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MetaCyc Pathway: sphingolipid biosynthesis (plants)

Pathway diagram: sphingolipid biosynthesis (plants)

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

Synonyms: ceramide biosynthesis (plants)

Superclasses: Biosynthesis Fatty Acid and Lipid Biosynthesis Sphingolipid Biosynthesis

Some taxa known to possess this pathway include ? : Aquilegia vulgaris , Arabidopsis thaliana col , Cucurbita pepo Early Prolific Straightneck , Gossypium arboreum , Phaseolus vulgaris , Solanum lycopersicum , Zea mays

Expected Taxonomic Range: Viridiplantae

Summary:
General Background

Sphingolipids are ubiquitous components of eukaryotic cells. They are composed of a long-chain base (amino alcohol), an amide linked fatty acyl chain, and a polar head. The predominant long-chain bases in plants are C18 amino alcohols, with sphinganine, 4-hydroxysphinganine, and 4-hydroxy-8-sphingenine being the prevalent long-chain bases. Whilst, the prevalent long-chain bases of many mammalian sphingolipids, sphingosine (4-sphingenine), is found only in trace amounts in plants. The predominant fatty acyl chains in plants are alpha-hydroxy fatty acids, with saturated C22 to C26 hydroxy fatty acyl chains, especially 2-hydroxylignoceric acid, are the most common ones. Ceramide (without a polar head group), glucosylceramide, and derivatives of inositolphosphorylceramide are the predominant plant sphingolipids. Sphingomyelin, which has phosphocholine as the polar head group and is the major phosphosphingolipid in animals, has not been detected in plants. On the other hand, yeast contains exclusively inositolphosphorylceramides.

Species- and tissue-specific diversity of the long-chain base and fatty acyl chain exists in plant glucosylceramides. In general, seed glucosylceramides are enriched with dihydroxy long-chain bases and C16 to C20 saturated hydroxy fatty acids. In contrast, leaves are enriched with trihydroxy long-chain bases and very long-chain (C20 to C26) saturated and monoenoic hydroxy fatty acids. Monoenoic hydroxyl fatty acids are predominantly found in glucosylceramides from cold hardy crops and Arabidopsis.

It is estimated that sphingolipids account for up to 10% of total lipids in plants. Glucosylceramide is the major sphingolipid. It is a significant lipid component of the plant cell plasma and tonoplast. While our knowledge of sphingolipid functions are mainly learned from studies in mammals and yeast, plant sphingolipids are thought to serve as membrane structural components and signal molecules.

About This Pathway

Two mechanisms were shown for ceramide formation via condensation of a fatty acyl group with the amino group of a long chain base. One utilizes acyl-CoAs and is catalyzed by sphinganine N-acyltransferase, the other uses free fatty acids by ceramide synthase. The sphinganine N-acyltransferase route is most likely the major route in plants. The relative activity of sphinganine N-acyltransferase using acyl-CoA of varying chain length from 16 to 24 carbons parallel the distribution of fatty acyl chains in glucosylceramides from different plant sources [Lynch00]. It suggests that sphinganine N-acyltransferase plays a key role in determining the respective acyl chain composition of naturally occurring plant glucosylceramides.

Although hydroxylation of the long chain base can occur with free sphinganine, hydroxylation and desaturation of long chain bases, as well as alpha-hydroxylation of fatty acyl chains, occur primarily after the formation of ceramides.

Citations: [Lynch04]

Variants: ceramide de novo biosynthesis , ceramide phosphoethanolamine biosynthesis , sphingolipid biosynthesis (mammals) , sphingolipid biosynthesis (yeast)

Unification Links: AraCyc:PWY-5129

Credits:
Revised 24-Mar-2010 by Zhang P


References

Lynch00: Lynch, Daniel V (2000). "Enzymes of sphingolipid metabolism in plants." Methods in enzymology, 311:130-149.

Lynch04: Lynch, Daniel V, Dunn, Teresa M (2004). "An introduction to plant sphingolipids and a review of recent advances in understanding their metabolism and function." New Phytologist, 161:677-702.

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

Beeler98: Beeler T, Bacikova D, Gable K, Hopkins L, Johnson C, Slife H, Dunn T (1998). "The Saccharomyces cerevisiae TSC10/YBR265w gene encoding 3-ketosphinganine reductase is identified in a screen for temperature-sensitive suppressors of the Ca2+-sensitive csg2Delta mutant." J Biol Chem 273(46);30688-94. PMID: 9804843

Bromley03: Bromley, Pamela E, Li, Yuneng, Murphy, Shawn M, Sumner, Catherine, Lynch, Daniel V (2003). "Complex sphingolipid synthesis in plants: characterization of inositolphosphorylceramide synthase activity in bean microsomes." Archives of Biochemistry and Biophysics, 417:219-226.

Chao11: Chao DY, Gable K, Chen M, Baxter I, Dietrich CR, Cahoon EB, Guerinot ML, Lahner B, Lu S, Markham JE, Morrissey J, Han G, Gupta SD, Harmon JM, Jaworski JG, Dunn TM, Salt DE (2011). "Sphingolipids in the root play an important role in regulating the leaf ionome in Arabidopsis thaliana." Plant Cell 23(3);1061-81. PMID: 21421810

Chen09a: Chen, M., Saucedo-Garcia, M., Plasencia, J., Gavilanes-Ruiz, M., Cahoon, E.B. (2009). "Plant Sphingolipids: Structure, Synthesis and Function. ." In Lipids in Photosynthesis: Essential and Regulatory Functions (Wada, H. and Murata, N., eds). New York: Springer Science, pp. 77-115.

Chen12a: Chen M, Markham JE, Cahoon EB (2012). "Sphingolipid Δ8 unsaturation is important for glucosylceramide biosynthesis and low-temperature performance in Arabidopsis." Plant J 69(5);769-81. PMID: 22023480

Gable02: Gable K, Han G, Monaghan E, Bacikova D, Natarajan M, Williams R, Dunn TM (2002). "Mutations in the yeast LCB1 and LCB2 genes, including those corresponding to the hereditary sensory neuropathy type I mutations, dominantly inactivate serine palmitoyltransferase." J Biol Chem 277(12);10194-200. PMID: 11781309

Grilley00: Grilley MM, Takemoto JY (2000). "Assay of the Saccharomyces cerevisiae dihydrosphingosine C-4 hydroxylase." Methods Enzymol 311;9-14. PMID: 10563305

Grilley98: Grilley MM, Stock SD, Dickson RC, Lester RL, Takemoto JY (1998). "Syringomycin action gene SYR2 is essential for sphingolipid 4-hydroxylation in Saccharomyces cerevisiae." J Biol Chem 273(18);11062-8. PMID: 9556590

Haak97: Haak D, Gable K, Beeler T, Dunn T (1997). "Hydroxylation of Saccharomyces cerevisiae ceramides requires Sur2p and Scs7p." J Biol Chem 272(47);29704-10. PMID: 9368039

Hillig03: Hillig, Inga, Leipelt, Martina, Ott, Claudia, Zahringer, Ulrich, Warnecke, Dirk, Heinz, Ernst (2003). "Formation of glucosylceramide and sterol glucoside by a UDP-glucose-dependent glucosylceramide synthase from cotton expressed in Pichia pastoris." FEBS Letters, 553:365-369.

Kihara04: Kihara A, Igarashi Y (2004). "FVT-1 is a mammalian 3-ketodihydrosphingosine reductase with an active site that faces the cytosolic side of the endoplasmic reticulum membrane." J Biol Chem 279(47);49243-50. PMID: 15328338

Kim10e: Kim SK, Noh YH, Koo JR, Yun HS (2010). "Effect of expression of genes in the sphingolipid synthesis pathway on the biosynthesis of ceramide in Saccharomyces cerevisiae." J Microbiol Biotechnol 20(2);356-62. PMID: 20208441

Kwalombota02: Kwalombota M (2002). "The effect of pregnancy in HIV-infected women." AIDS Care 14(3);431-3. PMID: 12042089

Lahner03: Lahner B, Gong J, Mahmoudian M, Smith EL, Abid KB, Rogers EE, Guerinot ML, Harper JF, Ward JM, McIntyre L, Schroeder JI, Salt DE (2003). "Genomic scale profiling of nutrient and trace elements in Arabidopsis thaliana." Nat Biotechnol 21(10);1215-21. PMID: 12949535

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

Lazarowski03: Lazarowski ER, Shea DA, Boucher RC, Harden TK (2003). "Release of cellular UDP-glucose as a potential extracellular signaling molecule." Mol Pharmacol 63(5);1190-7. PMID: 12695547

Lederer94: Lederer F (1994). "The cytochrome b5-fold: an adaptable module." Biochimie 76(7);674-92. PMID: 7893819

Leipelt01: Leipelt M, Warnecke D, Zahringer U, Ott C, Muller F, Hube B, Heinz E (2001). "Glucosylceramide synthases, a gene family responsible for the biosynthesis of glucosphingolipids in animals, plants, and fungi." J Biol Chem 276(36);33621-9. PMID: 11443131

Liang03: Liang H, Yao N, Song JT, Luo S, Lu H, Greenberg JT (2003). "Ceramides modulate programmed cell death in plants." Genes Dev 17(21);2636-41. PMID: 14563678

Lubert: Lubert Stryer "Biochemistry." ISBN 0-7167-1226-1.

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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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