Subsystem: D-gluconate and ketogluconates metabolism
This subsystem's description is:
The ketogenic properties of a variety of microorganisms have been known for many years and are of industrial importance. For example, 2-keto-L-gulonate is a key intermediate in the industrial biosynthesis of ascorbic acid (vitamin C) by the glucose pathway (Sonoyama et al., 1982, Grindley et al., 1998); and 5-keto-D-gluconate (5-KDG) can be converted to industrially important L-(+)-tartaric acid (Merfort et al., 2006). On the other hand, production of 2,5-DKG by P. citrea appears to be responsible for the dark color characteristic of the pink disease of pineapple (Pujol and Kado, 2000).
Oxidation of D-glucose to the ketogluconates [2-keto-D-gluconate (2-KDG), 5-keto-D-gluconate (5-KDG), and 2,5-diketo-D-gluconate (2,5-DKG)] is mediated by specialized membrane-bound dehydrogenases (consisting of 3 subunits) linked to the cytochrome chain (Pujol, Kado, 2000; Tsuya et al., 2006; Matsushita et al., 2003). An effort has been made in this SS to disambiguate these closely related enzymes via projecting substrate specificity from a few experimentally characterized ones to their orthologs in other organisms using phylogenetic trees. However, the results presented here should be taken very cautiously, since omissions and errors are unavoidable.
The subsequent metabolism of the ketogluconates (some of which can serve as the sole source of carbon and energy for various bacteria) proceeds via convertion to 6-phosphogluconate, which is further metabolized through the Entner-Doudoroff (EDP) and/or Pentose Phosphate pathways (PPP).
Two different metabolic routes from the ketogluconates to 6-PGA have been described. The first, nonphosphorylative pathway, observed for example in Erwinia herbicola, begins with reduction of the ketogluconate by NAD(P)H to gluconate by soluble NAD(P)H-dependent enzymes capable of reducing either 2-KDG, 5-KDG, or 2,5-DKG. This step is followed by phosphorylation to 6-PGA. The second route, present in genera Pseudomonas and Burkholderia (Var.code 4), begins with the phosphorylation of 2-KDG at the 6 position followed by reduction to 6-PGA (this pathway is not included in this Subsystem (SS), see SS: “2-Ketogluconate Utilization” for details.
The first, nonphosphorylative pathway, can proceed either through 2-keto-L-gulonate//L-idonate route, described for example in Erwinia (Truesdell et al., 1991) and E. coli (Bausch et al., 1998); or via broad specificity 2-ketoaldonate reductase, which is able to reduce 2,5-diketo-D-gluconate, 2-keto-D-gluconate and 2-keto-L-gulonate (Yum et al., 1998 , Yum et al., 1999).
Variant codes:
1 = Minimal functional SS variant: organism is capable of uptake (and in some cases of production) of D-gluconate (but not ketogluconates), possessing: (1) Glucose DH (PQQ-dependent), (2) one or more gluconate transporter(s), and (3) gluconokinase (GlcK) or Gluconate dehydratase (GLD), channeling external or internally produced D-gluconate to EDP or PPP pathways. Note, that this variant code is still assigned if either (1) OR (2) is missing (due to the fact that prediction of substrate specificities of these enzymes from genome sequence alone are notoriously unreliable). Hence, false-positive assignments of var.code 1 are more likely than omissions.
1.1 = PPP is utilized for D-gluconate utilization (PglDH is present) via GlcK
1.2 = EDP is utilized for D-gluconate utilization (KDPGA is present) via GlcK
1.3 = both, EDP and PPP are utilized for D-gluconate utilization
1.4 = GlcK is absent, but D-gluconate is utilized via Gluconate dehydratase (GLD) in place of phosphorylation
1.4* = GlcK is absent, but gluconate is likely utilized via Gluconate dehydratase (GLD) in place of phosphorylation, however, a gene for GLD has not been identified in this organisms yet, e.g. Rhodobacter sphaeroides (Szymona, Doudoroff, 1958) or E. coli (Zablotny et al., 1967). Such cases when GLD activity has been demonstrated in an organism (or inferred), but a gene is not known, are common apparently.
3 = in addition to D-gluconate, organism is capable of 2-KDG, and/or 5-KDG, and/or 2,5-DKG production due to predicted presence of specialized membrane-bound dehydrogenases (2KGK is absent). Numbers after the dot have the same meaning as above.
4 = organism is capable of 2-KDG, and/or 5-KDG, and/or 2,5-DKG production due to predicted presence of specialized membrane-bound dehydrogenases; and 2-KDG can be utilized via phosphorylative pathway (2KGK is present)
5 = L-idonate, 5-keto-D-gluconate uptake and catabolism can be asserted
6 = rich variety of several ketogluconate reductases are present, but not L-idonate reductase + 5-keto-D-gluconate pathway
8 = glucose oxidation via 2-KDG, and/or 5-KDG, and/or 2,5-DKG membrane-bound dehydrogenases can be asserted, but ketogluconates produced are apparently excreted since enzymes required for their downstream metabolism via EDP or PPP are missing??
9 = No known glucose DH [NAD(P)H, or PQQ, or 3-subunit FAD-dependent] or gluconate transporter of any kind can be asserted. However, GlcK or GLD are present. The source of D-gluconate (which is apparently being channeling by these enzymes to EDP or PPP pathways) is not clear at the moment. Unidentified D-gluconate transporter or a novel internal source of D-gluconate is present?? Over-annotation of GlcK?? Numbers after the dot have the same meaning as above
-1 = none of ketogluconate dehydrogenases or reductases can be asserted, and both, gluconokinase (GlcK) and gluconate dehydratase (GLD) are absent
References
Bausch C, Peekhaus N, Utz C, Blais T, Murray E, Lowary T, Conway T. Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli. J Bacteriol. 1998 Jul;180(14):3704-10.
Grindley JF, Payton MA, van de Pol, and Hardy KG. 1988. Conversion of Glucose to 2-Keto-L-Gulonate, Intermediate in L-Ascorbate Synthesis, by a Recombinant Strain of Erwinia citreus. Applied Environ. Microbiol., 54(7):1770-1775
Matsushita K et al., 2003. 5-keto-D-gluconate production is catalyzed by a quinoprotein glycerol dehydrogenase, major polyol dehydrogenase, in gluconobacter species. Appl Environ Microbiol. 2003 Apr;69(4):1959-66.
Merfort M, Herrmann U, Bringer-Meyer S, Sahm H. 2006. High-yield 5-keto-D-gluconic acid formation is mediated by soluble and membrane-bound gluconate-5-dehydrogenases of Gluconobacter oxydans. Appl Microbiol Biotechnol, 73(2):443-51.
Porco A, Peekhaus N, Bausch C, Tong S, Isturiz T, Conway T. Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism. J Bacteriol. 1997 Mar;179(5):1584-90.
Pujol C.J. and Kado C.I. 2000. Genetic and Biochemical Characterization of the Pathway in Pantoea citrea Leading to Pink Disease of Pineapple. J.Bact., 182(8): 2230–2237.
Sonoyama T, Tani H, et al., and Mitsushima K. 1982. Production of 2-Keto-l-Gulonic Acid from D-Glucose by Two-Stage Fermentation. Appl Environ Microbiol, 43(5):1064-1069
Szymona, M. and Doudoroff, M. (1958) Carbohydrate metabolism in Rhodopseudomonas sphaeroides. J. Gen. Microbiol. 22, 167–183
Truesdell SJ, Sims JC, Boerman PA, Seymour JL, Lazarus RA. Pathways for metabolism of ketoaldonic acids in an Erwinia sp. J Bacteriol. 1991 Nov;173(21):6651-6.
Tsuya T, Ferri S, Fujikawa M, Yamaoka H, Sode K. 2006. Cloning and functional expression of glucose dehydrogenase complex of Burkholderia cepacia in Escherichia coli. J Biotechnol, 123(2):127-36.
Yum DY, Lee BY, Pan JG. Identification of the yqhE and yafB genes encoding two 2, 5-diketo-D-gluconate reductases in Escherichia coli. Appl Environ Microbiol. 1999 Aug;65(8):3341-6.
For more information, please check out the description and the additional notes tabs, below
| Diagram | Functional Roles | Subsystem Spreadsheet | Description | Scenarios | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The ketogenic properties of a variety of microorganisms have been known for many years and are of industrial importance. For example, 2-keto-L-gulonate is a key intermediate in the industrial biosynthesis of ascorbic acid (vitamin C) by the glucose pathway (Sonoyama et al., 1982, Grindley et al., 1998); and 5-keto-D-gluconate (5-KDG) can be converted to industrially important L-(+)-tartaric acid (Merfort et al., 2006). On the other hand, production of 2,5-DKG by P. citrea appears to be responsible for the dark color characteristic of the pink disease of pineapple (Pujol and Kado, 2000). Oxidation of D-glucose to the ketogluconates [2-keto-D-gluconate (2-KDG), 5-keto-D-gluconate (5-KDG), and 2,5-diketo-D-gluconate (2,5-DKG)] is mediated by specialized membrane-bound dehydrogenases (consisting of 3 subunits) linked to the cytochrome chain (Pujol, Kado, 2000; Tsuya et al., 2006; Matsushita et al., 2003). An effort has been made in this SS to disambiguate these closely related enzymes via projecting substrate specificity from a few experimentally characterized ones to their orthologs in other organisms using phylogenetic trees. However, the results presented here should be taken very cautiously, since omissions and errors are unavoidable. The subsequent metabolism of the ketogluconates (some of which can serve as the sole source of carbon and energy for various bacteria) proceeds via convertion to 6-phosphogluconate, which is further metabolized through the Entner-Doudoroff (EDP) and/or Pentose Phosphate pathways (PPP). Two different metabolic routes from the ketogluconates to 6-PGA have been described. The first, nonphosphorylative pathway, observed for example in Erwinia herbicola, begins with reduction of the ketogluconate by NAD(P)H to gluconate by soluble NAD(P)H-dependent enzymes capable of reducing either 2-KDG, 5-KDG, or 2,5-DKG. This step is followed by phosphorylation to 6-PGA. The second route, present in genera Pseudomonas and Burkholderia (Var.code 4), begins with the phosphorylation of 2-KDG at the 6 position followed by reduction to 6-PGA (this pathway is not included in this Subsystem (SS), see SS: “2-Ketogluconate Utilization” for details. The first, nonphosphorylative pathway, can proceed either through 2-keto-L-gulonate//L-idonate route, described for example in Erwinia (Truesdell et al., 1991) and E. coli (Bausch et al., 1998); or via broad specificity 2-ketoaldonate reductase, which is able to reduce 2,5-diketo-D-gluconate, 2-keto-D-gluconate and 2-keto-L-gulonate (Yum et al., 1998 , Yum et al., 1999). Variant codes: 1 = Minimal functional SS variant: organism is capable of uptake (and in some cases of production) of D-gluconate (but not ketogluconates), possessing: (1) Glucose DH (PQQ-dependent), (2) one or more gluconate transporter(s), and (3) gluconokinase (GlcK) or Gluconate dehydratase (GLD), channeling external or internally produced D-gluconate to EDP or PPP pathways. Note, that this variant code is still assigned if either (1) OR (2) is missing (due to the fact that prediction of substrate specificities of these enzymes from genome sequence alone are notoriously unreliable). Hence, false-positive assignments of var.code 1 are more likely than omissions. 1.1 = PPP is utilized for D-gluconate utilization (PglDH is present) via GlcK 1.2 = EDP is utilized for D-gluconate utilization (KDPGA is present) via GlcK 1.3 = both, EDP and PPP are utilized for D-gluconate utilization 1.4 = GlcK is absent, but D-gluconate is utilized via Gluconate dehydratase (GLD) in place of phosphorylation 1.4* = GlcK is absent, but gluconate is likely utilized via Gluconate dehydratase (GLD) in place of phosphorylation, however, a gene for GLD has not been identified in this organisms yet, e.g. Rhodobacter sphaeroides (Szymona, Doudoroff, 1958) or E. coli (Zablotny et al., 1967). Such cases when GLD activity has been demonstrated in an organism (or inferred), but a gene is not known, are common apparently. 3 = in addition to D-gluconate, organism is capable of 2-KDG, and/or 5-KDG, and/or 2,5-DKG production due to predicted presence of specialized membrane-bound dehydrogenases (2KGK is absent). Numbers after the dot have the same meaning as above. 4 = organism is capable of 2-KDG, and/or 5-KDG, and/or 2,5-DKG production due to predicted presence of specialized membrane-bound dehydrogenases; and 2-KDG can be utilized via phosphorylative pathway (2KGK is present) 5 = L-idonate, 5-keto-D-gluconate uptake and catabolism can be asserted 6 = rich variety of several ketogluconate reductases are present, but not L-idonate reductase + 5-keto-D-gluconate pathway 8 = glucose oxidation via 2-KDG, and/or 5-KDG, and/or 2,5-DKG membrane-bound dehydrogenases can be asserted, but ketogluconates produced are apparently excreted since enzymes required for their downstream metabolism via EDP or PPP are missing?? 9 = No known glucose DH [NAD(P)H, or PQQ, or 3-subunit FAD-dependent] or gluconate transporter of any kind can be asserted. However, GlcK or GLD are present. The source of D-gluconate (which is apparently being channeling by these enzymes to EDP or PPP pathways) is not clear at the moment. Unidentified D-gluconate transporter or a novel internal source of D-gluconate is present?? Over-annotation of GlcK?? Numbers after the dot have the same meaning as above -1 = none of ketogluconate dehydrogenases or reductases can be asserted, and both, gluconokinase (GlcK) and gluconate dehydratase (GLD) are absent References Bausch C, Peekhaus N, Utz C, Blais T, Murray E, Lowary T, Conway T. Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L-idonic acid catabolism in Escherichia coli. J Bacteriol. 1998 Jul;180(14):3704-10. Grindley JF, Payton MA, van de Pol, and Hardy KG. 1988. Conversion of Glucose to 2-Keto-L-Gulonate, Intermediate in L-Ascorbate Synthesis, by a Recombinant Strain of Erwinia citreus. Applied Environ. Microbiol., 54(7):1770-1775 Matsushita K et al., 2003. 5-keto-D-gluconate production is catalyzed by a quinoprotein glycerol dehydrogenase, major polyol dehydrogenase, in gluconobacter species. Appl Environ Microbiol. 2003 Apr;69(4):1959-66. Merfort M, Herrmann U, Bringer-Meyer S, Sahm H. 2006. High-yield 5-keto-D-gluconic acid formation is mediated by soluble and membrane-bound gluconate-5-dehydrogenases of Gluconobacter oxydans. Appl Microbiol Biotechnol, 73(2):443-51. Porco A, Peekhaus N, Bausch C, Tong S, Isturiz T, Conway T. Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism. J Bacteriol. 1997 Mar;179(5):1584-90. Pujol C.J. and Kado C.I. 2000. Genetic and Biochemical Characterization of the Pathway in Pantoea citrea Leading to Pink Disease of Pineapple. J.Bact., 182(8): 2230–2237. Sonoyama T, Tani H, et al., and Mitsushima K. 1982. Production of 2-Keto-l-Gulonic Acid from D-Glucose by Two-Stage Fermentation. Appl Environ Microbiol, 43(5):1064-1069 Szymona, M. and Doudoroff, M. (1958) Carbohydrate metabolism in Rhodopseudomonas sphaeroides. J. Gen. Microbiol. 22, 167–183 Truesdell SJ, Sims JC, Boerman PA, Seymour JL, Lazarus RA. Pathways for metabolism of ketoaldonic acids in an Erwinia sp. J Bacteriol. 1991 Nov;173(21):6651-6. Tsuya T, Ferri S, Fujikawa M, Yamaoka H, Sode K. 2006. Cloning and functional expression of glucose dehydrogenase complex of Burkholderia cepacia in Escherichia coli. J Biotechnol, 123(2):127-36. Yum DY, Lee BY, Pan JG. Identification of the yqhE and yafB genes encoding two 2, 5-diketo-D-gluconate reductases in Escherichia coli. Appl Environ Microbiol. 1999 Aug;65(8):3341-6. Currently selected organism: Anabaena variabilis ATCC 29413 (open scenarios overview page for organism)
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
