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MetaCyc Pathway: superpathway of glucose and xylose degradation
Inferred from experiment

Pathway diagram: superpathway of glucose and xylose degradation

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

Superclasses: Degradation/Utilization/AssimilationCarbohydrates DegradationSugars Degradation

Some taxa known to possess this pathway include : Bacillus coagulans

Expected Taxonomic Range: Bacteria


There is renewed interest in lignocellulosic biomass as a renewable feedstock for the production of ethanol and other chemicals as result of increasing fuel costs and limited resources for fossil fuels [Patel06]. Ethanol production from lignocellulose is not a straightforward process. Cellulose and hemicellulose form a complex with lignin and need to be liberated first by delignification. Cellulose and hemicellulose then need to be depolymerized to release free sugars such as glucose and xylose. These mixed hexose and pentose sugars then require fermentation to produce ethanol [Lee97].

With the release of cellulose and hemicellulose from delignification, low acid concentrations will hydrolyze hemicellulose into monomeric sugars, while fungal cellulases are required to hydrolyze cellulose to glucose in a process called saccharification [Patel]. Fermentation of glucose to ethanol is also carried out by fungal cellulases which function optimally at 50°C and pH 5.0 [Wooley99]. The component pentose sugar of hemicellulose, xylose is not easily converted to ethanol by any organism but can be converted to lactate by lactic acid bacteria using the heterolactic fermentation pathway [Lokman91]. Lactate can be used as a source of lactic acid polymers to create biodegradeable plastics [Patel04]. The conversion of xylose to lactate by lactic acid bacteria has limitations industrially as two of the five carbons in the pentose are converted to acetate [Garde02].

About this Pathway

Bacillus coagulans is a newly identified Gram-positive thermophilic bacterial strain that can grow and ferment at pH 5.0 and temperatures of 60°C, conditions optimal for the hydrolysis of cellulose by fungal cellulases [Patel04]. This strain can convert both glucose and xylose to lactate [Patel06]. The conversion of xylose to lactate in Bacillus coagulans utilizes the pentose phosphate pathway (non-oxidative branch), unlike in other lactic acid bacteria which utilize the heterolactic fermentation pathway [Lokman91].

It should be noted that while Bacillus coagulans is thermophilic, and fungal cellulases function optimally at 50°C, one of the enzymes in this pathway glyceraldehyde-3-phosphate dehydrogenase is thermolabile, and is rendered non-functional at 55°C [Crabb81].

Subpathways: pentose phosphate pathway (oxidative branch), pentose phosphate pathway (non-oxidative branch), pentose phosphate pathway, xylose degradation I

Created 19-Sep-2011 by Weerasinghe D, SRI International


Crabb81: Crabb JW, Murdock AL, Suzuki T, Hamilton JW, McLinden JH, Amelunxen RE (1981). "Sequence homology in the amino-terminal and active-site regions of thermolabile glyceraldehyde-3-phosphate dehydrogenase from a thermophile." J Bacteriol 145(1);503-12. PMID: 7462149

Ewaschuk05: Ewaschuk JB, Naylor JM, Zello GA (2005). "D-lactate in human and ruminant metabolism." J Nutr 135(7);1619-25. PMID: 15987839

Garde02: Garde A, Jonsson G, Schmidt AS, Ahring BK (2002). "Lactic acid production from wheat straw hemicellulose hydrolysate by Lactobacillus pentosus and Lactobacillus brevis." Bioresour Technol 81(3);217-23. PMID: 11800488

Lee97: Lee J (1997). "Biological conversion of lignocellulosic biomass to ethanol." J Biotechnol 56(1);1-24. PMID: 9246788

Lokman91: Lokman BC, van Santen P, Verdoes JC, Kruse J, Leer RJ, Posno M, Pouwels PH (1991). "Organization and characterization of three genes involved in D-xylose catabolism in Lactobacillus pentosus." Mol Gen Genet 230(1-2);161-9. PMID: 1660563

Patel: Patel MA, Ou MS, Ingram LO, Shanmugam KT "Simultaneous saccharification and co-fermentation of crystalline cellulose and sugar cane bagasse hemicellulose hydrolysate to lactate by a thermotolerant acidophilic Bacillus sp." Biotechnol Prog 21(5);1453-60. PMID: 16209550

Patel04: Patel M, Ou M, Ingram LO, Shanmugam KT (2004). "Fermentation of sugar cane bagasse hemicellulose hydrolysate to L(+)-lactic acid by a thermotolerant acidophilic Bacillus sp." Biotechnol Lett 26(11);865-8. PMID: 15269531

Patel06: Patel MA, Ou MS, Harbrucker R, Aldrich HC, Buszko ML, Ingram LO, Shanmugam KT (2006). "Isolation and characterization of acid-tolerant, thermophilic bacteria for effective fermentation of biomass-derived sugars to lactic acid." Appl Environ Microbiol 72(5);3228-35. PMID: 16672461

Wooley99: Wooley R, Ruth M, Glassner D, Sheehan J (1999). "Process Design and Costing of Bioethanol Technology: A Tool for Determining the Status and Direction of Research and Development." Biotechnol Prog 15(5);794-803. PMID: 10514249

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

Abbe83: Abbe K, Takahashi S, Yamada T (1983). "Purification and properties of pyruvate kinase from Streptococcus sanguis and activator specificity of pyruvate kinase from oral streptococci." Infect Immun 39(3);1007-14. PMID: 6840832

Anderson64: Anderson, SR, Florini, JR, Vestling, CS (1964). "Rat liver lactate dehydrogenase. 3. Kinetics and specificity." J Biol Chem 239;2991-7. PMID: 14217887

Ashizawa91: Ashizawa K, McPhie P, Lin KH, Cheng SY (1991). "An in vitro novel mechanism of regulating the activity of pyruvate kinase M2 by thyroid hormone and fructose 1, 6-bisphosphate." Biochemistry 30(29);7105-11. PMID: 1854723

Bairoch93a: Bairoch A, Boeckmann B (1993). "The SWISS-PROT protein sequence data bank, recent developments." Nucleic Acids Res. 21:3093-3096. PMID: 8332529

Banerjee72: Banerjee S, Fraenkel DG (1972). "Glucose-6-phosphate dehydrogenase from Escherichia coli and from a "high-level" mutant." J Bacteriol 110(1);155-60. PMID: 4401601

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

Beaucamp97: Beaucamp N, Hofmann A, Kellerer B, Jaenicke R (1997). "Dissection of the gene of the bifunctional PGK-TIM fusion protein from the hyperthermophilic bacterium Thermotoga maritima: design and characterization of the separate triosephosphate isomerase." Protein Sci 1997;6(10);2159-65. PMID: 9336838

Beaucamp97a: Beaucamp N, Schurig H, Jaenicke R (1997). "The PGK-TIM fusion protein from Thermotoga maritima and its constituent parts are intrinsically stable and fold independently." Biol Chem 1997;378(7);679-85. PMID: 9278147

Beebee82: Beebee TJ, Carty DS (1982). "Purification and radioimmunoassay of rat lactate dehydrogenase A and B subunits." Biochem J 205(2);313-20. PMID: 7138505

Benov99: Benov L, Fridovich I (1999). "Why superoxide imposes an aromatic amino acid auxotrophy on Escherichia coli. The transketolase connection." J Biol Chem 274(7);4202-6. PMID: 9933617

Beutler85: Beutler E, Kuhl W, Gelbart T (1985). "6-Phosphogluconolactonase deficiency, a hereditary erythrocyte enzyme deficiency: possible interaction with glucose-6-phosphate dehydrogenase deficiency." Proc Natl Acad Sci U S A 82(11);3876-8. PMID: 3858849

Boiteux83: Boiteux A, Markus M, Plesser T, Hess B, Malcovati M (1983). "Analysis of progress curves. Interaction of pyruvate kinase from Escherichia coli with fructose 1,6-bisphosphate and calcium ions." Biochem J 1983;211(3);631-40. PMID: 6349612

Botha86: Botha FC, Dennis DT (1986). "Isozymes of phosphoglyceromutase from the developing endosperm of Ricinus communis: isolation and kinetic properties." Arch Biochem Biophys 245(1);96-103. PMID: 3004361

Branny98: Branny P, de la Torre F, Garel JR (1998). "An operon encoding three glycolytic enzymes in Lactobacillus delbrueckii subsp. bulgaricus: glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase and triosephosphate isomerase." Microbiology 144 ( Pt 4);905-14. PMID: 9579064

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Briggs84: Briggs KA, Lancashire WE, Hartley BS (1984). "Molecular cloning, DNA structure and expression of the Escherichia coli D-xylose isomerase." EMBO J 3(3);611-6. PMID: 6325179

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

Bugg91: Bugg TD, Wright GD, Dutka-Malen S, Arthur M, Courvalin P, Walsh CT (1991). "Molecular basis for vancomycin resistance in Enterococcus faecium BM4147: biosynthesis of a depsipeptide peptidoglycan precursor by vancomycin resistance proteins VanH and VanA." Biochemistry 30(43);10408-15. PMID: 1931965

Busto84: Busto F, Soler J, de Arriaga D, Cadenas E (1984). "In situ behaviour of D(-)-lactate dehydrogenase from Escherichia coli." Arch Microbiol 139(2-3);255-9. PMID: 6393891

Chae11: Chae, Lee (2011). "The functional annotation of protein sequences was performed by the in-house Ensemble Enzyme Prediction Pipeline (E2P2, version 1.0). E2P2 systematically integrates results from three molecular function annotation algorithms using an ensemble classification scheme. For a given genome, all protein sequences are submitted as individual queries against the base-level annotation methods. The individual methods rely on homology transfer to annotate protein sequences, using single sequence (BLAST, E-value cutoff <= 1e-30, subset of SwissProt 15.3) and multiple sequence (Priam, November 2010; CatFam, version 2.0, 1% FDR profile library) models of enzymatic functions. The base-level predictions are then integrated into a final set of annotations using an average weighted integration algorithm, where the weight of each prediction from each individual method was determined via a 0.632 bootstrap process over 1000 rounds of testing. The training and testing data for E2P2 and the BLAST reference database were drawn from protein sequences with experimental support of existence, compiled from SwissProt release 15.3."

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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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