumulating threonine resulting from mutation in a new dihydrodipicolinate synthase gene. Plant J. 2000 Nov;24(3):357-67.
Pubmed: 11069709
Yoshioka Y, Kurei S, Machida Y: Identification of a monofunctional aspartate kinase gene of Arabidopsis thaliana with spatially and temporally regulated expression. Genes Genet Syst. 2001 Jun;76(3):189-98.
Pubmed: 11569502
Park SJ, Cho YD: Identification of functionally important residues of Arabidopsis thaliana S-adenosylmethionine decarboxylase. J Biochem. 1999 Dec;126(6):996-1003.
Pubmed: 10578049
Araujo WL, Ishizaki K, Nunes-Nesi A, Larson TR, Tohge T, Krahnert I, Witt S, Obata T, Schauer N, Graham IA, Leaver CJ, Fernie AR: Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases as alternative electron donors linking lysine catabolism to the electron transport chain of Arabidopsis mitochondria. Plant Cell. 2010 May;22(5):1549-63. doi: 10.1105/tpc.110.075630. Epub 2010 May 25.
Pubmed: 20501910
Boex-Fontvieille ER, Gauthier PP, Gilard F, Hodges M, Tcherkez GG: A new anaplerotic respiratory pathway involving lysine biosynthesis in isocitrate dehydrogenase-deficient Arabidopsis mutants. New Phytol. 2013 Aug;199(3):673-82. doi: 10.1111/nph.12319. Epub 2013 May 30.
Pubmed: 23718121
Engqvist M, Drincovich MF, Flugge UI, Maurino VG: Two D-2-hydroxy-acid dehydrogenases in Arabidopsis thaliana with catalytic capacities to participate in the last reactions of the methylglyoxal and beta-oxidation pathways. J Biol Chem. 2009 Sep 11;284(37):25026-37. doi: 10.1074/jbc.M109.021253. Epub 2009 Jul 7.
Pubmed: 19586914
Rubio S, Larson TR, Gonzalez-Guzman M, Alejandro S, Graham IA, Serrano R, Rodriguez PL: An Arabidopsis mutant impaired in coenzyme A biosynthesis is sugar dependent for seedling establishment. Plant Physiol. 2006 Mar;140(3):830-43. doi: 10.1104/pp.105.072066. Epub 2006 Jan 13.
Pubmed: 16415216
Zhu X, Tang G, Galili G: Characterization of the two saccharopine dehydrogenase isozymes of lysine catabolism encoded by the single composite AtLKR/SDH locus of Arabidopsis. Plant Physiol. 2000 Nov;124(3):1363-72.
Pubmed: 11080311
Goepfert S, Hiltunen JK, Poirier Y: Identification and functional characterization of a monofunctional peroxisomal enoyl-CoA hydratase 2 that participates in the degradation of even cis-unsaturated fatty acids in Arabidopsis thaliana. J Biol Chem. 2006 Nov 24;281(47):35894-903. doi: 10.1074/jbc.M606383200. Epub 2006 Sep 18.
Pubmed: 16982622
Jin H, Song Z, Nikolau BJ: Reverse genetic characterization of two paralogous acetoacetyl CoA thiolase genes in Arabidopsis reveals their importance in plant growth and development. Plant J. 2012 Jun;70(6):1015-32. doi: 10.1111/j.1365-313X.2012.04942.x. Epub 2012 Mar 31.
Pubmed: 22332816
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