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MetaCyc Pathway: choline biosynthesis III
Inferred from experimentTraceable author statement to experimental support

Enzyme View:

Pathway diagram: choline biosynthesis III

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: BiosynthesisFatty Acid and Lipid BiosynthesisCholine Biosynthesis

Some taxa known to possess this pathway include : Arabidopsis thaliana col, Glycine max, Pisum sativum, Ricinus communis

Expected Taxonomic Range: Archaea, Bacteria , Eukaryota

General Background

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].

About This Pathway

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 pathway variant displayed (nucleotide pathway) represents the biosynthetic route as found in diverse plant families. 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 [Datko88c, Datko88b, Hitz81].

The synthesis of intermediates on both the phospho-base and phosphatidyl-base level includes the nucleotide pathway via CDP-phosphoaminoalcohol and the methylation pathway. However, it has been pointed out that the synthesis of phosphatidylethanolamine and phosphatidylcholine is characterized by a high degree of interaction and furcation on the various levels of arising intermediates. Consequently, it has been assumed that the reactions embedded in the nucleotide and methylation pathways may be two characteristics of one overall phosphoaminoalcohol pathway for the formation of phosphatidylcholine in plants [Kinney93].

The release of choline from the different pathway levels is also species-specific. Phosphocholine can either be directly dephosphorylated to release choline as observed in spinach [Summers93a] or incorporated into phosphatidylcholine with the subsequent release of choline, as in tobacco [McNeil00]. The latter reaction has been shown to be specifically catalyzed by phospholipase D ( phospholipases) in castor bean [Wang94]. Although a well-defined physiological role of phospholipase D (PLD) still await further research, progress has been made to assign some members of the heterogeneous family of PLD's to distinct cellular functions [Kirk99]. The remaining enzymes involved in this pathway, phosphoaminoalcohol cytidylyltransferase and CDP-aminoalcohol phosphotransferase, cover a broader spectrum of substrates. This may be beneficial to process the heterogeneous mixture of possible substrates but it also indicates that the pathway flux is probably controlled more upstream [Kinney93].

Superpathways: superpathway of choline biosynthesis

Variants: choline biosynthesis I, choline biosynthesis II

Unification Links: AraCyc:PWY-3561

Created 05-May-2005 by Foerster H, TAIR


Datko88b: Datko AH, Mudd SH (1988). "Enzymes of phosphatidylcholine synthesis in Lemna, soybean, and carrot." Plant Physiol. 88; 1338-1348.

Datko88c: Datko AH, Mudd SH (1988). "Phosphatidylcholine synthesis. Differing patterns in soybean and carrot." Plant Physiol. 88; 854-861.

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.

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.

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

Summers93a: Summers PS, Weretilnyk EA (1993). "Choline Synthesis in Spinach in Relation to Salt Stress." Plant Physiol 103(4);1269-1276. PMID: 12232019

Wang94: Wang X, Xu L, Zheng L (1994). "Cloning and expression of phosphatidylcholine-hydrolyzing phospholipase D from Ricinus communis L." J Biol Chem 269(32);20312-7. PMID: 8051126

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

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.

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

Jones98c: 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

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

Moore83a: 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.

Nishida96: Nishida I, Swinhoe R, Slabas AR, Murata N (1996). "Cloning of Brassica napus CTP: phosphocholine cytidylyltransferase cDNAs by complementation in a yeast cct mutant." Plant Mol Biol 31(2);205-11. PMID: 8756587

Qin02a: Qin C, Wang X (2002). "The Arabidopsis phospholipase D family. Characterization of a calcium-independent and phosphatidylcholine-selective PLD zeta 1 with distinct regulatory domains." Plant Physiol 2002;128(3);1057-68. PMID: 11891260

Slack85: Slack CR, Roughan PG, Browse JA, Gardiner SE (1985). "Some properties of cholinephosphotransferase from developing safflower cotyledons." Biochim. Biophys. Acta 833; 438-448.

Wang01d: Wang C, Wang X (2001). "A novel phospholipase D of Arabidopsis that is activated by oleic acid and associated with the plasma membrane." Plant Physiol 2001;127(3);1102-12. PMID: 11706190

Wang90: Wang X, Moore TS Jr (1990). "Phosphatidylcholine biosynthesis in castor bean endosperm. Purification and properties of cytidine 5'-triphosphate:choline-phosphate cytidylyltransferase." Plant Physiol. 93; 250-255.

Report Errors or Provide Feedback
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 Pathway Tools version 19.5 (software by SRI International) on Wed Jan 2, 2002, biocyc12.