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 [Mojzita10, 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
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
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
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
Mojzita10: 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
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
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
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
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
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
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
Bouvier14a: Bouvier JT, Groninger-Poe FP, Vetting M, Almo SC, Gerlt JA (2014). "Galactaro δ-lactone isomerase: lactone isomerization by a member of the amidohydrolase superfamily." Biochemistry 53(4);614-6. PMID: 24450804
Showing only 20 references. To show more, press the button "Show all references".
©2014 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493