MetaCyc Pathway: L-lysine degradation III
Traceable author statement to experimental supportInferred from experiment

Enzyme View:

Pathway diagram: L-lysine degradation III

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/AssimilationAmino Acids DegradationProteinogenic Amino Acids DegradationL-lysine Degradation

Some taxa known to possess this pathway include : Candida maltosa L4, Candida tropicalis, Cyberlindnera saturnus, Neurospora crassa 15069, Neurospora crassa 33933, Rhizoctonia leguminicola, Saccharomyces cerevisiae, Yarrowia lipolytica

Expected Taxonomic Range: Fungi

At least 9 pathways exist for the degradation of lysine in mammals, plants, bacteria and fungi. The initial products of lysine degradation in these pathways include: L-saccharopine in mammals and plants; β-L-lysine, 5-aminovaleramide, N6-hydroxylysine, cadaverine, and α-aminoadipate-δ-semialdehyde in bacteria; and α-aminoadipate-δ-semialdehyde, D-lysine, N6-acetyl-L-lysine, and 6-amino-2-oxocaproic acid in yeasts and fungi (reviewed in [Zabriskie00]). See MetaCyc pathways L-lysine degradation I to cadaverine, and L-lysine degradation XI (mammalian) via L-saccharopine.

In the fungal pathway shown here, lysine is degraded to glutarate via acetylation of the 6-amino group to the initial product N6-acetyl-L-lysine. This is followed by transamination, oxidative decarboxylation, deacetylation, transamination with loss of the second amino group, and oxidation to glutarate. Glutarate may be metabolized to other carboxylic acids (see below).

Evidence for this pathway was obtained for the fungus Rhizoctonia leguminicola [Guengerich76]. When variously radiolabeled lysine preparations were added to cell-free extracts of Rhizoctonia leguminicola, N6-acetyl-L-lysine was formed. Acetyl-CoA was required and acetyl-phosphate was not utilized. Another experiment using DL-{4,5-3H}lysine showed 5-acetamidovalerate as the major product. If radiolabeled N6-acetyl-L-lysine was used with added α-ketoglutarate, and pyridoxal phosphate, radiolabeled 2-keto-6-acetamidocaproate was produced. α-Ketoglutarate was preferred over pyruvate, and there was little or no dependence on pyridoxal phosphate. If thiamine pyrophosphate and NAD were added to a similar reaction, virtually all of the label was in 5-acetamidovalerate. If labeled 5-acetamidovalerate was used, labeled 5-aminovalerate (5-aminopentanoate) was identified. In addition, whole cell cultures of Rhizoctonia leguminicola incubated with labeled 5-acetamidovalerate accumulated radiolabeled glutarate. Whole cell cultures incubated with radiolabeled glutarate produced a mixture of tricarboxylic acid cycle acids and other carboxylic acids [Guengerich76].

Evidence for this pathway was also obtained in other yeasts and fungi [Guengerich76]. In whole cell cultures, formation of the initial product, N6-acetyl-L-lysine, was demonstrated in the fungus Neurospora crassa 33933, and the yeasts Saccharomyces cerevisiae and Cyberlindnera saturnus (previously known as Hansenula saturnus or Williopsis saturnus) ATCC 2579. In these experiments, whole cell cultures of Rhizoctonia leguminicola, N. crassa, S. cerevisiae and C. saturnus incubated with radiolabeled L-lysine all produced labeled N6-acetyl-L-lysine. Whole cell cultures of N. crassa 33933 and S. cerevisiae incubated with DL-[4,5-3H]lysine were shown to accumulate radiolabeled 5-acetamidovalerate. When N. crassa strains 33933 and 15069, and S. cerevisiae were incubated with DL-[2-14C]lysine, DL-[6-14C]lysine, or DL-[4,5-3H]lysine, radiolabeled 5-aminovalerate (5-aminopentanoate) was shown to accumulate. Species differences in the results, depending upon the radiolabel used, may be attributable to the presence of a racemase and a deacylase in Rhizoctonia leguminicola. These experiments provided evidence for a generalized pathway of lysine degradation in yeasts and fungi [Guengerich76].

Evidence for this acetylation pathway of lysine degradation has also been found in Yarrowia lipolytica (gene LYC1, the structural gene for lysine N6-acetyltransferase) [Beckerich94, Dujon04]; Candida maltosa (lysine N6 acetyltransferase characterization [Schmidt88a], and N6-acetyllysine aminotransferase characterization [Schmidt92]); and Candida tropicalis (evidence for lysine N6 acetyltransferase, N6-acetyllysine aminotransferase, and 5-aminovalerate aminotransferase activities) [Large91]. Earlier evidence for the pathway in Hansenula saturnus has also been described [Rothstein64]. The S. cerevisiae lysine N6-acetyltransferase has been purified and characterized [Bode93].

Superpathways: superpathway of L-lysine degradation

Variants: L-lysine degradation I, L-lysine degradation II (L-pipecolate pathway), L-lysine degradation IV, L-lysine degradation V, L-lysine degradation VI, L-lysine degradation VII, L-lysine degradation VIII, L-lysine degradation IX, L-lysine degradation X, L-lysine degradation XI (mammalian), L-lysine fermentation to acetate and butanoate

Unification Links: KEGG:MAP00310

Created 26-Jan-1999 by Iourovitski I, SRI International
Revised 29-Apr-2005 by Fulcher CA, SRI International


Beckerich94: Beckerich JM, Lambert M, Gaillardin C (1994). "LYC1 is the structural gene for lysine N-6-acetyl transferase in yeast." Curr Genet 25(1);24-9. PMID: 8082161

Bode93: Bode R, Thurau AM, Schmidt H (1993). "Characterization of acetyl-CoA: L-lysine N6-acetyltransferase, which catalyses the first step of carbon catabolism from lysine in Saccharomyces cerevisiae." Arch Microbiol 160(5);397-400. PMID: 8257283

Dujon04: Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004). "Genome evolution in yeasts." Nature 430(6995);35-44. PMID: 15229592

Guengerich76: Guengerich FP, Broquist HP (1976). "Lysine catabolism in Rhizoctonia leguminicola and related fungi." J Bacteriol 126(1);338-47. PMID: 131119

Large91: Large PJ, Robertson A (1991). "The route of lysine breakdown in Candida tropicalis." FEMS Microbiol Lett 66(2);209-13. PMID: 1682209

Rothstein64: Rothstein, M., Hart, J.L. (1964). "Products of lysine metabolism in yeast." Biochim Biophys Acta 93;439-41. PMID: 14251331

Schmidt88a: Schmidt H, Bode R, Birnbaum D (1988). "Lysine degradation in Candida maltosa: occurrence of a novel enzyme, acetyl-CoA:L-lysine N-acetyltransferase." Arch. Microbiol. 150:215-218.

Schmidt92: Schmidt H, Bode R (1992). "Characterization of a novel enzyme, N6-acetyl-L-lysine: 2-oxoglutarate aminotransferase, which catalyses the second step of lysine catabolism in Candida maltosa." Antonie Van Leeuwenhoek 62(4);285-90. PMID: 1285645

Zabriskie00: Zabriskie TM, Jackson MD (2000). "Lysine biosynthesis and metabolism in fungi." Nat Prod Rep 17(1);85-97. PMID: 10714900

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Chang77: Chang YF, Adams E (1977). "Factors influencing growth on L-lysine by Pseudomonas. Regulation of terminal enzymes in the delta-aminovalerate pathway and growth stimulation by alpha ketoglutarate." J Biol Chem 252(22);7987-91. PMID: 914858

EspinosaUrgel01: Espinosa-Urgel M, Ramos JL (2001). "Expression of a Pseudomonas putida aminotransferase involved in lysine catabolism is induced in the rhizosphere." Appl Environ Microbiol 67(11);5219-24. PMID: 11679348

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Rubio06: Rubio S, Larson TR, Gonzalez-Guzman M, Alejandro S, Graham IA, Serrano R, Rodriguez PL (2006). "An Arabidopsis mutant impaired in coenzyme A biosynthesis is sugar dependent for seedling establishment." Plant Physiol 140(3);830-43. PMID: 16415216

Yamanishi07: Yamanishi Y, Mihara H, Osaki M, Muramatsu H, Esaki N, Sato T, Hizukuri Y, Goto S, Kanehisa M (2007). "Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa." FEBS J 274(9);2262-73. PMID: 17388807

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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