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Isoprenoids: 3. Other Membrane-Associated Isoprenoids

By some definitions, all isoprenoids from simple monoterpenes such as geraniol to complex polymers such as natural rubber should be classified as ‘lipids’. As discussed in my web page “A Lipid Primer”, I prefer a more practical definition of lipids for these web pages. Here, only those isoprenoids that have a functional role in cellular membranes are discussed, i.e. plastoquinone, ubiquinone (coenzyme Q), phylloquinone (vitamin K) and menaquinone, dolichol and polyprenols, undecaprenyl phosphate and lipid II, and farnesyl pyrophosphate. The nature and function of tocopherols and tocotrienols (vitamin E) and of retinoids (vitamin A) are relevant here, but these are large subjects best described in separate web documents.

1.   Plastoquinone

Formula of a plastoquinoneA molecule that is related to the tocopherols, plastoquinone, is found in cyanobacteria and plant chloroplasts, and it is produced in plants by analogous biosynthetic pathways to those of tocopherols in the inner chloroplast envelope with solanesol diphosphate as the biosynthetic precursor of the side chain; there appears to be a somewhat different mechanism in cyanobacteria. The molecule is sometimes designated - 'plastoquinone-n' (or PQ-n), where 'n' is the number of isoprene units, which can vary from 6 to 9.

Plastoquinone has a key role in photosynthesis, by providing an electronic connection between photosystems I and II, generating an electrochemical proton gradient across the thylakoid membrane. This provides energy for the synthesis of adenosine triphosphate (ATP). The reduced dihydroplastoquinone (plastoquinol) that results transfers further electrons to the photosynthesis enzymes before being re-oxidized by a specific cytochrome complex; the redox state of the plastoquinone pool regulates the expression of many of the genes encoding photosystem proteins. X-Ray crystallography studies of photosystem II from cyanobacteria show two molecules of plastoquinone forming two membrane-spanning branches. In addition, plastoquinone has antioxidant activity comparable to that of the tocopherols, protecting especially against excess light energy and photooxidative damage. Similarly, in thylakoid membranes, plastoquinol is able to scavenge superoxide with production of H2O2. Plastoquinone is a cofactor participating in desaturation of phytoene in carotenoid biosynthesis, and the biosynthetic precursor of plastochromanols (see our web page on tocopherols).

2.   Ubiquinone (Coenzyme Q)

The ubiquinones, which are also known as coenzyme Q (CoQ) or mitoquinones, have obvious biosynthetic and functional relationships to plastoquinone and they are found in all the domains of life. They have a 2,3‑dimethoxy-5-methylbenzoquinone nucleus and a side chain of six to ten isoprenoid units; the human form illustrated has ten units (coenzyme Q10), while that of the rat has nine, Escherichia coli has eight and Saccharomyces cerevisiae has six. In plants, ubiquinones tend to have nine or ten isoprenoid units. In mitochondria, it is present both as the oxidized (ubiquinone) and reduced (ubiquinol) forms. Because of their hydrophobic properties, ubiquinones are located entirely in membrane bilayers in most eukaryote organelles.

Ubiquinones are synthesised de novo in most cells in animal, plant and bacterial tissues by a complex sequence of reactions from the essential amino acid phenylalanine and then tyrosine to generate p-hydroxybenzoic acid, which is the key precursor that is condensed with the polyprenyl unit via a specific transferase; this is followed by decarboxylation, hydroxylation and methylation steps, depending on the specific organism, although many of the required enzymes have yet to be identified. In fact, a complex of enzymes, termed 'complex Q', is believed to contain the proteins required for the terminal stage of coenzyme Q biosynthesis together with lipids, small molecule cofactors and metal ions, although again the full composition is not yet known. Forms with a second chromanol ring, resembling the structures of tocopherols, are also produced (ubichromanols), but not in animal tissues. They are generated on an industrial scale by yeast fermentation.

In mitochondria, ubiquinones are essential components of the respiratory electron transport system, taking part in the oxidation of succinate or NADH via the cytochrome system, reactions that are coupled to the generation of ATP. In this process, coenzyme Q transfers electrons from the primary substrates to the oxidase system while simultaneously transferring protons to the outside of the mitochondrial membrane, resulting in a proton gradient across the membrane; as a consequence, it is reduced to ubiquinol. Thus, it is an essential component of the cycle that generates the proton motive force driving ATP production via oxidative phosphorylation. Mitochondrial coenzyme Q is also implicated in the production of reactive oxygen species by a mechanism involving the formation of superoxide from ubisemiquinone radicals, and in this way is responsible for causing some of the oxidative damage behind many degenerative diseases. In this action, it is a pro-oxidant.

Ubiquinone - conversion to  ubiquinol

In complete contrast in its reduced form (ubiquinol), it acts as an endogenous antioxidant, the only lipid-soluble antioxidant to be synthesised endogenously. It inhibits lipid peroxidation in biological membranes and serum low-density lipoproteins, and it may also protect mitochondrial membrane proteins and DNA against oxidative damage. Although it only has about one tenth of the antioxidant activity of vitamin E (α-tocopherol), it is able to stimulate the effects of the latter by regenerating it from its oxidized form. However, ubiquinones and tocopherols appear to exhibit both cooperative and competitive effects under different conditions. There are also suggestions that coenzyme Q may be involved in redox control of cell signalling and gene expression. In addition, it is a regulator of mitochondrial permeability and it is required for pyrimidine nucleotide biosynthesis and as an electron acceptor for β-oxidation of fatty acids. Similarly, in bacteria and other prokaryotes, ubiquinones participate a large number of redox reaction, notably in the respiratory electron transport system but also in other enzyme reactions that require electron donation including the formation of disulfide bonds.

Dietary ubiquinone, i.e. that in food or dietary supplements, leads to elevated levels in blood, enhancing protection against lipid peroxidation with apparent beneficial effects to health, especially in relation to cardiac function, sperm motility and neurodegenerative diseases. In contrast, CoQ10 deficiency syndrome is associated with inherited pathological diseases defined by a decrease of the CoQ10 content in muscle and/or cultured skin fibroblasts.

3. Phylloquinone (Vitamin K) and Menaquinones

Phylloquinone or 2-methyl-3-phytyl-1,4-naphthoquinone is synthesised in the inner chloroplast envelope of cyanobacteria, algae and higher plants by a mechanism analogous to that of the tocopherols, i.e. from chorismate in the shikimate pathway with a prenyl side chain derived from phytyldiphosphate. In this membrane, it is a key component of the photosystem I complex where it receives an electron from the chlorophyll a acceptor molecule and then donates an electron to the membrane-associated iron-sulfur protein acceptor cluster in the complex. In an obvious parallel to the plastoquinones (above), two molecules of phylloquinone form two membrane-spanning branches, as demonstrated by X-ray crystallography studies of photosystem I from cyanobacteria. Plastoglobules associated with the thylakoid membrane are believed to function as a reservoir for excess phylloquinone, and may also function in its metabolism.

Phylloquinone and menaquinones

The menaquinones are related bacterial products, which function in the respiratory and photosynthetic electron transport chains of bacteria. They have a variable number (4 to 10) of isoprenoid units in the tail, and they are sometimes designated ‘MK-4’ to ‘MK-10’. In contrast to phylloquinone, these are usually highly unsaturated. In some species, there are methyl or other groups attached to the naphthoquinone moiety. Remarkably high concentrations of menaquinones are present in membranes of some extremophiles such as the haloarchaea, where it has been suggested that they act as ion permeability barriers and as a powerful shield against oxidative stress in addition to their functions as electron and proton transporters.

Phylloquinone is an essential component of the diet of animals and has been termed 'vitamin K1'. It must be supplied by green plant tissues, where it occurs in the range 400-700 μg/100 g, or seed oils. The menaquinones, the main source of which in the human diet is cheese and yoghurt, also have vitamin K activity and are termed 'vitamin K2'. They account for about 10-25% of the vitamin K content of the Western diet. A synthetic saturated form of this, which is used in animal feeds, is known as 'vitamin K3 or menadione', though strictly speaking it is not a vitamin but a pro-vitamin in that it can be converted to the menaquinone MK-4 in animal tissues by addition of a phytyl unit; it is too toxic for human nutrition. Vitamin K forms are absorbed from the intestines and transported in plasma in the form of lipoproteins in a similar manner to the other fat-soluble vitamins. Different tissues have differing storage capacities and presumably requirements for the various forms of vitamin K. As a high proportion is excreted, there appears to be a requirement for a constant intake. Vitamin K1 is taken up rapidly by the liver, but vitamin K2 remains in the plasma for much longer and may be the main source of the vitamin in peripheral tissues. In addition, it has been established that some dietary phylloquinone is converted to menaquinone-4 in animals, although the quantitative significance has still to be established; the mechanism involves conversion to menadione in the intestines followed by transport to tissues where a geranylgeranyl side-chain is attached by a specific prenyl transferase.

The primary role of vitamin K in animal tissues is to act as a cofactor specific to the vitamin K-dependent enzyme γ-glutamyl carboxylase in the endoplasmic reticulum in the liver mainly. Its function is the post-translational carboxylation of glutamate residues to form γ-carboxyglutamic acid in proteins, such as prothrombin. In this way, prothrombin and three related proteins are activated to promote blood clotting. The γ-carboxyglutamic acid residues are located at the binding site for Ca2+, and are vital for the activity of the enzyme. Phylloquinone must first be converted to the reduced form, phylloquinol, which is the actual cofactor for the enzyme; molecular oxygen and carbon dioxide are both required also. Phylloquinol donates hydrogen to the glutamic acid residue and is oxidized in the process to 2,3-epoxyphylloquinone. A further enzyme, vitamin K epoxide reductase, regenerates phylloquinone by reduction of the epoxide in a dithiol-dependent reaction so that this can be re-utilized many times ("the vitamin K cycle"); menaquinones undergo the same cycle of reaction. By interfering with the last step in the metabolic cycle, warfarin, the rodenticide, prevents blood clotting. In the same way, a deficiency in vitamin K results in inhibition of blood clotting and can lead to brain haemorrhaging in malnourished newborn infants, though this is not seen in adult humans, presumably because intestinal bacteria produce sufficient for our needs. Vitamin K-dependent proteins are also known to have important functions in the central and peripheral nervous systems, and vitamin K influences sphingolipid biosynthesis in brain.

The vitamin K cycle

Menaquinones differ from phylloquinone with respect to their chemical structure and pharmacokinetics, and it is now apparent that vitamin K2 (MK-4 especially) has a number of different actions, some with specificities for particular tissues. For example, osteocalcin is a γ-carboxyglutamic acid-containing protein, which forms a strong complex with the mineral hydroxyapatite (calcium phosphate) of bone; it must be carboxylated to function properly and vitamin K2 appears to be of particular importance in this instance. Vitamin K2 also regulates bone remodelling by osteoclasts to remove old or damaged bone and its replacement by new bone. In addition, vitamin K2 is involved in vascular calcification, cell growth and apoptosis. Side effects of the use of anticoagulants that bind to vitamin K can be osteoporosis and increased risk of vascular calcification. Although careful control of the dosage is necessary, vitamin K2 may be a useful adjunct for the treatment of osteoporosis, and it may reduce morbidity and mortality in cardiovascular health by reducing vascular calcification.

Excess vitamin K1 and the menaquinones are catabolized in the liver by a common degradative pathway in which the isoprenoid side chain is shortened to yield carboxylic acid aglycones such as menadiol, which can be excreted in bile and urine as glucuronides or sulfates.

4.   Dolichols and Polyprenols

Polyisoprenoid alcohols, such as dolichols, are ubiquitous if minor components, relative to the glycerolipids, of membranes of most living organisms from bacteria to mammals. They are hydrophobic linear polymers, consisting of up to twenty isoprene residues or a hundred carbon atoms (or many more in plants especially), linked head-to-tail, with a hydroxy group at one end (α-residue) and a hydrogen atom at the other (ω-end). In dolichols (or dihydropolyprenols), the double bond in the α-residue is hydrogenated, and this distinguishes them from the polyprenols with a double bond in the α-residue.

Formulae of polyprenols and dolichols

Polyisoprenoid alcohols are further differentiated by the geometrical configuration of the double bonds into three subgroups, i.e. di-trans-poly-cis, tri-trans-poly-cis, and all-trans. For many years, it was assumed that polyprenols were only present in bacteria and plants, especially photosynthetic tissues, while dolichols were found in mammals or yeasts, but it is now known that dolichols can also occur at low levels in bacteria and plants, while polyprenols have been detected in animal cells. Solanesol is a related and distinctive plant product with trans double bonds only and is a precursor of plastoquinone.

Scottish thistleWithin a given species, components of one chain-length may predominate, but other homologues are usually present. The chain length of the main polyisoprenoid alcohols varies from 11 isoprene units in eubacteria, to 16 or 17 in Drosophila, 15 and 16 in yeasts, 19 in hamsters and 20 in pigs and humans. In plants, the range is from 8 to 22 units, but some species of plant have an additional class of polyprenols with up to 40 units. In tissues, polyisoprenoid alcohols can be present in the free form, esterified with acetate or fatty acids, phosphorylated or monoglycosylated phosphorylated (various forms), depending on species and tissue. Polyisoprenoid alcohols per se do not form bilayers in aqueous solution, but rather a type of lamellar structure. However, they are found in most membranes, especially the plasma membrane of liver cells and the chloroplasts of plants.

Dolichoic acids, i.e. related molecules with a terminal carboxyl group and containing 14–20 isoprene units, have been isolated from the substantia nigra of the human brain. However, they were barely detectable in pig brain.

Biosynthesis of the basic building block of dolichols, e.g. isopentenyl diphosphate, follows either the mevalonate pathway or a more recently described methylerythritol phosphate pathway discussed in relation to cholesterol biosynthesis elsewhere on this site. Farnesyl pyrophosphate is the primary precursor in the biosynthesis of polyprenols and is the branch-point in sterol/isoprene biosynthesis (see our web page on plant sterols), depending on the nature of the organism (see a further note below). Subsequent formation of the linear prenyl chain is accomplished by cis-prenyl transferases that catalyse the condensation of isopentenyl pyrophosphate and farnesyl pyrophosphate and then the growing the allylic prenyl diphosphate chain. The end products are polyprenyl pyrophosphates, which are dephosphorylated first to polyprenol phosphate and thence to the free alcohol. Finally, a specific reductase has been identified from human tissues that catalyses the reduction of the double bond in position 2 to produce dolichols. There is a family of cis-prenyl transferases, present in both eukaryotes and bacteria, that in addition to the synthesis of dolichols can catalyse the formation of isoprenoid carbon skeletons from neryl pyrophosphate (C10) to natural rubber (C>10,000), including the polyisoprenoid phosphates involved in protein glycosylation as discussed in the next section.

Biosynthesis of dolichols

Although polyprenols and dolichols were first considered to be simply secondary metabolites, they are now known to have important biological functions. Glycosylation of asparagine residues is the main protein modification in all three domains of life, and phosphorylated polyisoprenoids, including dolichols, are essential to this process (next section). There is also a suggestion that free dolichol may have a beneficial antioxidant function in cell membranes.

5.  Polyisoprenoid Phosphates and Glycosylation of Proteins

Glycosylated phosphopolyisoprenoid alcohols are the carriers of oligosaccharide units for transfer to proteins and as glycosyl donors, i.e. they are substrates for glycosyl transferases for the biosynthesis of glycans in a similar manner to the cytosolic sugar nucleotides. They differ from the latter in their intracellular location, with the lipid portion in the membrane of the endoplasmic reticulum and the oligosaccharide portion specifically located either on the cytosolic or lumenal face of the membrane. The degree of unsaturation and chain-length of the product are important for recognition by the enzymes in the next stage of the pathway.

Dolichol phosphates: In eukaryotes, N-glycosylation begins on the cytoplasmic side of the endoplasmic reticulum with the transfer of carbohydrate moieties from nucleotide-activated sugar donors, such as uridine diphosphate N-acetylglucosamine, onto dolichol phosphate. Then, N-acetylglucosamine phosphate is added to give dolichol-pyrophosphate linked to N-acetylglucosamine, to which a further N-acetylglucosamine unit is added followed by five mannose units, the last catalysed by dolichol phosphate mannose synthase, which is also essential for GPI-anchor biosynthesis. The resulting dolichol-pyrophosphate-heptasaccharide is then flipped across the endoplasmic reticulum membrane to the luminal face with the aid of a “flippase”. Four further mannose and three glucose residues are added to the oligosaccharide chain by means of glycosyltransferases, which utilize as donors dolichol-phospho-mannose and dolichol-phospho-glucose, which are also synthesised on the cytosolic face of the membrane and flipped across to the luminal face. In humans, the final lipid product is a C95-dolichol pyrophosphate-linked tetradecasaccharide, the oligosaccharide unit of which is transferred from the dolichol carrier onto specific asparagine residues on a developing polypeptide in the membrane. The carrier dolichol-pyrophosphate is dephosphorylated to dolichol-phosphate then diffuses or is flipped back across the endoplasmic reticulum to the cytoplasmic face.

Formula of dolichol-pyrophosphate oligosaccharide

The Archaea use dolichol in their synthesis of lipid-linked oligosaccharide donors with both dolichol phosphate (Euryarchaeota) and pyrophosphate (Crenarchaeota) as carriers; these can have variable numbers of isoprene units many of which can be saturated. In the haloarchaeon Haloferax volcanii, for example, a series of C55 and C60 dolichol phosphates with saturated isoprene subunits at the α- and ω-positions is involved in the glycosylation reaction of target proteins, while similar lipid carriers of oligosaccharide units appear to be present in methanogens. Archaea of course use isoprenyl ethers linked to glycerol as major membrane lipid components in addition to unusual carotenoids such as the C50 bacterioruberins. In many of these species, isoprenoid biosynthesis is via the 'classical' mevalonate pathway (see our web page on cholesterol), but in other species some aspects of this pathway differ.

Undecaprenylphosphate: Most other bacteria use undecaprenyl-diphosphate-oligosaccharide as a glycosylation agent in a similar way for the biosynthesis of peptidoglycan, the main component of most bacterial cell walls and a structure unique to bacteria, of many other cell-wall polysaccharides, including lipopolysaccharides, O-antigenic polysaccharides and capsular polysaccharides, and of N-linked protein glycosylation in both in Gram-negative and Gram-positive bacteria. Undecaprenyl phosphate (a C55 isoprenoid), also referred to as bactoprenol, is the essential lipid intermediate. It is synthesised by the addition of eight units of isopentenyl pyrophosphate to farnesyl pyrophosphate, a reaction catalysed by undecaprenyl pyrophosphate synthase, followed by the removal of a phosphate group. Undecaprenyl phosphate is required for the synthesis and transport of hydrophilic GlcNAc-MurNAc-peptide monomers across the cytoplasmic membrane to external sites for polymer formation. It differs from the dolichol phosphates mainly in that the terminal unit is unsaturated.

Formula of undecaprenyl phosphate

Lipid II: Undecaprenyl diphosphate-MurNAc-pentapeptide-GlcNAc, often simply termed lipid II, is the last significant lipid intermediate in the construction of the peptidoglycan cell wall in bacteria (Lipid I is the biosynthetic precursor lacking the N-acetylgluosamine residue). This molecule must be translocated from the cytosolic to the exterior membrane of the organism, and three different protein classes have been identified that can accomplish this of which ATP-binding cassette (ABC) transporters are best characterized. Once across the membrane, lipid II is cleaved to provide the MurNAc-pentapeptide-GlcNAc monomer, which undergoes polymerization and cross linking to form the complex peptidoglycan polymer that provides strength and shape to bacteria. The undecaprenyl-pyrophosphate remaining is hydrolysed to undecaprenyl phosphate by a membrane-integrated member of the type II phosphatidic acid phosphatase family and is recycled back to the interior of the membrane. The turnover rate is very high so the lipid II cycle is considered to be the rate-limiting step in peptidoglycan biosynthesis. There is also some evidence that lipid II has a function on the inner leaflet of the cytoplasmic membrane in organizing the proteins of the cytoskeleton. Because of its highly conserved structure and accessibility on the surface membrane, synthesis and transport of lipid II is considered an important target for the development of novel antibiotics.

Formula of Lipid II

In a few prokaryotes, the membrane intermediate has a polyprenyl-monophosphate-glycan structure instead of lipid II, and undecaprenyl-phosphate-L-4-amino-4-deoxyarabinose is involved in lipid A modification in Gram-negative bacteria, for example. There are obvious parallels with the involvement of glycosylated phosphopolyisoprenoid alcohols as carriers of oligosaccharide units for transfer to proteins and as glycosyl donors in higher organisms (see above).

6.  Farnesyl Pyrophosphate and Related Compounds

Farnesyl pyrophosphate is a key intermediate in the biosynthesis of sterols such as cholesterol, and it is the donor of the farnesyl group in the biosynthesis of dolichols and polyprenols (see above) as well as for the isoprenylation of many proteins (see the web page on proteolipids). However, it is also known to mediate various biological reactions in its own right via interaction with a specific receptor. It is synthesised by two successive phosphorylation reactions of farnesol.

Farnesyl pyrophosphate and presqualene diphosphate

Presqualene diphosphate is unique among the isoprenoid phosphates in that it contains a cyclopropylcarbinyl ring. In addition to being a biosynthetic precursor of squalene, and thence of cholesterol, it is a natural anti-inflammatory agent, which functions by inhibiting the activity of phospholipase D and the generation of superoxide anions in neutrophils.

Recommended Reading

Lipid listings Credits/disclaimer Updated: February 15th, 2018 Author: William W. Christie LipidWeb icon