MetaCyc Pathway: superpathway of choline biosynthesis

Pathway diagram: superpathway of choline biosynthesis

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

Superclasses: Biosynthesis Fatty Acid and Lipid Biosynthesis

Some taxa known to possess this pathway include ? : Arabidopsis thaliana col , Brassica napus , Glycine max , Pisum sativum , Ricinus communis , Spinacia oleracea

Expected Taxonomic Range: Viridiplantae

Choline is a fundamental metabolite in plants because of its contribution to the synthesis of the membrane phospholipid phosphatidylcholine, which accounts for 40 to 60% of lipids in non-plastid plant membranes [Mou02]. Choline is also a precursor for the formation of glycine betaine (glycine betaine biosynthesis III (plants)) in certain plants such as spinach, where this osmoprotectant is accumulated and confers also tolerance to salinity, drought, and other environmental stresses. In addition choline has been recognized as an essential nutrient for humans [McNeil01].

The choline biosynthetic pathway enables plants to decouple choline synthesis from lipid metabolism (Kennedy pathway - diacylglycerol and triacylglycerol biosynthesis) and provides them with the metabolic flexibility to adapt to environmental conditions where large and variable amounts of choline are beneficial for survival [Rontein01].

The first step in choline biosynthesis is the direct decarboxylation of serine to ethanolamine [Rontein01], which is catalyzed by a serine decarboxylase unique to plants [Rontein03]. Ethanolamine is widely recognized as the entrance compound to choline biosynthesis. The synthesis of choline from ethanolamine may take place at three parallel pathways, where three consecutive N-methylation steps are carried out either on free-bases [Prudhomme92], phospho-bases [Nuccio00], phosphatidyl-bases [McNeil01] or a mixture of the latter [Datko88a] [Datko88].

The biosynthesis of choline appears to be regulated by a feedback response of phosphocholine inhibiting its own synthesis by decreasing N-methyltransferase (PEAMT) activities involved in the pathway [Nuccio00]. The activity of PEAMT was considerably increased when plants were exposed to salt stress [Nuccio00] [Summers93], which is consistent with the high demand for choline as osmoprotectant precursor in such plants.

The release of choline from the different pathway levels is species-specific. Phosphocholine can either be directly dephosphorylated to release choline as observed in spinach [Summers93] or incorporated into phosphatidylcholine with the subsequent release of choline, as in tobacco [McNeil00].

Subpathways: choline biosynthesis I , choline biosynthesis II , choline biosynthesis III

Unification Links: AraCyc:PWY-4762

Created 09-Sep-2005 by Foerster H , TAIR


Datko88: Datko AH, Mudd SH (1988). "Enzymes of phosphatidylcholine synthesis in Lemna, soybean, and carrot." Plant Physiol. 88; 1338-1348.

Datko88a: Datko AH, Mudd SH (1988). "Phosphatidylcholine synthesis. Differing patterns in soybean and carrot." Plant Physiol. 88; 854-861.

McNeil00: McNeil SD, Nuccio ML, Rhodes D, Shachar-Hill Y, Hanson AD (2000). "Radiotracer and computer modeling evidence that phospho-base methylation is the main route of choline synthesis in tobacco." Plant Physiol 123(1);371-80. PMID: 10806254

McNeil01: McNeil SD, Nuccio ML, Ziemak MJ, Hanson AD (2001). "Enhanced synthesis of choline and glycine betaine in transgenic tobacco plants that overexpress phosphoethanolamine N-methyltransferase." Proc Natl Acad Sci U S A 98(17);10001-5. PMID: 11481443

Mou02: Mou Z, Wang X, Fu Z, Dai Y, Han C, Ouyang J, Bao F, Hu Y, Li J (2002). "Silencing of phosphoethanolamine N-methyltransferase results in temperature-sensitive male sterility and salt hypersensitivity in Arabidopsis." Plant Cell 14(9);2031-43. PMID: 12215503

Nuccio00: Nuccio ML, Ziemak MJ, Henry SA, Weretilnyk EA, Hanson AD (2000). "cDNA cloning of phosphoethanolamine N-methyltransferase from spinach by complementation in Schizosaccharomyces pombe and characterization of the recombinant enzyme." J Biol Chem 275(19);14095-101. PMID: 10799484

Prudhomme92: Prud'homme M-P, Moore TS Jr. (1992). "Phosphatidylcholine synthesis in castor bean endosperm. Free bases as intermediates." Plant Physiol. 100; 1527-1535.

Rontein01: Rontein D, Nishida I, Tashiro G, Yoshioka K, Wu WI, Voelker DR, Basset G, Hanson AD (2001). "Plants synthesize ethanolamine by direct decarboxylation of serine using a pyridoxal phosphate enzyme." J Biol Chem 276(38);35523-9. PMID: 11461929

Rontein03: Rontein D, Rhodes D, Hanson AD (2003). "Evidence from engineering that decarboxylation of free serine is the major source of ethanolamine moieties in plants." Plant Cell Physiol 44(11);1185-91. PMID: 14634155

Summers93: Summers PS, Weretilnyk EA (1993). "Choline Synthesis in Spinach in Relation to Salt Stress." Plant Physiol 103(4);1269-1276. PMID: 12232019

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

Bolognese00: Bolognese CP, McGraw P (2000). "The isolation and characterization in yeast of a gene for Arabidopsis S-adenosylmethionine:phospho-ethanolamine N-methyltransferase." Plant Physiol 124(4);1800-13. PMID: 11115895

COMMUNICATION: TIGR Arabidopsis annotation team Communication,

Datko88b: Datko AH, Mudd SH (1988). "Enzymes of Phosphatidylcholine Synthesis in Lemna, Soybean, and Carrot." Plant Physiol 88(4);1338-1348. PMID: 16666464

Dewey94: Dewey RE, Wilson RF, Novitzky WP, Goode JH (1994). "The AAPT1 gene of soybean complements a cholinephosphotransferase-deficient mutant of yeast." Plant Cell 6(10);1495-507. PMID: 7994181

Fan99: Fan L, Zheng S, Cui D, Wang X (1999). "Subcellular distribution and tissue expression of phospholipase Dalpha, Dbeta, and Dgamma in Arabidopsis." Plant Physiol 1999;119(4);1371-8. PMID: 10198096

Friesen01: Friesen JA, Park YS, Kent C (2001). "Purification and kinetic characterization of CTP:phosphocholine cytidylyltransferase from Saccharomyces cerevisiae." Protein Expr Purif 21(1);141-8. PMID: 11162399

Goode99: Goode JH, Dewey RE (1999). "Characterization of aminoalcoholphosphotransferases from Arabidopsis thaliana and soybean." Plant Physiol. Biochem. 37(6): 445-457.

Hanson83: Hanson AD, Rhodes D, (1983) "14C Tracer evidence for synthesis of choline and betaine via phosphoryl base intermediates in salinized sugarbeet leaves." Plant Physiol. (1983), 71, 692-700.

Hanson95: Hanson AD, Rivoal J, Burnet M, Rathinasabapathi B, (1995) "Biosynthesis of quarternary ammonium and tertiary sulphonium compounds in response to water deficit." In: Smirnoff, N (ed.) Environment and plant metabolism. Flexibility and acclimation. Bios Scientific Publishers Ltd. (1995), 189-198 .

Hitz81: Hitz WD, Rhodes D, Hanson AD (1981). "Radiotracer evidence implicating phosphoryl and phosphatidyl bases as intermediates in betaine synthesis by water-stressed barley leaves." Plant Physiol. 68; 814-822.

Hjelmstad91: Hjelmstad RH, Bell RM (1991). "sn-1,2-diacylglycerol choline- and ethanolaminephosphotransferases in Saccharomyces cerevisiae. Mixed micellar analysis of the CPT1 and EPT1 gene products." J Biol Chem 266(7);4357-65. PMID: 1847919

Jones98: Jones PL, Willey DL, Gacesa P, Harwood JL (1998). "Isolation, characterisation and expression of a cDNA for pea cholinephosphate cytidylyltransferase." Plant Mol Biol 37(1);179-85. PMID: 9620275

Kinney87: Kinney AJ, Moore TS Jr., (1987) "Phosphatidylcholine synthesis in castor bean endosperm. I. Metabolism of L-serine." Plant Physiol. (1987) 84, 78-81.

Kinney88: Kinney AJ, Moore TS Jr., (1988) "Phosphatidylcholine synthesis in castor bean endosperm: characteristics and reversibility of the choline kinase reaction." Archives of Biochemistry and Biophysics (1988), 260(1), 102-108.

Kinney93: Kinney AJ (1993). "Phospholipid head groups." In: Moore, TS Jr. (ed.) Lipid metabolism in plants. CRC Press Boca Raton Ann Arbor London Tokyo, 259-284.

Kirk99: Kirk Pappan, Xuemin Wang "Molecular and biochemical properties and physiological roles of plant phospholipase D." Biochimica Biophysica Acta (1999) 1439: 151-166.

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

Macher76: Macher BA, Mudd JB (1976). "Partial purification and properties of ethanolamine kinase from spinach leaf." Arch Biochem Biophys 177(1);24-30. PMID: 187122

Moore83: Moore TS Jr, Price-Jones MJ, Harwood JL, (1983) "The effect of indoleacetic acid on phospholipid metabolism in pea stems." Phytochemistry (1983), 22, 2421-2425.

Mudd89: Mudd SH, Datko AH (1989). "Synthesis of methylated ethanolamine moieties. Regulation by choline in Lemna." Plant Physiol. 90; 296-305.

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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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