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A re-evaluation of the archaeal membrane lipid biosynthetic pathway

Key Points

  • Archaea were initially thought to be confined to extreme environments, but they are now known to occur ubiquitously in nature and to be important players in global biogeochemical cycles. Archaea are characterized by their unique membrane lipids, which contain isoprene units that are linked to the glycerol backbone by ether bonds (archaeol; C20) in a bilayer and glycerol dialkyl glycerol tetraether (GDGT; C40) in a monolayer.

  • Comparison of the phylogenetic composition of Archaea with the distribution of membrane ether lipids shows that most lipids are not specific for a certain phylogenetic group. Only the GDGT crenarchaeol, which contains four cyclopentane moieties and a cyclohexane moiety, is considered to be characteristic of the Thaumarchaeota, which suggests that the biosynthesis of the cyclohexane moiety is unique to this phylum.

  • The current conception of the archaeal membrane ether lipid biosynthetic pathway involves the condensation of units of isopentenyl diphosphate to form geranylgeranyl diphosphate (GGPP; C20) by a GGPP synthase. The formation of the two ether bonds is catalysed by the geranylgeranylglyceryl phosphate (GGGP) synthase and the digeranylgeranylglyceryl phosphate (DGGGP) synthase. The formation of GDGTs is thought to involve a head-to-head coupling between the two archaeol lipids, followed by internal cyclization to form cyclopentane moieties. These reactions are highly unusual and the enzymes that are involved are unknown.

  • The analysis of the amino acid sequence of most of the archaeal GGGP synthases suggests that they could accommodate substrates >C20 that already have rings present.

  • The synthesis of the unique cyclohexane moiety-containing GDGT crenarchaeol by Thaumarchaeota might explain the inability to annotate DGGGP synthases in thaumarchaeotal genomes, as a currently unknown, highly divergent DGGGP synthase would be required to accommodate the isoprenyl chain containing the 'bulky' cyclohexane moiety.

  • An alternative archaeal lipid biosynthetic pathway pathway is presented, which is based on a 'multiple-key, multiple-lock' mechanism for which multiple keys with different configurations (owing to the presence of rings) would need to accommodate and specifically interact at the molecular level with different locks (isoprenylglyceryl phosphate synthase and di-isoprenylglyceryl phosphate synthase). This pathway is consistent with most of the phylogenetic relationships that were observed in our study as well as with most of the experimental evidence for the different GDGT biosynthetic steps, and it is supported by possible intermediates that have previously been described.


Archaea produce unique membrane lipids in which isoprenoid alkyl chains are bound to glycerol moieties via ether linkages. As cultured representatives of the Archaea have become increasingly available throughout the past decade, archaeal genomic and membrane lipid-composition data have also become available. In this Analysis article, we compare the amino acid sequences of the key enzymes of the archaeal ether-lipid biosynthesis pathway and critically evaluate past studies on the biochemical functions of these enzymes. We propose an alternative archaeal lipid biosynthetic pathway that is based on a 'multiple-key, multiple-lock' mechanism.

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Figure 1: Current understanding of the archaeal lipid biosynthetic pathway.
Figure 2: Partial IPP synthase protein alignment.
Figure 3: Partial GGGP synthase protein alignment.
Figure 4: Maximum likelihood tree based on the protein sequences of archaeal putative GGGP synthases.
Figure 5: Maximum likelihood tree based on the protein sequences of putative archaeal DGGGP synthases and thaumarchaeotal UbiA prenyltransferases.
Figure 6: An alternative archaeal lipid biosynthesis scheme.


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Correspondence to Laura Villanueva.

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Supplementary information

Supplementary information S1 (table)

Isoprenyl diphosphate (IPP) synthases in archaeal genomes. (PDF 353 kb)

Supplementary information S2 (table)

Squalene/phytoene synthase homologues annotated in archaeal genomes. (PDF 257 kb)



Organisms that have an optimal growth temperature of at least 80 °C.


Microorganisms that thrive in acidic, sulphur-rich and high-temperature environments. The name is a combination of thermophile and acidophile.


A term used to describe extremophilic organisms that thrive at high concentrations of salt.


A term used to describe Archaea that produce methane under anoxic conditions.

Horizontal gene transfer

(HGT). The transfer of genetic material between different species of microorganisms; the acquired genes are transmitted to the next generation as the cell divides.

Phytanyl chains

Saturated chains that are composed of four head-to-tail-linked isoprene units (that is, C20 isoprenoids).


(Also known as isoprene). A term used to describe a group of natural products that have diverse structures composed of various numbers of isopentenyl (C5) pyrophosphate units.


Enzymes that transfer (iso)prenyl moieties to acceptor molecules.

Head-to-head condensation

The coupling of two isoprenyl units at the C1 position of both units.


A biochemical precursor of the steroid and triterpenoid families; it is synthesized by tail-to-tail condensation of farnesyl pyrophosphate (C15) by squalene synthase.


An acyclic diterpene (terpene consists of two or more isoprene C5H8 units) alcohol.


A diterpenoid alcohol (also known as 3,7,11,15-tetramethyl-2,6,10,14-hexadecatraen-1-ol)


An isopropyl moiety with a terminal double bond.


A term used to describe a double bond at the terminal position of a carbon chain.


A molecule that is composed of two head-to-head-condensed phytanyl units (C40 isoprenoid).


A C40 intermediate in the biosynthesis of carotenoids; it is produced from two molecules of geranylgeranyl pyrophosphate (GGPP) by the action of the enzyme phytoene synthase.

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Villanueva, L., Damsté, J. & Schouten, S. A re-evaluation of the archaeal membrane lipid biosynthetic pathway. Nat Rev Microbiol 12, 438–448 (2014).

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