MetaCyc Pathway: D-galacturonate degradation III
Inferred from experimentTraceable author statement to experimental support

Enzyme View:

Pathway diagram: D-galacturonate 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/AssimilationCarboxylates DegradationSugar Acids DegradationD-Galacturonate Degradation
Degradation/Utilization/AssimilationSecondary Metabolites DegradationSugar Derivatives DegradationSugar Acids DegradationD-Galacturonate Degradation

Some taxa known to possess this pathway include : Aspergillus nidulans, Aspergillus niger, Trichoderma reesei

Expected Taxonomic Range: Fungi

General Background

The uronic acid D-galacturonate is an aldose sugar containing a carboxyl group. It is the main monomeric constituent of pectin (see a pectin), a heteropolymer present the cell walls of dicotyledonous plants. In pectin the D-galacturonate monomers are in the α-pyranose form connected through a 1,4 linkage to form long chains. Homogalacturonan (see a homogalacturonan) is the simplest form of pectin. Other forms are rhamnogalacturonan-I, rhamnogalacturonan-II and xylogalacturonan (see a xylogalacturonan) (see pathways homogalacturonan degradation homogalacturonan biosynthesis xylogalacturonan biosynthesis). In natural pectin the majority of the carboxyl groups of D-galacturonate are methyl esters. Some plants also contain acetylated galacturonate residues. Non-esterified carboxyl groups may be linked through divalent cations such as Mg2+ or Ca2+, causing pectin to form a gel.

The complete biodegradation of pectin requires a variety of enzymes including hydrolases for polygalacturonan, rhamnogalacturonans and xylogalacturonan; lyases for pectin, pectate (see a pectate) and rhamnogalacturonan; and pectin methylesterases and acetyl esterases. Saprophytic and phytopathogenic fungi and bacteria can produce variety of extracellular and intracellular enzymes that degrade pectin and its homogalacturonan, rhamnogalacturonan and xylogalacturonan derivatives. In [MartensUzunova09] and reviewed in [Richard09, Reginault08, HugouvieuxCotte96].

Pectin is used in the animal feed industry and in the food industry as a gelling agent. In ruminants, bacterial and fungal enzymes in the digestive tract aid its digestion. There is commercial interest in pectin-degrading enzymes to convert the pectin-rich by-products from citrus peel and sugar beet processing to higher value material. Pectinolytic enzymes such as esterases, hydrolases and lyases, are also used in other industries that require the processing of pectin. Reviewed in [Richard09].

D-galacturonate is an important carbon source for microorganisms that catabolize plant material. Bacterial pathways for D-galacturonate degradation have been described. Escherichia coli uses the isomerase pathway (see D-galacturonate degradation I). Agrobacterium tumefaciens and Delftia acidovorans use an oxidative pathway (see D-galacturonate degradation II). A different pathway for D-galacturonate degradation has been described for eukaryotic filamentous fungi which appears to be evolutionarily conserved in the fungal subphylum Pezizomycotina which includes Aspergillus niger, Emericella nidulans (previously known as Aspergillus nidulans) and Trichoderma reesei. In [MartensUzunova08] and reviewed in [Richard09] (this pathway).

About This Pathway

In this fungal pathway the degradation of D-galacturonate occurs via L-compounds [MartensUzunova08]. The first step is reductive. In Aspergillus niger a reversible reaction catalyzed by a reductase that can utilize NADH or NADPH converts D-galacturonate to aldehydo-L-galactonate. This reductase is the product of gene GAAA in Aspergillus niger, with an ortholog GAR2 in Trichoderma reesei. It is co-expressed in Aspergillus niger along with GAAB encoding a L-galactonate dehydratase, and GAAC and GAAD encoding the putative aldolase and L-glyceraldehyde reductase, respectively. These genes are evolutionarily conserved in pectin-degrading filamentous fungi [MartensUzunova08]. However, a previously identified enzyme encoded by GAR1 in Trichoderma reesei that only uses NADPH may also participate this pathway [Kuorelahti05]. It showed no nucleotide sequence similarity with GAAA [MartensUzunova08].

The second step is a dehydration, followed by a reversible aldolase splitting of 2-dehydro-3-deoxy-L-galactonate to produce L-glyceraldehyde and pyruvate. pyruvate is utilized in many pathways. L-glyceraldehyde is reduced to glycerol, which can be catabolized as indicated in the pathway link [Hondmann91]. In Trichoderma reesei the product of gene gld1 was shown to catalyze this reaction and was NADPH-specific making it a likely candidate for this pathway. Overall, it appears that the two physiologically unidirectional enzymes drive the pathway forward. Reviewed in [Richard09].

Superpathways: superpathway of microbial D-galacturonate and D-glucuronate degradation

Variants: D-galacturonate degradation I, D-galacturonate degradation II

Created 13-Apr-2010 by Fulcher CA, SRI International


Abbott08: Abbott DW, Boraston AB (2008). "Structural biology of pectin degradation by Enterobacteriaceae." Microbiol Mol Biol Rev 72(2);301-16, table of contents. PMID: 18535148

Caffall09: Caffall KH, Mohnen D (2009). "The structure, function, and biosynthesis of plant cell wall pectic polysaccharides." Carbohydr Res 344(14);1879-900. PMID: 19616198

Hondmann91: Hondmann DH, Busink R, Witteveen CF, Visser J (1991). "Glycerol catabolism in Aspergillus nidulans." J Gen Microbiol 137(3);629-36. PMID: 2033381

HugouvieuxCotte96: Hugouvieux-Cotte-Pattat N, Condemine G, Nasser W, Reverchon S (1996). "Regulation of pectinolysis in Erwinia chrysanthemi." Annu Rev Microbiol 50;213-57. PMID: 8905080

Kuorelahti05: Kuorelahti S, Kalkkinen N, Penttila M, Londesborough J, Richard P (2005). "Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase." Biochemistry 44(33);11234-40. PMID: 16101307

MartensUzunova08: Martens-Uzunova ES, Schaap PJ (2008). "An evolutionary conserved d-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation." Fungal Genet Biol 45(11);1449-57. PMID: 18768163

MartensUzunova09: Martens-Uzunova ES, Schaap PJ (2009). "Assessment of the pectin degrading enzyme network of Aspergillus niger by functional genomics." Fungal Genet Biol 46 Suppl 1;S170-S179. PMID: 19618506

Reginault08: Reginault, Ph., Valette-Collet , O., Boccara, M. (2008). "The importance of fungal pectinolytic enzymes in plant invasion, host adaptability and symptom type." Eur. J. Plant Pathol.

Richard09: Richard P, Hilditch S (2009). "D-galacturonic acid catabolism in microorganisms and its biotechnological relevance." Appl Microbiol Biotechnol 82(4);597-604. PMID: 19159926

Zandleven07: Zandleven J, Sorensen SO, Harholt J, Beldman G, Schols HA, Scheller HV, Voragen AJ (2007). "Xylogalacturonan exists in cell walls from various tissues of Arabidopsis thaliana." Phytochemistry 68(8);1219-26. PMID: 17336350

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

Agius03: Agius F, Gonzalez-Lamothe R, Caballero JL, Munoz-Blanco J, Botella MA, Valpuesta V (2003). "Engineering increased vitamin C levels in plants by overexpression of a D-galacturonic acid reductase." Nat Biotechnol 21(2);177-81. PMID: 12524550

Hilditch07: Hilditch S, Berghall S, Kalkkinen N, Penttila M, Richard P (2007). "The missing link in the fungal D-galacturonate pathway: identification of the L-threo-3-deoxy-hexulosonate aldolase." J Biol Chem 282(36);26195-201. PMID: 17609199

Ishikawa06: Ishikawa T, Masumoto I, Iwasa N, Nishikawa H, Sawa Y, Shibata H, Nakamura A, Yabuta Y, Shigeoka S (2006). "Functional characterization of D-galacturonic acid reductase, a key enzyme of the ascorbate biosynthesis pathway, from Euglena gracilis." Biosci Biotechnol Biochem 70(11);2720-6. PMID: 17090924

Kuorelahti06: Kuorelahti S, Jouhten P, Maaheimo H, Penttila M, Richard P (2006). "L-galactonate dehydratase is part of the fungal path for D-galacturonic acid catabolism." Mol Microbiol 61(4);1060-8. PMID: 16879654

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

Liepins06: Liepins J, Kuorelahti S, Penttila M, Richard P (2006). "Enzymes for the NADPH-dependent reduction of dihydroxyacetone and D-glyceraldehyde and L-glyceraldehyde in the mould Hypocrea jecorina." FEBS J 273(18);4229-35. PMID: 16930134

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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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