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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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MetaCyc Pathway: Rubisco shunt

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

Superclasses: Generation of Precursor Metabolites and Energy

Some taxa known to possess this pathway include ? : Arabidopsis lyrata , Arabidopsis thaliana col , Arabidopsis thaliana ler , Brassica napus , Ricinus communis , Zea mays

Expected Taxonomic Range: Spermatophyta

Summary:
Oil is a major carbon reserve in most plant seeds. Conversion of carbohydrates to oil generally starts by glycolysis (either mitochondrial or cytosolic). Pyruvate, the end product of glycolysis, is further decarboxylated to acetyl-CoA, the precursor for fatty acid and oil biosynthesis. In the process, one-third of carbon is lost as CO2. An elegant experiment illustrated the existence of a Rubisco shunt [Schwender04]. Comparing to glycolysis, the Rubisco shunt results in an increase of carbon conversion efficiency, yielding 20% more acetyl-CoA with 40% less carbon loss. In oilseed rape, the Rubisco shunt is responsible for the production of 37% -75% of phosphoglycerate in the developing embryo.

There are three stages in the Rubisco shunt.

Stage I is composed of the non-oxidative pentose phosphate pathway (in reverse direction of what is shown in pentose phosphate pathway (non-oxidative branch)), where a series of re-arrangements of the carbon skeleton convert the six-carbon sugar β-D-fructofuranose 6-phosphate to the five-carbon sugar D-ribulose 5-phosphate, which is further converted to D-ribulose-1,5-bisphosphate. The net change is:

5 β-D-fructofuranose 6-phosphate = 6 D-ribulose-1,5-bisphosphate

Stage II is catalyzed by the carboxylase activity of Rubisco, which fixes one molecule of CO2 with one molecule of D-ribulose-1,5-bisphosphate, yielding two molecules three-carbon 3-phospho-D-glycerate. The net change is:

6 D-ribulose-1,5-bisphosphate + 6 CO2 = 12 3-phospho-D-glycerate

In stage III 3-phospho-D-glycerate is converted to pyruvate via the later steps of glycolysis. Pyruvate is further metabolized to acetyl-CoA which fuels fatty acid biosynthesis (fatty acid biosynthesis initiation I) and seed oil (triacylglycerol biosynthesis) accumulation. The net change is:

12 3-phospho-D-glycerate = 12 acetyl-CoA + 12 CO2

Overall, the net carbon stoichiometry via the Rubisco shunt is:

5 β-D-fructofuranose 6-phosphate = 12 acetyl-CoA + 6 CO2

Comparing to glycolysis (5 β-D-fructofuranose 6-phosphate = 10 acetyl-CoA + 10 CO2), the Rubisco shunt allows the conversion of carbohydrate into 20% more acetyl-CoA than glycolysis, and has 40% less carbon loss as CO2.

Note that there is no active Calvin-Benson-Bassham cycle following the Rubisco step in developing seeds. This allows the continuation of Rubisco shunt to stage III.

The whole pathway is located in the plastid.

Credits:
Created 20-Nov-2007 by Zhang P , TAIR


References

Andre07: Andre C, Froehlich JE, Moll MR, Benning C (2007). "A heteromeric plastidic pyruvate kinase complex involved in seed oil biosynthesis in Arabidopsis." Plant Cell 19(6);2006-22. PMID: 17557808

Ruuska04: Ruuska SA, Schwender J, Ohlrogge JB (2004). "The capacity of green oilseeds to utilize photosynthesis to drive biosynthetic processes." Plant Physiol 136(1);2700-9. PMID: 15347783

Schwender04: Schwender J, Goffman F, Ohlrogge JB, Shachar-Hill Y (2004). "Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds." Nature 432(7018);779-82. PMID: 15592419

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

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

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

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

Bowien: Bowien B, editor, Schlegel HG, editor "Autotrophic Bacteria." Science Tech Publishers Madison, WI.

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

Comi01: Comi GP, Fortunato F, Lucchiari S, Bordoni A, Prelle A, Jann S, Keller A, Ciscato P, Galbiati S, Chiveri L, Torrente Y, Scarlato G, Bresolin N (2001). "Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis." Ann Neurol 50(2);202-7. PMID: 11506403

DAlessio71: D'Alessio G, Josse J (1971). "Glyceraldehyde phosphate dehydrogenase, phosphoglycerate kinase, and phosphoglyceromutase of Escherichia coli. Simultaneous purification and physical properties." J Biol Chem 1971;246(13);4319-25. PMID: 4932978

David70: David J, Wiesmeyer H (1970). "Regulation of ribose metabolism in Escherichia coli. II. Evidence for two ribose-5-phosphate isomerase activities." Biochim Biophys Acta 208(1);56-67. PMID: 4909663

Dedonder93: Dedonder A, Rethy R, Fredericq H, Van Montagu M, Krebbers E (1993). "Arabidopsis rbcS genes are differentially regulated by light." Plant Physiol 1993;101(3);801-8. PMID: 8310058

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).

deZwaan72: de Zwaan A (1972). "Pyruvate kinase in muscle extracts of the sea mussel Mytilus edulis L." Comp Biochem Physiol B 42(1);7-14. PMID: 4342452

deZwaan75: de Zwaan A, Holwerda DA, Addink AD (1975). "The influence of divalent cations on allosteric behaviour of muscle pyruvate kinase from the sea mussel Mytilus edulis L." Comp Biochem Physiol B 52(4);469-72. PMID: 1203

Essenberg75a: Essenberg MK, Cooper RA (1975). "Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles." Eur J Biochem 55(2);323-32. PMID: 1104357

Ezaki99: Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T (1999). "Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1." J Biol Chem 274(8);5078-82. PMID: 9988755

Foster10: Foster JM, Davis PJ, Raverdy S, Sibley MH, Raleigh EA, Kumar S, Carlow CK (2010). "Evolution of bacterial phosphoglycerate mutases: non-homologous isofunctional enzymes undergoing gene losses, gains and lateral transfers." PLoS One 5(10);e13576. PMID: 21187861

Fraser99: Fraser HI, Kvaratskhelia M, White MF (1999). "The two analogous phosphoglycerate mutases of Escherichia coli." FEBS Lett 1999;455(3);344-8. PMID: 10437801

Grana89: Grana X, Urena J, Ludevid D, Carreras J, Climent F (1989). "Purification, characterization and immunological properties of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase from maize (Zea mays) seeds." Eur J Biochem 186(1-2);149-53. PMID: 2480892

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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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