MetaCyc Pathway: benzoate biosynthesis III (CoA-dependent, non-β-oxidative)
Inferred from experiment

Pathway diagram: benzoate biosynthesis III (CoA-dependent, non-beta-oxidative)

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.

Synonyms: benzoic acid biosynthesis, benzoate biosynthesis III (CoA-dependent, β-oxidative-independent)

Superclasses: BiosynthesisSecondary Metabolites BiosynthesisPhenylpropanoid Derivatives BiosynthesisBenzenoids BiosynthesisBenzoate Biosynthesis

Some taxa known to possess this pathway include : Hypericum androsaemum

Expected Taxonomic Range: Viridiplantae

General Background

Benzoate is derived from the phenylpropanoid biosynthesis pathway. A subset of the benzoate-derived compounds, such as phenylethylbenzoate, benzylbenzoate methyl benzoate, are volatile and are often important constituents of floral scents [Boatright04, Azuma02, DAuria02, Negre02]. In addition, salicylic acid (SA) and methylsalicylate (MeSA) contribute significantly to plant defense signaling [Vlot09] and benzoate-derived secondary metabolites, such as xanthones [ElSeedi10, Dharmaratne09], may also help to protect plants from attack [Wildermuth06].

An important step in the creation of these volatile compounds is the shortening of the 3-carbon side-chain present on trans-cinnamic acid. At least three different biosynthetic routes for volatile benzenoid biosynthesis have been proposed and there is evidence that a subset of the different pathways may operate in individual species. For example, Petunia x hybrida has at least two pathways present ( beta-oxidative, CoA-dependent and non-beta-oxidative, non-CoA-dependent), whereas cucumber ( Cucumis sativus) and Nicotiana attenuata seem to lack the "non-oxidative" variant [Jarvis00]. Meanwhile, this pathway, a hybrid between the other two, exists in Hypericum androsaemum.

A greater understanding of the metabolic pathways involved in benzenoid biosynthesis may contribute to genetic engineering efforts aimed at altering floral scents [Pichersky07], modifying SA-based defense responses, or changing the levels of other secondary defense metabolites and pigment compounds, such as xanthones [Abd02], that derive from this pathway.

About This Pathway

In this benzoate biosynthesis variant, the removal of the 2-carbon unit from the side chain is accomplished by adding a water across the double bond in (E)-cinnamoyl-CoA and then removing acetyl-CoA. Thus, this pathway is CoA-dependent but does not involve the other enzymatic steps associated with β-oxidation [Abd02]. Although all enzymatic activities associated with all of the steps in this pathway have been observed experimentally in Hypericum androsaemum, none of the genes encoding the enzymes have been cloned to date [Abd02].

The activity of several enzymes in this pathway appears to be up-regulated by methyl jasmonate and precedes a rise in the production of xanthones, a class of secondary metabolites made in Hypericum androsaemum [Abd02].

Subpathways: trans-cinnamoyl-CoA biosynthesis

Variants: benzoate biosynthesis I (CoA-dependent, β-oxidative), benzoate biosynthesis II (CoA-independent, non-β-oxidative), salicin biosynthesis, salicortin biosynthesis

Unification Links: PlantCyc:PWY-6446

Created 01-Mar-2010 by Dreher KA, TAIR


Abd01: Abd El-Mawla AM, Schmidt W, Beerhues L (2001). "Cinnamic acid is a precursor of benzoic acids in cell cultures of Hypericum androsaemum L. but not in cell cultures of Centaurium erythraea RAFN." Planta 212(2);288-93. PMID: 11216850

Abd02: Abd El-Mawla AM, Beerhues L (2002). "Benzoic acid biosynthesis in cell cultures of Hypericum androsaemum." Planta 214(5);727-33. PMID: 11882941

Azuma02: Azuma H, Toyota M, Asakawa Y, Takaso T, Tobe H (2002). "Floral scent chemistry of mangrove plants." J Plant Res 115(1117);47-53. PMID: 12884048

Boatright04: Boatright J, Negre F, Chen X, Kish CM, Wood B, Peel G, Orlova I, Gang D, Rhodes D, Dudareva N (2004). "Understanding in vivo benzenoid metabolism in petunia petal tissue." Plant Physiol 135(4);1993-2011. PMID: 15286288

DAuria02: D'Auria JC, Chen F, Pichersky E (2002). "Characterization of an acyltransferase capable of synthesizing benzylbenzoate and other volatile esters in flowers and damaged leaves of Clarkia breweri." Plant Physiol 130(1);466-76. PMID: 12226525

Dharmaratne09: Dharmaratne HR, Napagoda MT, Tennakoon SB (2009). "Xanthones from roots of Calophyllum thwaitesii and their bioactivity." Nat Prod Res 23(6);539-45. PMID: 19384730

ElSeedi10: El-Seedi HR, El-Barbary MA, El-Ghorab DM, Bohlin L, Borg-Karlson AK, Goransson U, Verpoorte R (2010). "Recent Insights into the Biosynthesis and Biological Activities of Natural Xanthones." Curr Med Chem. PMID: 20156171

Jarvis00: Jarvis AP, Schaaf O, Oldham NJ (2000). "3-hydroxy-3-phenylpropanoic acid is an intermediate in the biosynthesis of benzoic acid and salicylic acid but benzaldehyde is not." Planta 212(1);119-26. PMID: 11219576

Negre02: Negre F, Kolosova N, Knoll J, Kish CM, Dudareva N (2002). "Novel S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme responsible for biosynthesis of methyl salicylate and methyl benzoate, is not involved in floral scent production in snapdragon flowers." Arch Biochem Biophys 406(2);261-70. PMID: 12361714

Pichersky07: Pichersky E, Dudareva N (2007). "Scent engineering: toward the goal of controlling how flowers smell." Trends Biotechnol 25(3);105-10. PMID: 17234289

Vlot09: Vlot AC, Dempsey DA, Klessig DF (2009). "Salicylic Acid, a multifaceted hormone to combat disease." Annu Rev Phytopathol 47;177-206. PMID: 19400653

Wildermuth06: Wildermuth MC (2006). "Variations on a theme: synthesis and modification of plant benzoic acids." Curr Opin Plant Biol 9(3);288-96. PMID: 16600669

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

Colquhoun12: Colquhoun TA, Marciniak DM, Wedde AE, Kim JY, Schwieterman ML, Levin LA, Van Moerkercke A, Schuurink RC, Clark DG (2012). "A peroxisomally localized acyl-activating enzyme is required for volatile benzenoid formation in a Petuniaxhybrida cv. 'Mitchell Diploid' flower." J Exp Bot 63(13);4821-33. PMID: 22771854

Gaid12: Gaid MM, Sircar D, Muller A, Beuerle T, Liu B, Ernst L, Hansch R, Beerhues L (2012). "Cinnamate:CoA Ligase Initiates the Biosynthesis of a Benzoate-Derived Xanthone Phytoalexin in Hypericum calycinum Cell Cultures." Plant Physiol 160(3);1267-80. PMID: 22992510

Gasson98: Gasson MJ, Kitamura Y, McLauchlan WR, Narbad A, Parr AJ, Parsons EL, Payne J, Rhodes MJ, Walton NJ (1998). "Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester." J Biol Chem 273(7);4163-70. PMID: 9461612

Guranowski10: Guranowski A, Wojdyla AM, Zimny J, Wypijewska A, Kowalska J, Jemielity J, Davis RE, Bieganowski P (2010). "Dual activity of certain HIT-proteins: A. thaliana Hint4 and C. elegans DcpS act on adenosine 5'-phosphosulfate as hydrolases (forming AMP) and as phosphorylases (forming ADP)." FEBS Lett 584(1);93-8. PMID: 19896942

Hegeman66: Hegeman GD (1966). "Synthesis of the enzymes of the mandelate pathway by Pseudomonas putida. I. Synthesis of enzymes by the wild type." J Bacteriol 91(3);1140-54. PMID: 5929747

Ibdah09: Ibdah M, Chen YT, Wilkerson CG, Pichersky E (2009). "An aldehyde oxidase in developing seeds of Arabidopsis converts benzaldehyde to benzoic Acid." Plant Physiol 150(1);416-23. PMID: 19297586

Inoue95: Inoue J, Shaw JP, Rekik M, Harayama S (1995). "Overlapping substrate specificities of benzaldehyde dehydrogenase (the xylC gene product) and 2-hydroxymuconic semialdehyde dehydrogenase (the xylG gene product) encoded by TOL plasmid pWW0 of Pseudomonas putida." J Bacteriol 177(5);1196-201. PMID: 7868591

James98: James KD, Williams PA (1998). "ntn genes determining the early steps in the divergent catabolism of 4-nitrotoluene and toluene in Pseudomonas sp. strain TW3." J Bacteriol 1998;180(8);2043-9. PMID: 9555884

Katsuyama09: Katsuyama Y, Kita T, Funa N, Horinouchi S (2009). "Curcuminoid biosynthesis by two type III polyketide synthases in the herb Curcuma longa." J Biol Chem 284(17);11160-70. PMID: 19258320

Kim01c: Kim SH, Virmani D, Wake K, MacDonald K, Kronstad JW, Ellis BE (2001). "Cloning and disruption of a phenylalanine ammonia-lyase gene from Ustilago maydis." Curr Genet 40(1);40-8. PMID: 11570515

Klempien12: Klempien A, Kaminaga Y, Qualley A, Nagegowda DA, Widhalm JR, Orlova I, Shasany AK, Taguchi G, Kish CM, Cooper BR, D'Auria JC, Rhodes D, Pichersky E, Dudareva N (2012). "Contribution of CoA ligases to benzenoid biosynthesis in petunia flowers." Plant Cell 24(5);2015-30. PMID: 22649270

Koukol61: Koukol, J., Conn, E.E. (1961). "The metabolism of aromatic compounds in higher plants. IV. Purification and properties of the phenylalanine deaminase of Hordeum vulgare." J Biol Chem 236;2692-8. PMID: 14458851

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

Liu06: Liu R, Xu S, Li J, Hu Y, Lin Z (2006). "Expression profile of a PAL gene from Astragalus membranaceus var. Mongholicus and its crucial role in flux into flavonoid biosynthesis." Plant Cell Rep 25(7);705-10. PMID: 16456646

Long09: Long MC, Nagegowda DA, Kaminaga Y, Ho KK, Kish CM, Schnepp J, Sherman D, Weiner H, Rhodes D, Dudareva N (2009). "Involvement of snapdragon benzaldehyde dehydrogenase in benzoic acid biosynthesis." Plant J 59(2);256-65. PMID: 19292760

MacDonald07: MacDonald MJ, D'Cunha GB (2007). "A modern view of phenylalanine ammonia lyase." Biochem Cell Biol 85(3);273-82. PMID: 17612622

Moore02: Moore BS, Hertweck C, Hopke JN, Izumikawa M, Kalaitzis JA, Nilsen G, O'Hare T, Piel J, Shipley PR, Xiang L, Austin MB, Noel JP (2002). "Plant-like biosynthetic pathways in bacteria: from benzoic acid to chalcone." J Nat Prod 65(12);1956-62. PMID: 12502351

Narbad98: Narbad A, Gasson MJ (1998). "Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens." Microbiology 144 ( Pt 5);1397-405. PMID: 9611814

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

Vannelli07: Vannelli T, Wei Qi W, Sweigard J, Gatenby AA, Sariaslani FS (2007). "Production of p-hydroxycinnamic acid from glucose in Saccharomyces cerevisiae and Escherichia coli by expression of heterologous genes from plants and fungi." Metab Eng 9(2);142-51. PMID: 17204442

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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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