MetaCyc Pathway: L-arabinose degradation II
Inferred from experiment

Enzyme View:

Pathway diagram: L-arabinose degradation II

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Degradation/Utilization/AssimilationCarbohydrates DegradationSugars DegradationL-arabinose Degradation

Some taxa known to possess this pathway include : Aspergillus niger, Aspergillus oryzae, Penicillium chrysogenum, Trichoderma reesei

Expected Taxonomic Range: Fungi

General Background

Bacteria and fungi generally utilize L-arabinose derived from plant matter via different pathways. The bacterial pathways are shown in L-arabinose degradation I which involves isomerase, kinase and epimerase steps; and in L-arabinose degradation III which involves oxidative, non-phosphorylative steps. The fungal pathway, which involves oxidation and reduction steps followed by a kinase step, is shown here and in the pathway link. The end product of the phosphorylative pathways is D-xylulose 5-phosphate which enters the non-oxidative pentose phosphate pathway as shown in the pathway link ( [Richard01] and in [Verho04, deGroot05] and reviewed in [Seiboth11]).

L-arabinose is present in plants as arabinan, a polysaccharide constituent of plant cell wall heteropolysaccharides. Fungi such as Aspergillus niger initially degrade arabinan to the pentose sugar L-arabinose using an extracellular arabinanolytic enzyme system. They can then catabolize L-arabinose as a carbon source intracellularly (in [deGroot05]). Expression of the extracellular and intracellular enzymes is specifically and coordinately induced by L-arabinose or L-arabitol (reviewed in [Seiboth11]).

About This Pathway

The initial steps in this pathway involve reduction and oxidation reactions that produce xylitol which is degraded as shown in the pathway link. In the fungi Aspergillus niger and Trichoderma reesei, deletion analysis suggested that the first step may be catalyzed by at least two enzymes. In Aspergillus niger it is catalyzed by a reductase encoded by gene larA that has a preferred specificity for L-arabinose. A candidate for the remaining activity in this organism is D-xylose reductase encoded by gene xyrA (not shown). In Trichoderma reesei the first step appears to be mainly catalyzed by aldose reductase encoded by gene xyl1 which also catalyzes the first step in α-D-xylopyranose catabolism (see pathway xylose degradation II). As shown in pathway xylose degradation II, α-D-xylopyranose is also catabolized by fungi to xylitol. The reduction of L-xylulose to xylitol has been shown to be catalyzed by the product of gene lxrA in Aspergillus niger and by the product of gene lxr3 in Trichoderma reesei, with both enzymes being phylogenetically distinct ( [Mojzita10, Metz13] and in [Seiboth11]). Pathway D-galactose degradation IV shows that some fungi also catabolize the hexose D-galactose to galactitol. Reviewed in [Seiboth11].

Superpathways: superpathway of pentose and pentitol degradation

Variants: L-arabinose degradation I, L-arabinose degradation III, L-arabinose degradation IV

Created 18-May-2007 by Fulcher CA, SRI International
Revised 18-Jan-2011 by Fulcher CA, SRI International


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

Metz13: Metz B, Mojzita D, Herold S, Kubicek CP, Richard P, Seiboth B (2013). "A novel L-xylulose reductase essential for L-arabinose catabolism in Trichoderma reesei." Biochemistry 52(14);2453-60. PMID: 23506391

Mojzita10: Mojzita D, Vuoristo K, Koivistoinen OM, Penttila M, Richard P (2010). "The 'true' L-xylulose reductase of filamentous fungi identified in Aspergillus niger." FEBS Lett 584(16);3540-4. PMID: 20654618

Richard01: Richard P, Londesborough J, Putkonen M, Kalkkinen N, Penttila M (2001). "Cloning and expression of a fungal L-arabinitol 4-dehydrogenase gene." J Biol Chem 276(44);40631-7. PMID: 11514550

Seiboth11: Seiboth B, Metz B (2011). "Fungal arabinan and L: -arabinose metabolism." Appl Microbiol Biotechnol. PMID: 21212945

Verho04: Verho R, Putkonen M, Londesborough J, Penttila M, Richard P (2004). "A novel NADH-linked l-xylulose reductase in the l-arabinose catabolic pathway of yeast." J Biol Chem 279(15);14746-51. PMID: 14736891

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

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

Huang15: Huang H, Carter MS, Vetting MW, Al-Obaidi N, Patskovsky Y, Almo SC, Gerlt JA (2015). "A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis." J Am Chem Soc 137(46);14570-3. PMID: 26560079

Ishikura01: Ishikura S, Isaji T, Usami N, Kitahara K, Nakagawa J, Hara A (2001). "Molecular cloning, expression and tissue distribution of hamster diacetyl reductase. Identity with L-xylulose reductase." Chem Biol Interact 130-132(1-3);879-89. PMID: 11306103

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Martinez08a: Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Barbote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS (2008). "Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)." Nat Biotechnol 26(5);553-60. PMID: 18454138

Mojzita10a: Mojzita D, Penttila M, Richard P (2010). "Identification of an L-arabinose reductase gene in Aspergillus niger and its role in L-arabinose catabolism." J Biol Chem 285(31);23622-8. PMID: 20511228

Nakagawa02a: Nakagawa J, Ishikura S, Asami J, Isaji T, Usami N, Hara A, Sakurai T, Tsuritani K, Oda K, Takahashi M, Yoshimoto M, Otsuka N, Kitamura K (2002). "Molecular characterization of mammalian dicarbonyl/L-xylulose reductase and its localization in kidney." J Biol Chem 277(20);17883-91. PMID: 11882650

Rao06: Rao RS, Jyothi ChP, Prakasham RS, Sarma PN, Rao LV (2006). "Xylitol production from corn fiber and sugarcane bagasse hydrolysates by Candida tropicalis." Bioresour Technol 97(15);1974-8. PMID: 16242318

Seiboth07: Seiboth B, Gamauf C, Pail M, Hartl L, Kubicek CP (2007). "The D-xylose reductase of Hypocrea jecorina is the major aldose reductase in pentose and D-galactose catabolism and necessary for beta-galactosidase and cellulase induction by lactose." Mol Microbiol 66(4);890-900. PMID: 17924946

Witteveen94: Witteveen C. F. B., Weber F., Busink R., Visser J. (1994). "Isolation and characterization of two xylitol dehydrogenases from Aspergillus niger." Microbiology 140, 1679-1685.

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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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