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discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Pathway: starch biosynthesis

Note: a dashed line (without arrowheads) between two compound names is meant to imply that the two names are just different instantiations of the same compound -- i.e. one may be a specific name and the other a general name, or they may both represent the same compound in different stages of a polymerization-type pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Biosynthesis Carbohydrates Biosynthesis Polysaccharides Biosynthesis Glucogen and Starch Biosynthesis

Some taxa known to possess this pathway include ? : Arabidopsis thaliana col Inferred from experiment [Delatte05], Chlamydomonas reinhardtii Inferred from experiment [Zabawinski01], Hordeum vulgare Inferred from experiment [Burton02], Manihot esculenta , Nicotiana tabacum , Oryza sativa Inferred from experiment [Kubo99], Pisum sativum , Solanum tuberosum Inferred from experiment [Hussain03], Triticum aestivum , Zea mays Inferred from experiment [James95]

Expected Taxonomic Range: Cyanobacteria , Rhodophyta , Viridiplantae

Summary:
General Background

Starch and glycogen, megadalton-sized glucose polymers, are the major reservoir of readily available energy and carbon compounds in most living organisms, ranging from archaea, eubacteria and yeasts, up to higher eukaryotes including plants and animals [Zeeman10, Santelia11]. Only parasites seem to lack enzymes for the metabolism of these compounds [Henrissat02].

The structure of starch in higher plants differs from that of its counterpart a glycogen in animals and bacteria. Starch is a complex α-glucan that can be very difficult to adequately describe. Starch contains at least two different major sub-classes of α-glucans: amylose and amylopectin. Amylose contains up to several thousand α-glucosyl units linked almost exclusively in α(1->4) linkage with very few branches of α(1->6) linkage. Amylopectin, on the other hand is a much more branched molecule with many α(1->6) linkages and contains up to several million glucosyl residues. At least twelve different types of starch with different branching patterns and chain lengths have been reported [Robyt13]. To further complicate the situation, starch can appears in different crystalline and soluble forms which are difficult to define and depict using standard chemical structures.

It has been reported that cyanobacteria synthesize glycogen while red algae produce floridean-starch with structure that is intermediate between starch and glycogen, and that green algae accumulate amylopectin-like polysaccharides. However, some cyanobacteria have distinct α-polyglucans (which were designated as semi-amylopectin), making them a transition point between glycogen and starch biosynthesis [Nakamura05].

About This Pathway

Starch is synthesized in plastids, including chloroplasts in photosynthetic tissues and amyloplasts in non-photosynthetic tissues such as seeds, roots, and tubers. Starch synthesized in chloroplasts of photosynthetic tissues is degraded to maltose and glucose during the dark period (see starch degradation II). These sugars are exported to the cytosol and used in sucrose synthesis. Sucrose can be readily transported to non-photosynthetic tissues to support plant growth or for starch synthesis in amyloplasts.

The starch biosynthesis pathway depicted here includes both chloroplast and amyloplast pathways. The starting point for the chloroplast pathway is fructose-6-phosphate, a product of photosynthetic carbon fixation. The starting point for amyloplast pathway is glucose-1-phosphate, a product of sucrose degradation. Studies from potato, pea, and maize indicate that glucose-6-phosphate, in addition to glucose-1-phosphate, can be imported into the amyloplast and can serve as the starting point for starch biosynthesis [Tauberger00].

The role of plastidial α-phosphorylase enzymes (2.4.1.1) in starch biosynthesis remain controversial and may differ between species [Streb12, Ball09]. For example, mutations in the PHS1 gene of Arabidopsis have no effect on starch biosynthesis [Zeeman04].

Following the initial production of ADP-α-D-glucose, starch biosynthesis appears to involve reactions catalyzed by at least three classes of enzymes, i.e. starch synthases, starch branching enzymes and starch debranching enzymes [Ball09]. However, the exact steps involved and the order in which they are required for the formation of different types of starch may differ between species and even between different types of cells within the same species [Delatte05].

There is also evidence that Chlamydomonas reinhardtii might involve an additional enzyme in starch biosynthesis, namely, a disproportionating enzyme, DPE1. However the corresponding enzyme, DPE1 in Arabidopsis has been shown to play a part in starch degradation instead [Ball09, Streb12].

Developing a better understanding of starch biosynthesis and its regulation is an active area of research.

Citations: [Dey97a, Cathie95, Hannah08, Wattebled08]

Variants: glycogen biosynthesis I (from ADP-D-Glucose) , glycogen biosynthesis II (from UDP-D-Glucose)

Unification Links: AraCyc:PWY-622 , PlantCyc:PWY-622

Credits:
Revised 15-Mar-2013 by Dreher KA , PMN


References

Ball09: Ball, Steven J., Deschamps, Philippe (2009). "Chapter 1: Starch Metabolism." The Chlamydomonas Sourcebook (Second Edition). Edited by: Elizabeth H. Harris, Ph.D., David B. Stern, Ph.D., and George B. Witman, Ph.D. Volume 2:1-40.

Burton02: Burton RA, Jenner H, Carrangis L, Fahy B, Fincher GB, Hylton C, Laurie DA, Parker M, Waite D, van Wegen S, Verhoeven T, Denyer K (2002). "Starch granule initiation and growth are altered in barley mutants that lack isoamylase activity." Plant J 31(1);97-112. PMID: 12100486

Cathie95: Cathie Martin, Alison M. Smith "Starch synthesis." Plant Cell, 1995, 7:971-985.

Delatte05: Delatte T, Trevisan M, Parker ML, Zeeman SC (2005). "Arabidopsis mutants Atisa1 and Atisa2 have identical phenotypes and lack the same multimeric isoamylase, which influences the branch point distribution of amylopectin during starch synthesis." Plant J 41(6);815-30. PMID: 15743447

Dey97a: Dey, P. M., Harborne, J. B. (1997). "Plant Biochemistry." Academic Press Inc., San Diego, USA.

Hannah08: Hannah LC, James M (2008). "The complexities of starch biosynthesis in cereal endosperms." Curr Opin Biotechnol 19(2);160-5. PMID: 18400487

Henrissat02: Henrissat B, Deleury E, Coutinho PM (2002). "Glycogen metabolism loss: a common marker of parasitic behaviour in bacteria?." Trends Genet 18(9);437-40. PMID: 12175798

Hussain03: Hussain H, Mant A, Seale R, Zeeman S, Hinchliffe E, Edwards A, Hylton C, Bornemann S, Smith AM, Martin C, Bustos R (2003). "Three isoforms of isoamylase contribute different catalytic properties for the debranching of potato glucans." Plant Cell 15(1);133-49. PMID: 12509527

James95: James MG, Robertson DS, Myers AM (1995). "Characterization of the maize gene sugary1, a determinant of starch composition in kernels." Plant Cell 7(4);417-29. PMID: 7773016

Kubo99: Kubo A, Fujita N, Harada K, Matsuda T, Satoh H, Nakamura Y (1999). "The starch-debranching enzymes isoamylase and pullulanase are both involved in amylopectin biosynthesis in rice endosperm." Plant Physiol 121(2);399-410. PMID: 10517831

Mouille96: Mouille G, Maddelein ML, Libessart N, Talaga P, Decq A, Delrue B, Ball S (1996). "Preamylopectin Processing: A Mandatory Step for Starch Biosynthesis in Plants." Plant Cell 8(8);1353-1366. PMID: 12239416

Nakamura05: Nakamura Y, Takahashi J, Sakurai A, Inaba Y, Suzuki E, Nihei S, Fujiwara S, Tsuzuki M, Miyashita H, Ikemoto H, Kawachi M, Sekiguchi H, Kurano N (2005). "Some Cyanobacteria synthesize semi-amylopectin type alpha-polyglucans instead of glycogen." Plant Cell Physiol 46(3);539-45. PMID: 15695453

Robyt13: Robyt, J.F., Mukerjea, R. (2013). "Evolution of the development of how starch is biosynthesized." Starch. 65:8-21.

Santelia11: Santelia D, Zeeman SC (2011). "Progress in Arabidopsis starch research and potential biotechnological applications." Curr Opin Biotechnol 22(2);271-80. PMID: 21185717

Streb12: Streb S, Zeeman SC (2012). "Starch metabolism in Arabidopsis." Arabidopsis Book 10;e0160. PMID: 23393426

Tauberger00: Tauberger E, Fernie AR, Emmermann M, Renz A, Kossmann J, Willmitzer L, Trethewey RN (2000). "Antisense inhibition of plastidial phosphoglucomutase provides compelling evidence that potato tuber amyloplasts import carbon from the cytosol in the form of glucose-6-phosphate." Plant J 2000;23(1);43-53. PMID: 10929100

Wattebled08: Wattebled F, Planchot V, Dong Y, Szydlowski N, Pontoire B, Devin A, Ball S, D'Hulst C (2008). "Further evidence for the mandatory nature of polysaccharide debranching for the aggregation of semicrystalline starch and for overlapping functions of debranching enzymes in Arabidopsis leaves." Plant Physiol 148(3);1309-23. PMID: 18815382

Zabawinski01: Zabawinski C, Van Den Koornhuyse N, D'Hulst C, Schlichting R, Giersch C, Delrue B, Lacroix JM, Preiss J, Ball S (2001). "Starchless mutants of Chlamydomonas reinhardtii lack the small subunit of a heterotetrameric ADP-glucose pyrophosphorylase." J Bacteriol 183(3);1069-77. PMID: 11208806

Zeeman04: Zeeman SC, Thorneycroft D, Schupp N, Chapple A, Weck M, Dunstan H, Haldimann P, Bechtold N, Smith AM, Smith SM (2004). "Plastidial alpha-glucan phosphorylase is not required for starch degradation in Arabidopsis leaves but has a role in the tolerance of abiotic stress." Plant Physiol 135(2);849-58. PMID: 15173560

Zeeman10: Zeeman SC, Kossmann J, Smith AM (2010). "Starch: its metabolism, evolution, and biotechnological modification in plants." Annu Rev Plant Biol 61;209-34. PMID: 20192737

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

Ballicora02: Ballicora MA, Sesma JI, Iglesias AA, Preiss J (2002). "Characterization of chimeric ADPglucose pyrophosphorylases of Escherichia coli and Agrobacterium tumefaciens. Importance of the C-terminus on the selectivity for allosteric regulators." Biochemistry 41(30);9431-7. PMID: 12135365

Ballicora07: Ballicora MA, Erben ED, Yazaki T, Bertolo AL, Demonte AM, Schmidt JR, Aleanzi M, Bejar CM, Figueroa CM, Fusari CM, Iglesias AA, Preiss J (2007). "Identification of regions critically affecting kinetics and allosteric regulation of the Escherichia coli ADP-glucose pyrophosphorylase by modeling and pentapeptide-scanning mutagenesis." J Bacteriol 189(14);5325-33. PMID: 17496097

Baveja86: Baveja UK, Jyoti AS, Kaur M, Agarwal DS, Anand BS, Nanda R (1986). "Isoenzyme studies of Giardia lamblia isolated from symptomatic cases." Aust J Exp Biol Med Sci 64 ( Pt 2);119-26. PMID: 2943257

Bejar06: Bejar CM, Jin X, Ballicora MA, Preiss J (2006). "Molecular architecture of the glucose 1-phosphate site in ADP-glucose pyrophosphorylases." J Biol Chem 281(52);40473-84. PMID: 17079236

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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Buleon97: Buleon A, Gallant DJ, Bouchet B, Mouille G, D'Hulst C, Kossmann J, Ball S (1997). "Starches from A to C. Chlamydomonas reinhardtii as a model microbial system to investigate the biosynthesis of the plant amylopectin crystal." Plant Physiol 115(3);949-57. PMID: 9390431

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."

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

Dauvillee00: Dauvillee D, Mestre V, Colleoni C, Slomianny M, Mouille G, Delrue B, d'Hulst C, Bliard C, Nuzillard J, Ball S (2000). "The debranching enzyme complex missing in glycogen accumulating mutants of Chlamydomonas reinhardtii displays an isoamylase-type specificity." Plant Sci 157(2);145-156. PMID: 10960727

Dauvillee01: Dauvillee D, Colleoni C, Mouille G, Buleon A, Gallant DJ, Bouchet B, Morell MK, d'Hulst C, Myers AM, Ball SG (2001). "Two loci control phytoglycogen production in the monocellular green alga Chlamydomonas reinhardtii." Plant Physiol 125(4);1710-22. PMID: 11299352

Dauvillee01a: Dauvillee D, Colleoni C, Mouille G, Morell MK, d'Hulst C, Wattebled F, Lienard L, Delvalle D, Ral JP, Myers AM, Ball SG (2001). "Biochemical characterization of wild-type and mutant isoamylases of Chlamydomonas reinhardtii supports a function of the multimeric enzyme organization in amylopectin maturation." Plant Physiol 125(4);1723-31. PMID: 11299353

Delatte06: Delatte T, Umhang M, Trevisan M, Eicke S, Thorneycroft D, Smith SM, Zeeman SC (2006). "Evidence for distinct mechanisms of starch granule breakdown in plants." J Biol Chem 281(17);12050-9. PMID: 16495218

Delrue92: Delrue B, Fontaine T, Routier F, Decq A, Wieruszeski JM, Van Den Koornhuyse N, Maddelein ML, Fournet B, Ball S (1992). "Waxy Chlamydomonas reinhardtii: monocellular algal mutants defective in amylose biosynthesis and granule-bound starch synthase activity accumulate a structurally modified amylopectin." J Bacteriol 174(11);3612-20. PMID: 1592815

Delvalle05: Delvalle D, Dumez S, Wattebled F, Roldan I, Planchot V, Berbezy P, Colonna P, Vyas D, Chatterjee M, Ball S, Merida A, D'Hulst C (2005). "Soluble starch synthase I: a major determinant for the synthesis of amylopectin in Arabidopsis thaliana leaves." Plant J 43(3);398-412. PMID: 16045475

DeSantis89: DeSantis D, Tryon VV, Pollack JD "Metabolism of Mollicutes: the Embden-Meyerhof-Parnas Pathway and the Hexose Monophosphate Shunt." J General Microbiology 135:683-691 (1989).

deVries67: de Vries W, Gerbrandy SJ, Stouthamer AH (1967). "Carbohydrate metabolism in Bifidobacterium bifidum." Biochim Biophys Acta 136(3);415-25. PMID: 6048259

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

Dumez06: Dumez S, Wattebled F, Dauvillee D, Delvalle D, Planchot V, Ball SG, D'Hulst C (2006). "Mutants of Arabidopsis lacking starch branching enzyme II substitute plastidial starch synthesis by cytoplasmic maltose accumulation." Plant Cell 18(10);2694-709. PMID: 17028209

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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
Page generated by SRI International Pathway Tools version 18.5 on Thu Nov 27, 2014, biocyc13.