MetaCyc Pathway: starch degradation V
Inferred from experiment

Enzyme View:

Pathway diagram: starch degradation V

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 DegradationPolysaccharides DegradationStarch Degradation
Degradation/Utilization/AssimilationPolymeric Compounds DegradationPolysaccharides DegradationStarch Degradation

Some taxa known to possess this pathway include : Pyrococcus furiosus, Pyrococcus furiosus DSM 3638

Expected Taxonomic Range: Archaea

General Background

Many organisms including bacteria, fungi, metazoa, and plants can degrade glucose polymers derived from starch or glycogen (see pathways starch degradation II, starch degradation I, glycogen degradation I and glycogen degradation II). Some hyperthermophilic archaea have also been shown to produce starch-degrading enzymes, and pathways for the utilization of starch and its derivatives, such as a cyclodextrin, a maltodextrin, and maltose have been proposed. These hyperthermophilic archaea can utilize starch and its degradation products as primary carbon sources during anaerobic growth. Thermostable starch-degrading enzymes produced by hyperthermophilic organisms are of industrial interest [Lee06, Hashimoto01, Labes07, Labes01].

Pyrococcus furiosus DSM 3638 was shown to degrade starch mainly via maltodextrins in a pathway involving an extracellular amylopullulanase, a transporter, an intracellular 4-α-glucanotransferase, and a maltodextrin phosphorylase, as described below in About This Pathway ( [Lee06] and in [Labes07]).

The sulfate-reducing archaeon Archaeoglobus fulgidus 7324 has been shown to degrade starch via a unique pathway involving cyclodextrin intermediates [Labes07, Labes01] (see pathway starch degradation III).

In the hyperthermophilic archaeon Thermococcus sp. B1001 evidence suggested a starch degradation pathway via formation of cyclodextrins from starch extracellularly by a cyclomaltodextrin glucanotransferase, transport of cyclodextrins into the cell, and their degradation by a cyclodextrinase to the end products maltose and α-D-glucopyranose ( [Hashimoto01] and in [Labes07]) (see pathway starch degradation IV).

Among bacteria Escherichia coli cannot utilize starch, but it can metabolize short, linear maltodextrins (see pathway glycogen degradation I). However the enterobacterium Klebsiella oxytoca M5al can utilize starch as a sole source of carbon and energy. Mutant analysis suggested that it metabolizes starch by two pathways. The first was a proposed maltose/maltodextrin pathway involving extracellular degradation of starch by pullulanase and the disproportionation activity of cyclodextrin glucanotransferase to form linear maltodextins. After transport into the cell they are degraded to β-D-glucopyranose and α-D-glucopyranose 1-phosphate by the products of malP, malQ and malZ. The second was a proposed cyclodextrin pathway involving extracellular conversion of starch to cyclodextrins (see a cyclodextrin) by cyclodextrin glucanotransferase, transport into the cell, linearization by cyclodextrinase (CymH) [Feederle96], and further catabolism as in the maltose/maltodextrin pathway [Fiedler96, Pajatsch98].

About This Pathway

The hyperthermophilic archaeon Pyrococcus furiosus DSM 3638 is an obligately anaerobic heterotroph that is able to utilize a variety of sugars as a primary carbon source. Its genome encodes many glycosyl hydrolases and transferases, the physiological function of which are unclear. Using global transcriptional profiling data and biochemical studies [Lee06] have defined the pathway for starch metabolism in Pyrococcus furiosus DSM 3638. This pathway involves an amylopullulanase (PF1935*) acting extracellularly, and 4-α-glucanotransferase (PF0272), α-glucan/maltodextrin phosphorylase (maltodextrin phosphorylase) (PF1535) and phosphoglucomutase (PF0588) acting intracellularly. Although other candidates for starch degrading enzymes were annotated in the Pyrococcus furiosus DSM 3638 genome, they did not appear to be functionally involved in starch degradation ( [Lee06] and in [Labes07]).

In this pathway starch is degraded extracellularly by amylopullulanase which has both pullulanase and α-amylase activity. Products of its α-amylase activity include maltodextrins (see a maltodextrin), maltose and D-glucose [Kang05, Dong97]. Two active transporters Mal-II and Mal-I transport maltodextrins and maltose respectively, into the cell [Koning02]. A 4-α-glucanotransferase generates α-D-glucopyranose from maltose and maltodextrins. α-glucan/maltodextrin phosphorylase (maltodextrin phosphorylase) converts maltodextrins to α-D-glucopyranose 1-phosphate [Lee06].

The α-D-glucopyranose and α-D-glucopyranose 1-phosphate produced in the pathway are proposed to enter the novel glycolytic pathway of this organism after conversion of the latter compound to α-D-glucose 6-phosphate by phosphoglucomutase (EC [Lee06]. In aqueous solution the epimers α-D-glucopyranose and β-D-glucopyranose spontaneously interconvert, forming an equilibrium mixture [Franks87]. Likewise, α-D-glucose 6-phosphate exists in equilibrium with its epimer β-D-glucose 6-phosphate. These reactions can also be enzyme-catalyzed. Whether the α, β, or both α and β epimers are used depends upon the anomeric specificity of the enzymes that utilize these compounds.

Variants: starch degradation I, starch degradation II, starch degradation III, starch degradation IV

Created 25-Feb-2011 by Fulcher CA, SRI International


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Ball11: Ball S, Colleoni C, Cenci U, Raj JN, Tirtiaux C (2011). "The evolution of glycogen and starch metabolism in eukaryotes gives molecular clues to understand the establishment of plastid endosymbiosis." J Exp Bot 62(6);1775-801. PMID: 21220783

Buleon98: Buleon A, Colonna P, Planchot V, Ball S (1998). "Starch granules: structure and biosynthesis." Int J Biol Macromol 23(2);85-112. PMID: 9730163

DePinto68: DePinto JA, Campbell LL (1968). "Purification and properties of the amylase of Bacillus macerans." Biochemistry 7(1);114-20. PMID: 5758537

Dong97: Dong G, Vieille C, Zeikus JG (1997). "Cloning, sequencing, and expression of the gene encoding amylopullulanase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme." Appl Environ Microbiol 63(9);3577-84. PMID: 9293009

Feederle96: Feederle R, Pajatsch M, Kremmer E, Bock A (1996). "Metabolism of cyclodextrins by Klebsiella oxytoca m5a1: purification and characterisation of a cytoplasmically located cyclodextrinase." Arch Microbiol 165(3);206-12. PMID: 8599539

Fiedler96: Fiedler G, Pajatsch M, Bock A (1996). "Genetics of a novel starch utilisation pathway present in Klebsiella oxytoca." J Mol Biol 256(2);279-91. PMID: 8594196

Franks87: Franks F. (1987). "Physical chemistry of small carbohydrates-equilibrium solution properties." Pure & Appl. Chem. Vol. 59, No. 9, pp. 1189-1202.

Hashimoto01: Hashimoto Y, Yamamoto T, Fujiwara S, Takagi M, Imanaka T (2001). "Extracellular synthesis, specific recognition, and intracellular degradation of cyclomaltodextrins by the hyperthermophilic archaeon Thermococcus sp. strain B1001." J Bacteriol 183(17);5050-7. PMID: 11489857

Kang05: Kang S, Vieille C, Zeikus JG (2005). "Identification of Pyrococcus furiosus amylopullulanase catalytic residues." Appl Microbiol Biotechnol 66(4);408-13. PMID: 15599521

Koning02: Koning SM, Konings WN, Driessen AJ (2002). "Biochemical evidence for the presence of two alpha-glucoside ABC-transport systems in the hyperthermophilic archaeon Pyrococcus furiosus." Archaea 1(1);19-25. PMID: 15803655

Labes01: Labes A, Schonheit P (2001). "Sugar utilization in the hyperthermophilic, sulfate-reducing archaeon Archaeoglobus fulgidus strain 7324: starch degradation to acetate and CO2 via a modified Embden-Meyerhof pathway and acetyl-CoA synthetase (ADP-forming)." Arch Microbiol 176(5);329-38. PMID: 11702074

Labes07: Labes A, Schonheit P (2007). "Unusual starch degradation pathway via cyclodextrins in the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain 7324." J Bacteriol 189(24);8901-13. PMID: 17921308

Lee06: Lee HS, Shockley KR, Schut GJ, Conners SB, Montero CI, Johnson MR, Chou CJ, Bridger SL, Wigner N, Brehm SD, Jenney FE, Comfort DA, Kelly RM, Adams MW (2006). "Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus." J Bacteriol 188(6);2115-25. PMID: 16513741

Pajatsch98: Pajatsch M, Gerhart M, Peist R, Horlacher R, Boos W, Bock A (1998). "The periplasmic cyclodextrin binding protein CymE from Klebsiella oxytoca and its role in maltodextrin and cyclodextrin transport." J Bacteriol 180(10);2630-5. PMID: 9573146

Shearer02: Shearer J, Graham TE (2002). "New perspectives on the storage and organization of muscle glycogen." Can J Appl Physiol 27(2);179-203. PMID: 12179957

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

Accorsi89: Accorsi A, Piatti E, Piacentini MP, Gini S, Fazi A (1989). "Isoenzymes of phosphoglucomutase from human red blood cells: isolation and kinetic properties." Prep Biochem 19(3);251-71. PMID: 2533352

Boles94: Boles E, Liebetrau W, Hofmann M, Zimmermann FK (1994). "A family of hexosephosphate mutases in Saccharomyces cerevisiae." Eur J Biochem 220(1);83-96. PMID: 8119301

Britton68: Britton HG, Clarke JB (1968). "The mechanism of the phosphoglucomutase reaction. Studies on rabbit muscle phosphoglucomutase with flux techniques." Biochem J 110(2);161-80. PMID: 5726186

Csutora05: Csutora P, Strassz A, Boldizsar F, Nemeth P, Sipos K, Aiello DP, Bedwell DM, Miseta A (2005). "Inhibition of phosphoglucomutase activity by lithium alters cellular calcium homeostasis and signaling in Saccharomyces cerevisiae." Am J Physiol Cell Physiol 289(1);C58-67. PMID: 15703203

Duckworth73: Duckworth HW, Barber BH, Sanwal BD (1973). "The interaction of phosphoglucomutase with nucleotide inhibitors." J Biol Chem 248(4);1431-5. PMID: 4568817

Fu95: Fu L, Bounelis P, Dey N, Browne BL, Marchase RB, Bedwell DM (1995). "The posttranslational modification of phosphoglucomutase is regulated by galactose induction and glucose repression in Saccharomyces cerevisiae." J Bacteriol 177(11);3087-94. PMID: 7768805

Hashimoto67: Hashimoto T, Joshi JC, Del Rio C, Handler P (1967). "Phosphoglucomutase. IV. Inactivation by beryllium ions." J Biol Chem 242(8);1671-9. PMID: 4960829

Imamura01: Imamura H, Fushinobu S, Jeon BS, Wakagi T, Matsuzawa H (2001). "Identification of the catalytic residue of Thermococcus litoralis 4-alpha-glucanotransferase through mechanism-based labeling." Biochemistry 40(41);12400-6. PMID: 11591160

Imamura03: Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, Matsuzawa H (2003). "Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor." J Biol Chem 278(21);19378-86. PMID: 12618437

Jeon97: Jeon BS, Taguchi H, Sakai H, Ohshima T, Wakagi T, Matsuzawa H (1997). "4-alpha-glucanotransferase from the hyperthermophilic archaeon Thermococcus litoralis--enzyme purification and characterization, and gene cloning, sequencing and expression in Escherichia coli." Eur J Biochem 248(1);171-8. PMID: 9310375

Joshi64: Joshi JG, Handler P (1964). "Phosphoglucomutase. I. Purification and properties of phosphoglucomutase from Escherichia coli." J Biol Chem 239;2741-51. PMID: 14216423

Kofler00: Kofler H, Hausler RE, Schulz B, Groner F, Flugge UI, Weber A (2000). "Molecular characterisation of a new mutant allele of the plastid phosphoglucomutase in Arabidopsis, and complementation of the mutant with the wild-type cDNA." Mol Gen Genet 263(6);978-86. PMID: 10954083

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

Lazarevic05: Lazarevic V, Soldo B, Medico N, Pooley H, Bron S, Karamata D (2005). "Bacillus subtilis alpha-phosphoglucomutase is required for normal cell morphology and biofilm formation." Appl Environ Microbiol 71(1);39-45. PMID: 15640167

Masuda01: Masuda CA, Xavier MA, Mattos KA, Galina A, Montero-Lomeli M (2001). "Phosphoglucomutase is an in vivo lithium target in yeast." J Biol Chem 276(41);37794-801. PMID: 11500487

Mizanur08: Mizanur RM, Griffin AK, Pohl NL (2008). "Recombinant production and biochemical characterization of a hyperthermostable alpha-glucan/maltodextrin phosphorylase from Pyrococcus furiosus." Archaea 2(3);169-76. PMID: 19054743

Najjar54: Najjar VA, Pullman ME (1954). "The occurrence of a group transfer involving enzyme (phosphoglucomutase) and substrate." Science 119(3097);631-4. PMID: 13156640

Parche06: Parche S, Beleut M, Rezzonico E, Jacobs D, Arigoni F, Titgemeyer F, Jankovic I (2006). "Lactose-over-glucose preference in Bifidobacterium longum NCC2705: glcP, encoding a glucose transporter, is subject to lactose repression." J Bacteriol 188(4);1260-5. PMID: 16452407

Periappuram00: Periappuram C, Steinhauer L, Barton DL, Taylor DC, Chatson B, Zou J (2000). "The plastidic phosphoglucomutase from Arabidopsis. A reversible enzyme reaction with an important role in metabolic control." Plant Physiol 122(4);1193-9. PMID: 10759515

Qian94: Qian N, Stanley GA, Hahn-Hagerdal B, Radstrom P (1994). "Purification and characterization of two phosphoglucomutases from Lactococcus lactis subsp. lactis and their regulation in maltose- and glucose-utilizing cells." J Bacteriol 176(17);5304-11. PMID: 8071206

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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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