If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
|Superclasses:||Degradation/Utilization/Assimilation → Secondary Metabolites Degradation → Sugar 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
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.
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.
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.
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
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