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MetaCyc Chimeric Pathway: superpathway of microbial D-galacturonate and D-glucuronate degradation

Pathway diagram: superpathway of microbial D-galacturonate and D-glucuronate degradation

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

Superclasses: Degradation/Utilization/AssimilationSecondary Metabolites DegradationSugar Derivatives Degradation

Some taxa known to possess parts of the pathway include : Acinetobacter sp. ADP1, Agrobacterium fabrum C58, Agrobacterium tumefaciens, Aquifex aeolicus, Aspergillus nidulans, Aspergillus niger, Bacillus subtilis, Clostridium acetobutylicum, Deinococcus radiodurans, Delftia acidovorans, Dickeya chrysanthemi, Dickeya dadantii 3937, Erwinia chrysanthemi EC16, Escherichia coli K-12 substr. MG1655, Haemophilus influenzae, Pectobacterium carotovorum, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas sp., Pseudomonas syringae, Trichoderma reesei

Expected Taxonomic Range: Bacteria , Fungi

Note: This is a chimeric pathway, comprising reactions from multiple organisms, and typically will not occur in its entirety in a single organism. The taxa listed here are likely to catalyze only subsets of the reactions depicted in this pathway.

Please note: This pathway does not represent a single organism. Rather, it is a superpathway assembled from pathways found in a variety of organisms. Its purpose is to provide an overview of the diversity of ways that microorganisms can degrade D-galacturonate, D-glucuronate and their precursors or derivatives.

Degradation of the pectin metabolite 5-dehydro-4-deoxy-D-glucuronate:

In Dickeya dadantii 3937 (previously known as Erwinia chrysanthemi strain 3937) the main pathway for degradation of the polygalacturonate component of pectin involves production of the monomer 5-dehydro-4-deoxy-D-glucuronate. It is degraded intracellularly by isomerization to 3-deoxy-D-glycero-2,5-hexodiulosonate followed by reduction to the common metabolite 2-dehydro-3-deoxy-D-gluconate. 2-dehydro-3-deoxy-D-gluconate is phosphorylated and then cleaved by an aldolase encoded by gene kdgA which produces the central metabolites D-glyceraldehyde 3-phosphate and pyruvate. In Escherichia coli the aldolase encoded by gene eda is involved in the Entner-Doudoroff pathway I. However, in Dickeya chrysanthemi this enzyme does not appear to be involved in D-gluconate catabolism and no product of the edd gene that encodes the phosphogluconate dehydratase of the Entner-Doudoroff pathway I could be detected in various species of Erwinia. These observations question the existence of the Entner-Doudoroff pathway in these organisms ( [HugouvieuxCotte94] and reviewed in [HugouvieuxCotte96]). See subpathway 4-deoxy-L-threo-hex-4-enopyranuronate degradation.

a β-D-glucuronoside, D-glucuronate and D-galacturonate degradation in Escherichia coli:

In Escherichia coli K-12, degradation of a β-D-glucuronoside begins with hydrolysis to yield D-glucuronate. This compound is isomerized to D-fructuronate and reduced to D-mannonate. Analogous reactions occur in D-galacturonate degradation, forming D-tagaturonate and D-altronate. Dehydration of D-mannonate and D-altronate yields the common metabolite 2-dehydro-3-deoxy-D-gluconate. The product of gene kdgK phosphorylates it to yield 2-dehydro-3-deoxy-D-gluconate 6-phosphate, which enters central metabolism via the Entner-Doudoroff pathway I. See subpathways superpathway of β-D-glucuronide and D-glucuronate degradation and D-galacturonate degradation I.

Oxidative D-glucuronate and D-galacturonate degradation in bacteria:

In the oxidative pathway for D-galacturonate and D-glucuronate degradation found in some bacteria, these compounds are oxidized by an inducible uronate dehydrogenase [Yoon09]. This conversion may occur via a 1.4-lactone [Boer10, Wagner76]. The lactone is thought to spontaneously hydrolyze (in [Mojzita10b, Wagner76, Boer10]). It is not known if the lactone form can be utilized directly by the following enzyme, or if cleavage to the linear acid form is required. The pathway proceeds to 2-oxoglutarate (α-ketoglutarate) formation, which can be metabolized in the TCA cycle I (prokaryotic), or used in many other pathways. Reviewed in [Richard09]. In Acinetobacter sp. ADP1 (previously known as Acinetobacter baylyi ADP1) genes encoding enzymes for the degradation of D-glucarate and galactarate have been identified. Compound intermediates in the pathway were also identified [Aghaie08]. See subpathways D-glucuronate degradation II, D-galacturonate degradation II, D-glucarate degradation II and D-galactarate degradation II.

D-glucarate and galactarate degradation in Escherichia coli:

Escherichia coli can use both D-glucarate and galactarate as the sole source of carbon for growth. The initial step in their degradation is dehydration to 5-dehydro-4-deoxy-D-glucarate. The subsequent steps include cleavage of this compound into pyruvate and tartronate semialdehyde, reduction of tartronate semialdehyde to D-glycerate, and its phosphorylation to form 2-phospho-D-glycerate. See subpathways D-glucarate degradation I and D-galactarate degradation I.

Reductive D-galacturonate degradation in fungi:

In this 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. Reviewed in [Richard09]. See subpathway D-galacturonate degradation III.

Subpathways: 4-deoxy-L-threo-hex-4-enopyranuronate degradation, D-galactarate degradation I, D-glucarate degradation II, D-glucarate degradation I, D-galactarate degradation II, D-glucuronate degradation II, D-galacturonate degradation III, D-galacturonate degradation II, D-galacturonate degradation I, superpathway of β-D-glucuronide and D-glucuronate degradation, β-D-glucuronide and D-glucuronate degradation, D-fructuronate degradation

Created 27-May-2010 by Fulcher CA, SRI International


Aghaie08: Aghaie A, Lechaplais C, Sirven P, Tricot S, Besnard-Gonnet M, Muselet D, de Berardinis V, Kreimeyer A, Gyapay G, Salanoubat M, Perret A (2008). "New insights into the alternative D-glucarate degradation pathway." J Biol Chem 283(23);15638-46. PMID: 18364348

Boer10: Boer H, Maaheimo H, Koivula A, Penttila M, Richard P (2010). "Identification in Agrobacterium tumefaciens of the D-galacturonic acid dehydrogenase gene." Appl Microbiol Biotechnol 86(3);901-9. PMID: 19921179

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

HugouvieuxCotte94: Hugouvieux-Cotte-Pattat N, Robert-Baudouy J (1994). "Molecular analysis of the Erwinia chrysanthemi region containing the kdgA and zwf genes." Mol Microbiol 11(1);67-75. PMID: 8145647

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

Mojzita10b: Mojzita D, Wiebe M, Hilditch S, Boer H, Penttila M, Richard P (2010). "Metabolic engineering of fungal strains for conversion of D-galacturonate to meso-galactarate." Appl Environ Microbiol 76(1);169-75. PMID: 19897761

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

Wagner76: Wagner G, Hollmann S (1976). "Uronic acid dehydrogenase from Pseudomonas syringae. Purification and properties." Eur J Biochem 61(2);589-96. PMID: 2471

Yoon09: Yoon SH, Moon TS, Iranpour P, Lanza AM, Prather KJ (2009). "Cloning and characterization of uronate dehydrogenases from two pseudomonads and Agrobacterium tumefaciens strain C58." J Bacteriol 191(5);1565-73. PMID: 19060141

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

Adams90a: Adams MR, Grubb SM, Hamer A, Clifford MN (1990). "Colorimetric enumeration of Escherichia coli based on beta-glucuronidase activity." Appl Environ Microbiol 56(7);2021-4. PMID: 2202252

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

Aich01: Aich S, Delbaere LT, Chen R (2001). "Expression and purification of Escherichia coli beta-glucuronidase." Protein Expr Purif 22(1);75-81. PMID: 11388802

Akhtar13: Akhtar MK, Turner NJ, Jones PR (2013). "Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities." Proc Natl Acad Sci U S A 110(1);87-92. PMID: 23248280

Andberg12: Andberg M, Maaheimo H, Boer H, Penttila M, Koivula A, Richard P (2012). "Characterization of a novel Agrobacterium tumefaciens galactarolactone cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-deoxy-2-keto-L-threo-hexarate." J Biol Chem 287(21);17662-71. PMID: 22493433

Aradska13: Aradska J, Smidak R, Turkovicova L, Turna J, Lubec G (2013). "Proteomic differences between tellurite-sensitive and tellurite-resistant E.coli." PLoS One 8(11);e78010. PMID: 24244285

Ashwell58: Ashwell A, Wahba AJ, Hickman J (1958). "A new pathway of uronic acid metabolism." Biochim Biophys Acta 30(1);186-7. PMID: 13584413

Ashwell60: Ashwell G, Wahba AJ, Hickman J (1960). "Uronic acid metabolism in bacteria. I. Purification and properties of uronic acid isomerase in Escherichia coli." J Biol Chem. 235:1559-1565. PMID: 13794771

Atsumi10: Atsumi S, Wu TY, Eckl EM, Hawkins SD, Buelter T, Liao JC (2010). "Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes." Appl Microbiol Biotechnol 85(3);651-7. PMID: 19609521

Bartsch08: Bartsch O, Hagemann M, Bauwe H (2008). "Only plant-type (GLYK) glycerate kinases produce d-glycerate 3-phosphate." FEBS Lett 582(20);3025-8. PMID: 18675808

Bateman70: Bateman DF, Kosuge T, Kilgore WW (1970). "Purification and properties of uronate dehydrogenase from Pseudomonas syringae." Arch Biochem Biophys 136(1);97-105. PMID: 4392089

Blackwell99: Blackwell NC, Cullis PM, Cooper RA, Izard T (1999). "Rhombohedral crystals of 2-dehydro-3-deoxygalactarate aldolase from Escherichia coli." Acta Crystallogr D Biol Crystallogr 55(Pt 7);1368-9. PMID: 10393309

Blanco82: Blanco C, Ritzenthaler P, Mata-Gilsinger M (1982). "Cloning and endonuclease restriction analysis of uidA and uidR genes in Escherichia coli K-12: determination of transcription direction for the uidA gene." J Bacteriol 149(2);587-94. PMID: 6276362

Blanco83: Blanco C, Mata-Gilsinger M, Ritzenthaler P (1983). "Construction of hybrid plasmids containing the Escherichia coli uxaB gene: analysis of its regulation and direction of transcription." J Bacteriol 153(2);747-55. PMID: 6296052

Blanco87: Blanco C, Nemoz G (1987). "One step purification of Escherichia coli beta-glucuronidase." Biochimie 69(2);157-61. PMID: 3105604

Blot02: Blot N, Berrier C, Hugouvieux-Cotte-Pattat N, Ghazi A, Condemine G (2002). "The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family." J Biol Chem 277(10);7936-44. PMID: 11773048

BLUMENTHAL63: BLUMENTHAL HJ, FISH DC (1963). "Bacterial conversion of D-glucarate to glycerate and pyruvate." Biochem Biophys Res Commun 11;239-43. PMID: 13971911

Blumenthal64: Blumenthal HJ, Jepson T (1964). "Asymmetric dehydration of galactarate by bacterial galactarate dehydratase." Biochem Biophys Res Commun 1964;17(3);282-7. PMID: 4285952

Blumenthal66: Blumenthal, HJ, Jepson, T "Galactarate Dehydrase." Methods in Enzymology 9:665-669 (1966).

Blumenthal66a: Blumenthal H "D-Glucarate Dehydrase." Meth Enz 1966;9:660-665.

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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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