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MetaCyc Pathway: all-trans-farnesol biosynthesis
Inferred from experiment

Pathway diagram: all-trans-farnesol biosynthesis

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.

Synonyms: trans,trans-farnesol biosynthesis

Superclasses: Generation of Precursor Metabolites and Energy

Some taxa known to possess this pathway include : Saccharomyces cerevisiae

Expected Taxonomic Range: Eukaryota


There is growing need to find renewable biologically produced compounds as replacements for petroleum-based fuels. Due to the branched and ringed structures found in their hydrocarbon chain, isoprenoid compounds have the potential to be used as biofuels. The branching improves the cetane number (a measurement of the combustion quality) of fuel mixtures [Murley09]. The C15 isoprenoid compound farnesol is a putative biodiesel with a cetane number that falls withing the expected range for petroleum diesel.

Biodiesel has both disadvantages and advantages compared to petroleum diesel. The disadvantages include biodiesel having poorer cold weather characteristics, producing higher nitrous oxide emissions and a greater ability to oxidize. The advantages include biodiesel being derived from a renewable source, having a lower sulfur content and hence lower oxidized sulfur emissions, increased lubricity and lower carbon monoxide emissions.

Isoprenoid compounds are derived from isopentenyl pyrophosphate (IPP) and dimethyl alleyl diphosphate (DMAPP). These two compounds can be derived from two distinct pathways: the mevalonate pathway I (MVA) and the methylerythritol phosphate pathway I (MEP), also known as deoxyxylulose pathway. The MVA pathway is more energetically favorable than the MEP pathway as it generates protons which can be used to generate ATP, and does not require an input of ATP per se [Murley09].

About this Pathway

Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) are both derived from either the MVA or MEP pathways [Okada08]. These compounds are precursors to E,E farnesyl diphosphate, an intermediate in the putative biodiesel farnesol biosynthesis [Song06].

A soluble form of phosphatase capable of converting farnesyl diphosphate (FPP) to E,E-farnesol was identified in Saccharomyces cerevisiae [Song06]. The purified FPP phosphatase is a truncated form of alkaline phosphatase [Song06].

FPP can also be converted to farnesane, another valuable diesel fuel, but this does not occur naturally in a biological system.

Created 09-Aug-2011 by Weerasinghe D, SRI International


Murley09: Murley, A.C. (2009). "Aliphatic and isoprenoid hydrocarbon biosynthesis for diesel fuels." Basic Biotechnology eJournal.

Okada08: Okada K, Kasahara H, Yamaguchi S, Kawaide H, Kamiya Y, Nojiri H, Yamane H (2008). "Genetic evidence for the role of isopentenyl diphosphate isomerases in the mevalonate pathway and plant development in Arabidopsis." Plant Cell Physiol 49(4);604-16. PMID: 18303110

Song06: Song L (2006). "A soluble form of phosphatase in Saccharomyces cerevisiae capable of converting farnesyl diphosphate into E,E-farnesol." Appl Biochem Biotechnol 128(2);149-58. PMID: 16484724

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

Anderson89: Anderson MS, Muehlbacher M, Street IP, Proffitt J, Poulter CD (1989). "Isopentenyl diphosphate:dimethylallyl diphosphate isomerase. An improved purification of the enzyme and isolation of the gene from Saccharomyces cerevisiae." J Biol Chem 1989;264(32);19169-75. PMID: 2681212

Anderson89a: Anderson MS, Yarger JG, Burck CL, Poulter CD (1989). "Farnesyl diphosphate synthetase. Molecular cloning, sequence, and expression of an essential gene from Saccharomyces cerevisiae." J Biol Chem 1989;264(32);19176-84. PMID: 2681213

Barnard81: Barnard GF, Popjak G (1981). "Human liver prenyltransferase and its characterization." Biochim Biophys Acta 661(1);87-99. PMID: 7295734

Blanchard93: Blanchard L, Karst F (1993). "Characterization of a lysine-to-glutamic acid mutation in a conservative sequence of farnesyl diphosphate synthase from Saccharomyces cerevisiae." Gene 125(2);185-9. PMID: 8096487

Bouvier00: Bouvier F, Suire C, d'Harlingue A, Backhaus RA, Camara B (2000). "Molecular cloning of geranyl diphosphate synthase and compartmentation of monoterpene synthesis in plant cells." Plant J 24(2);241-52. PMID: 11069698

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Burke02: Burke C, Croteau R (2002). "Interaction with the small subunit of geranyl diphosphate synthase modifies the chain length specificity of geranylgeranyl diphosphate synthase to produce geranyl diphosphate." J Biol Chem 277(5);3141-9. PMID: 11733504

Burke04: Burke C, Klettke K, Croteau R (2004). "Heteromeric geranyl diphosphate synthase from mint: construction of a functional fusion protein and inhibition by bisphosphonate substrate analogs." Arch Biochem Biophys 422(1);52-60. PMID: 14725857

Burke99: Burke CC, Wildung MR, Croteau R (1999). "Geranyl diphosphate synthase: cloning, expression, and characterization of this prenyltransferase as a heterodimer." Proc Natl Acad Sci U S A 96(23);13062-7. PMID: 10557273

Campbell98: Campbell M, Hahn FM, Poulter CD, Leustek T (1998). "Analysis of the isopentenyl diphosphate isomerase gene family from Arabidopsis thaliana." Plant Mol Biol 36(2);323-8. PMID: 9484444

Carrigan03: Carrigan CN, Poulter CD (2003). "Zinc is an essential cofactor for type I isopentenyl diphosphate:dimethylallyl diphosphate isomerase." J Am Chem Soc 125(30);9008-9. PMID: 15369345

Chen93: Chen A, Poulter CD (1993). "Purification and characterization of farnesyl diphosphate/geranylgeranyl diphosphate synthase. A thermostable bifunctional enzyme from Methanobacterium thermoautotrophicum." J Biol Chem 268(15);11002-7. PMID: 8388380

Chooi10: Chooi YH, Cacho R, Tang Y (2010). "Identification of the viridicatumtoxin and griseofulvin gene clusters from Penicillium aethiopicum." Chem Biol 17(5);483-94. PMID: 20534346

Chooi12: Chooi YH, Fang J, Li Y, Wu K, Wang P, Tang Y (2012). "Discovery and characterization of a group of fungal polycyclic polyketide prenyltransferases." J Am Chem Soc 134(22);9428-37. PMID: 22590971

Clizbe07: Clizbe DB, Owens ML, Masuda KR, Shackelford JE, Krisans SK (2007). "IDI2, a second isopentenyl diphosphate isomerase in mammals." J Biol Chem 282(9);6668-76. PMID: 17202134

Cunillera96: Cunillera N, Arro M, Delourme D, Karst F, Boronat A, Ferrer A (1996). "Arabidopsis thaliana contains two differentially expressed farnesyl-diphosphate synthase genes." J Biol Chem 271(13);7774-80. PMID: 8631820

Daum98: Daum G, Lees ND, Bard M, Dickson R (1998). "Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae." Yeast 1998;14(16);1471-510. PMID: 9885152

Delourme94: Delourme D, Lacroute F, Karst F (1994). "Cloning of an Arabidopsis thaliana cDNA coding for farnesyl diphosphate synthase by functional complementation in yeast." Plant Mol Biol 26(6);1867-73. PMID: 7858223

deRuyck06: de Ruyck J, Durisotti V, Oudjama Y, Wouters J (2006). "Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography." J Biol Chem 281(26);17864-9. PMID: 16617181

Dhiman04: Dhiman RK, Schulbach MC, Mahapatra S, Baulard AR, Vissa V, Brennan PJ, Crick DC (2004). "Identification of a novel class of omega,E,E-farnesyl diphosphate synthase from Mycobacterium tuberculosis." J Lipid Res 45(6);1140-7. PMID: 15060088

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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 Pathway Tools version 19.5 (software by SRI International) on Sun May 1, 2016, biocyc14.