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MetaCyc Chimeric Pathway: superpathway of pentose and pentitol degradation

Pathway diagram: superpathway of pentose and pentitol degradation

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

Superclasses: Degradation/Utilization/AssimilationCarbohydrates DegradationSugars Degradation
Degradation/Utilization/AssimilationSecondary Metabolites DegradationSugar Derivatives DegradationSugar Alcohols Degradation

Some taxa known to possess parts of the pathway include : Aspergillus niger, Aspergillus oryzae, Azospirillum brasilense, Caulobacter crescentus CB15, Enterobacter aerogenes, Escherichia coli B, Escherichia coli C, Escherichia coli K-12 substr. MG1655, Haloarcula marismortui, Haloferax volcanii, Herbaspirillum seropedicae, Klebsiella pneumoniae, Morganella morganii, Pelomonas saccharophila, Penicillium chrysogenum, Providencia stuartii, Pseudomonas fluorescens, Serratia marcescens, Sinorhizobium meliloti, Sulfolobus solfataricus, Trichoderma reesei

Expected Taxonomic Range: Archaea, 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 different organisms. Its purpose is to provide an overview of the ways that they degrade pentoses and pentitols.

Pentose sugars and pentitol sugar alcohols can be grouped into several basic catabolic pathways. These pathways are relevant to the degradation of plant material in the environment. Bacteria have been shown to degrade pentoses using isomerases, kinases and epimerases; and pentitols using dehydrogenases and kinases. The L- or D-xylulose 5-phosphate formed is metabolized through the pentose phosphate pathway.

Some bacteria and archaea use an oxidative, nonphosphorylative pathway for pentoses involving dehydrogenases, lactonases and dehydratases, yielding the central metabolite α-ketoglutarate. In some organisms, an aldolase can yield pyruvate and glycolaldehyde, or glycolate (see Summary in L-arabinose degradation III).

Fungi commonly use reductases, dehydrogenases and kinases to metabolize these substrates through D-xylulose 5-phosphate and the pentose phosphate pathway. The fungal D-xylose and L-arabinose degradation pathways join at xylitol [Brouns06] and [deGroot05].

Citations: [Doten85, Reiner75, Charnetzky74, Scangos78, Heuel98, Charnetzky74a, Brunker98, Brunker97 , Brunker98a, Badia91, Sanchez94, Elsinghorst94 , Neidhardt87]

Subpathways: D-arabinose degradation II, xylose degradation I, ribitol degradation, D-arabitol degradation, xylitol degradation, L-lyxose degradation, L-arabinose degradation I, L-arabinose degradation II, L-arabinose degradation III, D-arabinose degradation I, xylose degradation II, D-arabinose degradation III, xylose degradation III, xylose degradation IV, L-arabinose degradation IV

Created 12-Jun-2006 by Fulcher CA, SRI International
Revised 17-Mar-2011 by Fulcher CA, SRI International


Badia91: Badia J, Gimenez R, Baldoma L, Barnes E, Fessner WD, Aguilar J (1991). "L-lyxose metabolism employs the L-rhamnose pathway in mutant cells of Escherichia coli adapted to grow on L-lyxose." J Bacteriol 1991;173(16);5144-50. PMID: 1650346

Brouns06: Brouns SJ, Walther J, Snijders AP, van de Werken HJ, Willemen HL, Worm P, de Vos MG, Andersson A, Lundgren M, Mazon HF, van den Heuvel RH, Nilsson P, Salmon L, de Vos WM, Wright PC, Bernander R, van der Oost J (2006). "Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment." J Biol Chem 281(37);27378-88. PMID: 16849334

Brunker97: Brunker P, Altenbuchner J, Kulbe KD, Mattes R (1997). "Cloning, nucleotide sequence and expression of a mannitol dehydrogenase gene from Pseudomonas fluorescens DSM 50106 in Escherichia coli." Biochim Biophys Acta 1351(1-2);157-67. PMID: 9116029

Brunker98: Brunker P, Altenbuchner J, Mattes R (1998). "Structure and function of the genes involved in mannitol, arabitol and glucitol utilization from Pseudomonas fluorescens DSM50106." Gene 206(1);117-26. PMID: 9461423

Brunker98a: Brunker P, Hils M, Altenbuchner J, Mattes R (1998). "The mannitol utilization genes of Pseudomonas fluorescens are regulated by an activator: cloning, nucleotide sequence and expression of the mtlR gene." Gene 215(1);19-27. PMID: 9666063

Charnetzky74: Charnetzky WT, Mortlock RP (1974). "Ribitol catabolic pathway in Klebsiella aerogenes." J Bacteriol 119(1);162-9. PMID: 4366025

Charnetzky74a: Charnetzky WT, Mortlock RP (1974). "D-Arabitol catabolic pathway in Klebsiella aerogenes." J Bacteriol 119(1);170-5. PMID: 4366026

deGroot05: de Groot MJ, Prathumpai W, Visser J, Ruijter GJ (2005). "Metabolic control analysis of Aspergillus niger L-arabinose catabolism." Biotechnol Prog 21(6);1610-6. PMID: 16321042

Doten85: Doten RC, Mortlock RP (1985). "Inducible xylitol dehydrogenases in enteric bacteria." J Bacteriol 162(2);845-8. PMID: 3886639

Elsinghorst94: Elsinghorst EA, Mortlock RP (1994). "Molecular cloning of the Escherichia coli B L-fucose-D-arabinose gene cluster." J Bacteriol 1994;176(23);7223-32. PMID: 7961494

Heuel98: Heuel H, Shakeri-Garakani A, Turgut S, Lengeler JW (1998). "Genes for D-arabinitol and ribitol catabolism from Klebsiella pneumoniae." Microbiology 144 ( Pt 6);1631-9. PMID: 9639934

Neidhardt87: Neidhardt FC, Ingraham J, Low KB, Magasanik B, Schaechter M, Umbarger HE "Escherichia coli and Salmonella typhimurium, Cellular and Molecular Biology, Volumes 1 & 2." Microbiology, Washington, D.C., 1987.

Reiner75: Reiner AM (1975). "Genes for ribitol and D-arabitol catabolism in Escherichia coli: their loci in C strains and absence in K-12 and B strains." J Bacteriol 123(2);530-6. PMID: 1097416

Sanchez94: Sanchez JC, Gimenez R, Schneider A, Fessner WD, Baldoma L, Aguilar J, Badia J (1994). "Activation of a cryptic gene encoding a kinase for L-xylulose opens a new pathway for the utilization of L-lyxose by Escherichia coli." J Biol Chem 1994;269(47);29665-9. PMID: 7961955

Scangos78: Scangos GA, Reiner AM (1978). "Ribitol and D-arabitol catabolism in Escherichia coli." J Bacteriol 134(2);492-500. PMID: 350825

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

Adams67: Adams E, Rosso G (1967). "Alpha-ketoglutaric semialdehyde dehydrogenase of Pseudomonas. Properties of the purified enzyme induced by hydroxyproline and of the glucarate-induced and constitutive enzymes." J Biol Chem 242(8);1802-14. PMID: 6024771

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

Aguayo13: Aguayo MF, Ampuero D, Mandujano P, Parada R, Munoz R, Gallart M, Altabella T, Cabrera R, Stange C, Handford M (2013). "Sorbitol dehydrogenase is a cytosolic protein required for sorbitol metabolism in Arabidopsis thaliana." Plant Sci 205-206;63-75. PMID: 23498864

Akel09: Akel E, Metz B, Seiboth B, Kubicek CP (2009). "Molecular regulation of arabinan and L-arabinose metabolism in Hypocrea jecorina (Trichoderma reesei)." Eukaryot Cell 8(12);1837-44. PMID: 19801419

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

Alizade76: Alizade MA, Brendel K, Gaede K (1976). "Chirality of xylitol-oxidizing enzymes from mammalian liver." FEBS Lett 67(1);41-4. PMID: 8339

ANALYSISREFEREN: Computational analysis, http://www.arabidopsis.org/servlets/TairObject?type=analysisreference&id=501719615.

Andersson95: Andersson A, Schneider G, Lindqvist Y (1995). "Purification and preliminary X-ray crystallographic studies of recombinant L-ribulose-5-phosphate 4-epimerase from Escherichia coli." Protein Sci 4(8);1648-50. PMID: 8520491

Anstrom03: Anstrom DM, Kallio K, Remington SJ (2003). "Structure of the Escherichia coli malate synthase G:pyruvate:acetyl-coenzyme A abortive ternary complex at 1.95 A resolution." Protein Sci 12(9);1822-32. PMID: 12930982

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

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

Autieri07: Autieri SM, Lins JJ, Leatham MP, Laux DC, Conway T, Cohen PS (2007). "L-fucose stimulates utilization of D-ribose by Escherichia coli MG1655 DeltafucAO and E. coli Nissle 1917 DeltafucAO mutants in the mouse intestine and in M9 minimal medium." Infect Immun 75(11);5465-75. PMID: 17709419

Badia89: Badia J, Baldoma L, Aguilar J, Boronat A (1989). "Identification of the rhaA, rhaB and rhaD gene products from Escherichia coli K-12." FEMS Microbiol Lett 53(3);253-7. PMID: 2558952

Badia98: Badia J, Ibanez E, Sabate M, Baldoma L, Aguilar J (1998). "A rare 920-kilobase chromosomal inversion mediated by IS1 transposition causes constitutive expression of the yiaK-S operon for carbohydrate utilization in Escherichia coli." J Biol Chem 273(14);8376-81. PMID: 9525947

Baldoma87: Baldoma L, Aguilar J (1987). "Involvement of lactaldehyde dehydrogenase in several metabolic pathways of Escherichia coli K12." J Biol Chem 262(29);13991-6. PMID: 3308886

Baldoma88: Baldoma L, Aguilar J (1988). "Metabolism of L-fucose and L-rhamnose in Escherichia coli: aerobic-anaerobic regulation of L-lactaldehyde dissimilation." J Bacteriol 170(1);416-21. PMID: 3275622

Banerjee95: Banerjee S, Anderson F, Farber GK (1995). "The evolution of sugar isomerases." Protein Eng 8(12);1189-95. PMID: 8869631

Batt90: Batt CA, Jamieson AC, Vandeyar MA (1990). "Identification of essential histidine residues in the active site of Escherichia coli xylose (glucose) isomerase." Proc Natl Acad Sci U S A 1990;87(2);618-22. PMID: 2405386

Bhaskar11: Bhaskar V, Kumar M, Manicka S, Tripathi S, Venkatraman A, Krishnaswamy S (2011). "Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis." Proteins 79(4);1132-42. PMID: 21294156

Boronat83: Boronat A, Caballero E, Aguilar J (1983). "Experimental evolution of a metabolic pathway for ethylene glycol utilization by Escherichia coli." J Bacteriol 1983;153(1);134-9. PMID: 6336729

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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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