MetaCyc Pathway: L-tryptophan degradation VII (via indole-3-pyruvate)
Inferred from experiment

Enzyme View:

Pathway diagram: L-tryptophan degradation VII (via indole-3-pyruvate)

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: BiosynthesisHormones BiosynthesisPlant Hormones BiosynthesisAuxins Biosynthesis
Degradation/Utilization/AssimilationAmino Acids DegradationProteinogenic Amino Acids DegradationL-tryptophan Degradation

Some taxa known to possess this pathway include : Agrobacterium tumefaciens, Azospirillum brasilense, Azospirillum lipoferum, Azotobacter vinelandii, Bradyrhizobium japonicum, Burkholderia pyrrocinia, Enterobacter cloacae, Escherichia coli K4, Pantoea agglomerans, Pseudomonas chlororaphis chlororaphis, Pseudomonas fluorescens, Sinorhizobium meliloti Rm2011, Sulfolobus tokodaii 7

Expected Taxonomic Range: Proteobacteria, Thermoprotei

The metabolism of tryptophan to indole-3-acetate (indole acetic acid, IAA) via indole-3-pyruvate and indole-3-acetaldehyde has been documented in several nonpathogenic plant-associated bacteria, such as Bradyrhizobium japonicum [Kaneshiro83], Rhizobium leguminosarum [BadenochJones82] and Azotobacter vinlandii [GarciaTabares87], as well as the tumorigenic Agrobacterium tumefaciens [Kaper58], Pseudomonas savastanoi [Kuo73], and Pantoea agglomerans pv. gypsophilae [Manulis91]. In addition, a recent report described the presence of this pathway in the archaeon Sulfolobus sp. strain 7, a hyperthermophilic organism which is not associated with plants.

Initially it was difficult to prove the existence of this pathway, due to low rate of IAA synthesis, and the fact that indole-3-pyruvate is converted to IAA non-enzymatically. However, work done with the organism Enterobacter cloacae, which produces IAA in a higher rate, enabled the elucidation of the pathway and the identification of its components.

The key enzyme of this pathway is indole-3-pyruvate carboxylase (IPDC), as the two other enzymes which participate in this pathway are usually present in most bacteria, including those that cannot produce IAA. Upon expression of the E. cloacae IPDC enzyme in the heterologous hosts Escherichia coli, Enterobacter aerogenes, Pantoea agglomerans, Pseudomonas putida, Pseudomonas fluorescens, and Agrobacterium tumefaciens, all of these organisms were able to convert L-tryptophan to IAA [Koga91, Koga95]. Furthermore, experiments have shown that IPDC is solely responsible for the regulation of this pathway, and that the first enzyme in the pathway, L-tryptophan aminotransferase, operates very close to equilibrium [Koga94].

There has been a report that in certain organisms ( Burkholderia pyrrocinia, formerly known as Pseudomonas pyrrocinia, and Pseudomonas chlororaphis, formerly known as Pseudomonas aureofaciens) the pathway continues further: IAA is metabolized to indole-3-caboxaldehyde, which is converted by dehydrogenation to indole-3-carboxylate. The later undergoes spontaneous decarboxylation into indole [Lubbe83].

Variants: indole-3-acetate activation I, indole-3-acetate activation II, indole-3-acetate biosynthesis I, indole-3-acetate biosynthesis II, indole-3-acetate biosynthesis III (bacteria), indole-3-acetate biosynthesis IV (bacteria), indole-3-acetate biosynthesis V (bacteria and fungi), L-tryptophan degradation I (via anthranilate), L-tryptophan degradation II (via pyruvate), L-tryptophan degradation III (eukaryotic), L-tryptophan degradation IV (via indole-3-lactate), L-tryptophan degradation VIII (to tryptophol), L-tryptophan degradation IX, L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde, L-tryptophan degradation V (side chain pathway), L-tryptophan degradation VI (via tryptamine), L-tryptophan degradation X (mammalian, via tryptamine), L-tryptophan degradation XI (mammalian, via kynurenine), L-tryptophan degradation XII (Geobacillus), methyl indole-3-acetate interconversion

Created 11-Aug-1998 by Ying HC, Marine Biological Laboratory
Revised 18-Apr-2005 by Caspi R, SRI International


BadenochJones82: Badenoch-Jones, J., Summons, R. E., Rolfe, B. G., Parker, C. W., Letham, D. S. (1982). "Mass spectrometric identification of indole compounds produced by Rhizobium strains." Biomed. Mass Spectrom. 9:429-437.

Brandl96: Brandl MT, Lindow SE (1996). "Cloning and characterization of a locus encoding an indolepyruvate decarboxylase involved in indole-3-acetic acid synthesis in Erwinia herbicola." Appl Environ Microbiol 62(11);4121-8. PMID: 8900003

GarciaTabares87: Garcia-Tabares, F., Herraiz-Tomico, T., Amat-Guerri, F., Garcia-Bilbao, J.L. (1987). "Production of 3-IAA and 3-indolelactic acid in Azotobacter vinelandii cultures supplemented with tryptophan." Appl. Microbiol. Biotechnol. 25:502-506.

Kaneshiro83: Kaneshiro, T., Slodki, M. E., Plattner, R. D. (1983). "Tryptophan catabolism to indolepyruvic and indoleacetic acid by Rhizobium japonicum L-259 mutants." Curr. Microbiol. 8:301-306.

Kaper58: Kaper, J. M., Veldstra, H (1958). "On the metabolism of tryptophan by Agrobacterium tumefaciens." Biochim Biophys Acta 30(2);401-20. PMID: 13607457

Koga91: Koga J, Adachi T, Hidaka H (1991). "Molecular cloning of the gene for indolepyruvate decarboxylase from Enterobacter cloacae." Mol Gen Genet 226(1-2);10-6. PMID: 2034209

Koga92: Koga J, Adachi T, Hidaka H (1992). "Purification and characterization of indolepyruvate decarboxylase. A novel enzyme for indole-3-acetic acid biosynthesis in Enterobacter cloacae." J Biol Chem 267(22);15823-8. PMID: 1639814

Koga94: Koga J, Syono K, Ichikawa T, Adachi T (1994). "Involvement of L-tryptophan aminotransferase in indole-3-acetic acid biosynthesis in Enterobacter cloacae." Biochim Biophys Acta 1209(2);241-7. PMID: 7811697

Koga95: Koga J (1995). "Structure and function of indolepyruvate decarboxylase, a key enzyme in indole-3-acetic acid biosynthesis." Biochim Biophys Acta 1249(1);1-13. PMID: 7766676

Kuo73: Kuo, T., Kosuge, T. (1973). "Role of aminotransferase and indole-3-pyruvic acid in the synthesis of indole-3-acetic acid in Pseudomonas savastanoi." J. Gen. Appl. Microbiol. 16:191-204.

Lubbe83: Lubbe C, van Pee KH, Salcher O, Lingens F (1983). "The metabolism of tryptophan and 7-chlorotryptophan in Pseudomonas pyrrocinia and Pseudomonas aureofaciens." Hoppe Seylers Z Physiol Chem 364(4);447-53. PMID: 6862384

Manulis91: Manulis, S., Valinski, L., Gafni, Y. (1991). "Indole-3-acetic acid biosynthetic pathways in Erwinia herbicola in relation to pathogenicity on Gypsophila paniculata." Physiol. Mol. Plant Pathol. 39:161-171.

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

Baca94: Baca, B. E., Soto-Urzua, L., Xochihua-Corona, Y. G., Cuervo-Garcia, A. (1994). "Characterization of two aromatic amino acid aminotransferases and production of indole-3-acetic acid in Azospirillum spp. strains." Soil Biol. Biochem. 26:57-63.

Cooney91: Cooney, T.P., Nonhebel, H.M. (1991). "Biosynthesis of indole-3-acetic acid in tomato shoots: Measurement, mass-spectral identification and incorporation of -2H from -2H2O into indole-3-acetic acid, d- and l-tryptophan, indole-3-pyruvate and tryptamine." Planta. 184 (3): 368-376.

Dickinson03: Dickinson JR, Salgado LE, Hewlins MJ (2003). "The catabolism of amino acids to long chain and complex alcohols in Saccharomyces cerevisiae." J Biol Chem 278(10);8028-34. PMID: 12499363

Gummalla99: Gummalla, S., Broadbent, J. R. (1999). "Tryptophan catabolism by Lactobacillus casei and Lactobacillus helveticus cheese flavor adjuncts." J. Dairy Sci 82:2070-2077.

Koiwai00: Koiwai H, Akaba S, Seo M, Komano T, Koshiba T (2000). "Functional expression of two Arabidopsis aldehyde oxidases in the yeast Pichia pastoris." J Biochem (Tokyo) 2000;127(4);659-64. PMID: 10739959

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

ONeil68: O'Neil SR, DeMoss RD (1968). "Tryptophan transaminase from Clostridium sporogenes." Arch Biochem Biophys 127(1);361-9. PMID: 5697992

Schutz03: Schutz A, Sandalova T, Ricagno S, Hubner G, Konig S, Schneider G (2003). "Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid." Eur J Biochem 270(10);2312-21. PMID: 12752451

Seo00a: Seo M, Koiwai H, Akaba S, Komano T, Oritani T, Kamiya Y, Koshiba T (2000). "Abscisic aldehyde oxidase in leaves of Arabidopsis thaliana." Plant J 23(4);481-8. PMID: 10972874

SotoUrzua96: Soto-Urzua L, Xochinua-Corona YG, Flores-Encarnacion M, Baca BE (1996). "Purification and properties of aromatic amino acid aminotransferases from Azospirillum brasilense UAP 14 strain." Can J Microbiol 42(3);294-8. PMID: 8868238

Stepanova08: Stepanova AN, Robertson-Hoyt J, Yun J, Benavente LM, Xie DY, Dolezal K, Schlereth A, Jurgens G, Alonso JM (2008). "TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development." Cell 133(1);177-91. PMID: 18394997

Tam98: Tam YY, Normanly J (1998). "Determination of indole-3-pyruvic acid levels in Arabidopsis thaliana by gas chromatography-selected ion monitoring-mass spectrometry." J Chromatogr A 800(1);101-8. PMID: 9561757

Tao08: Tao Y, Ferrer JL, Ljung K, Pojer F, Hong F, Long JA, Li L, Moreno JE, Bowman ME, Ivans LJ, Cheng Y, Lim J, Zhao Y, Ballare CL, Sandberg G, Noel JP, Chory J (2008). "Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants." Cell 133(1);164-76. PMID: 18394996

Truelsen72: Truelsen, T.A. (1972). "Indole-3-Pyruvic Acid as an Intermediate in the Conversion of Tryptophan to Indole-3-Acetic Acid. II. Distribution of Tryptophan Transaminase Activity in Plants." Physiologia Plantarum. 28 (1): 67-70.

Urrestarazu98: Urrestarazu A, Vissers S, Iraqui I, Grenson M (1998). "Phenylalanine- and tyrosine-auxotrophic mutants of Saccharomyces cerevisiae impaired in transamination." Mol Gen Genet 257(2);230-7. PMID: 9491082

Wakagi02: Wakagi T, Fukuda E, Ogawa Y, Kino H, Matsuzawa H (2002). "A novel bifunctional molybdo-enzyme catalyzing both decarboxylation of indolepyruvate and oxidation of indoleacetaldehyde from a thermoacidophilic archaeon, Sulfolobus sp. strain 7." FEBS Lett 510(3);196-200. PMID: 11801253

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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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