MetaCyc Pathway: indole-3-acetate biosynthesis II
Inferred from experiment

Pathway diagram: indole-3-acetate biosynthesis II

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: auxin biosynthesis, indole-3-acetic acid biosynthesis, IAA de novo synthesis, IAA biosynthesis II

Superclasses: BiosynthesisHormones BiosynthesisPlant Hormones BiosynthesisAuxins Biosynthesis

Some taxa known to possess this pathway include : Arabidopsis thaliana col, Zea mays

Expected Taxonomic Range: Viridiplantae

The phytohormone family of auxins regulates many plant biological processes including cell division, elongation, differentiation, root initiation, tropic responses, flowering, fruit ripening, and senescence [Woodward05]. Indole-3-acetic acid (IAA) is the most abundant natural plant auxin.

Several tryptophan-dependent pathways have been proposed for the biosynthesis of IAA in plants over the years. While it is now believed that the main pathway consists of only two steps (see indole-3-acetate biosynthesis I), this diagram describes the various other proposals and observations.

In addition, acumulation of IAA in Arabidopsis mutants which have tryptophan synthesis blocked at different steps suggests that IAA can be synthesized by a tryptophan independent route. Indole-3-glycerol phosphate is the branching point of the tryptophan independent route [Normanly93, Ouyang00].

IAA can be conjugated to a number of amino acids and other functional groups (see superpathway of indole-3-acetate conjugate biosynthesis). In some cases, these conjugates can be cleaved to release free IAA as well (see indole-3-acetate activation I and indole-3-acetate activation II).

Some bacterial plant pathogens, such as Agrobacteria, which carry IAA biosynthesis enzymes on the Ti-plasmid, also produce IAA in a different pathway. One such pathway includes the connversion of tryptophan to indoleacetamide (IAM) and then to IAA through the activity of an IAM hydrolase (see indole-3-acetate biosynthesis III (bacteria) and indole-3-acetate biosynthesis IV (bacteria)). Although the full bacterial pathway is not present in plants, IAM and IAM hydrolase activity have been detected in Arabidopsis thaliana and a number of other plant species, including rice, wheat, and pea (see references in [Neu07].

Variants: indole-3-acetate activation I, indole-3-acetate activation II, indole-3-acetate biosynthesis I, indole-3-acetate biosynthesis III (bacteria), indole-3-acetate biosynthesis IV (bacteria), indole-3-acetate biosynthesis V (bacteria and fungi), L-tryptophan degradation VII (via indole-3-pyruvate), methyl indole-3-acetate interconversion

Unification Links: AraCyc:PWY-581, PlantCyc:PWY-581

Revised 17-Aug-2012 by Caspi R, SRI International


Neu07: Neu D, Lehmann T, Elleuche S, Pollmann S (2007). "Arabidopsis amidase 1, a member of the amidase signature family." FEBS J 274(13);3440-51. PMID: 17555521

Normanly93: Normanly J, Cohen JD, Fink GR (1993). "Arabidopsis thaliana auxotrophs reveal a tryptophan-independent biosynthetic pathway for indole-3-acetic acid." Proc Natl Acad Sci U S A 1993;90(21);10355-9. PMID: 8234297

Ouyang00: Ouyang J, Shao X, Li J (2000). "Indole-3-glycerol phosphate, a branchpoint of indole-3-acetic acid biosynthesis from the tryptophan biosynthetic pathway in Arabidopsis thaliana." Plant J 2000;24(3);327-33. PMID: 11069706

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

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

Woodward05: Woodward AW, Bartel B (2005). "Auxin: regulation, action, and interaction." Ann Bot (Lond) 95(5);707-35. PMID: 15749753

Zhao01: Zhao Y, Christensen SK, Fankhauser C, Cashman JR, Cohen JD, Weigel D, Chory J (2001). "A role for flavin monooxygenase-like enzymes in auxin biosynthesis." Science 2001;291(5502);306-9. PMID: 11209081

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

Bertoldi00: Bertoldi M, Borri Voltattorni C (2000). "Reaction of dopa decarboxylase with L-aromatic amino acids under aerobic and anaerobic conditions." Biochem J 352 Pt 2;533-8. PMID: 11085948

Buki85: Buki KG, Vinh DQ, Horvath I (1985). "Partial purification and some properties of tryptophan decarboxylase from a Bacillus strain." Acta Microbiol Hung 32(1);65-73. PMID: 4036551

Burkhard01: Burkhard P, Dominici P, Borri-Voltattorni C, Jansonius JN, Malashkevich VN (2001). "Structural insight into Parkinson's disease treatment from drug-inhibited DOPA decarboxylase." Nat Struct Biol 8(11);963-7. PMID: 11685243

Chourey10: Chourey PS, Li QB, Kumar D (2010). "Sugar-hormone cross-talk in seed development: two redundant pathways of IAA biosynthesis are regulated differentially in the invertase-deficient miniature1 (mn1) seed mutant in maize." Mol Plant 3(6);1026-36. PMID: 20924026

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.

Fernandez89: Fernandez, J.A., Owen, T.G., Kurz, W.G.W., De Luca, V.D. (1989). "Immunological detection and quantitation of tryptophan decarboxylase in developing Catharanthus roseus seedlings." Plant Physiol. 91: 79-84.

Glawischnig04: Glawischnig E, Hansen BG, Olsen CE, Halkier BA (2004). "Camalexin is synthesized from indole-3-acetaldoxime, a key branching point between primary and secondary metabolism in Arabidopsis." Proc Natl Acad Sci U S A 101(21);8245-50. PMID: 15148388

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

Hashimoto91a: Hashimoto Y, Nishiyama M, Ikehata O, Horinouchi S, Beppu T (1991). "Cloning and characterization of an amidase gene from Rhodococcus species N-774 and its expression in Escherichia coli." Biochim Biophys Acta 1088(2);225-33. PMID: 2001397

Hull00: Hull AK, Vij R, Celenza JL (2000). "Arabidopsis cytochrome P450s that catalyze the first step of tryptophan-dependent indole-3-acetic acid biosynthesis." Proc Natl Acad Sci U S A 2000;97(5);2379-84. PMID: 10681464

Ichinose85: Ichinose H, Kojima K, Togari A, Kato Y, Parvez S, Parvez H, Nagatsu T (1985). "Simple purification of aromatic L-amino acid decarboxylase from human pheochromocytoma using high-performance liquid chromatography." Anal Biochem 150(2);408-14. PMID: 4091266

Jin10: Jin JM, Lee S, Lee J, Baek SR, Kim JC, Yun SH, Park SY, Kang S, Lee YW (2010). "Functional characterization and manipulation of the apicidin biosynthetic pathway in Fusarium semitectum." Mol Microbiol 76(2);456-66. PMID: 20233305

Kemper85: Kemper, E., Waffenschmidt, S., Weiler, E. W., Rausch, T., Schroeder, J (1985). "T-DNA coded auxin formation in crown gall cells." Planta 163, 257-262.

Kobayashi95: Kobayashi M, Suzuki T, Fujita T, Masuda M, Shimizu S (1995). "Occurrence of enzymes involved in biosynthesis of indole-3-acetic acid from indole-3-acetonitrile in plant-associated bacteria, Agrobacterium and Rhizobium." Proc Natl Acad Sci U S A 92(3);714-8. PMID: 11607511

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

Kumar63: Kumar, S.A., Mahadevan, S. (1963). "3-indoleacetaldoxime hydro-lyaseE: a pyridoxal-5'-phosphate activated enzyme." Arch Biochem Biophys 103;516-8. PMID: 14099566

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

LopezMeyer97: Lopez-Meyer M, Nessler CL (1997). "Tryptophan decarboxylase is encoded by two autonomously regulated genes in Camptotheca acuminata which are differentially expressed during development and stress." Plant J 11(6);1167-75. PMID: 9225462

Mashiguchi11: Mashiguchi K, Tanaka K, Sakai T, Sugawara S, Kawaide H, Natsume M, Hanada A, Yaeno T, Shirasu K, Yao H, McSteen P, Zhao Y, Hayashi K, Kamiya Y, Kasahara H (2011). "The main auxin biosynthesis pathway in Arabidopsis." Proc Natl Acad Sci U S A 108(45);18512-7. PMID: 22025724

Mikkelsen00: Mikkelsen MD, Hansen CH, Wittstock U, Halkier BA (2000). "Cytochrome P450 CYP79B2 from Arabidopsis catalyzes the conversion of tryptophan to indole-3-acetaldoxime, a precursor of indole glucosinolates and indole-3-acetic acid." J Biol Chem 275(43);33712-7. PMID: 10922360

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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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