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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.

Abstract

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.

References

  1. Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 74, 5088–5090 (1977).

    CAS  Article  Google Scholar 

  2. Koga, Y. & Morii, H. Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations. Microbiol. Mol. Biol. Rev. 71, 97–120 (2007). An extensive review of the different steps in the archaeal ether lipid biosynthetic pathway and the experimental data that support this.

    CAS  Article  Google Scholar 

  3. Kates, M. Biology of halophilic bacteria, Part, II. Membrane lipids of extreme halophiles: biosynthesis, function and evolutionary significance. Experientia 49, 1027–1036 (1993).

    CAS  Article  Google Scholar 

  4. Thompson, D. H. et al. Tetraether bolaform amphiphiles as models of archae-bacterial membrane lipids: Raman spectroscopy, 31P NMR, X-ray scattering, and electron microscopy. J. Am. Chem. Soc. 114, 9035–9042 (1992).

    CAS  Article  Google Scholar 

  5. Sinninghe Damsté, J. S., Hopmans, E. C., Schouten, S., van Duin, A. C. T. & Geenevasen, J. A. J. Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota. J. Lipid Res. 43, 1641–1651 (2002). The first description of crenarchaeol as a characteristic lipid of marine Thaumarchaeota.

    Article  Google Scholar 

  6. Jarrell, K. F. et al. Major players on the microbial stage: why archaea are important. Microbiology 157, 919–936 (2011).

    CAS  Article  Google Scholar 

  7. Wuchter, C. et al. Archaeal nitrification in the ocean. Proc. Natl Acad. Sci. USA 103, 12317–12322 (2006).

    CAS  Article  Google Scholar 

  8. Boucher, Y., Kamekura, M. & Doolittle, W. F. Origins and evolution of isoprenoid lipid biosynthesis in archaea. Mol. Microbiol. 52, 515–527 (2004).

    CAS  Article  Google Scholar 

  9. Lombard, J., Lopez-Garcia, P. & Moreira, D. Phylogenomic investigation of phospholipid synthesis on archaea. Archaea 2012, 630910 (2012).

    Article  Google Scholar 

  10. Schouten, S., Hopmans, E. C. & Sinninghe Damsté, J. S. The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: a review. Org. Geochem. 54, 19–61 (2013). A recent review on the sources, analysis methods and applications of archaeal ether lipids in organic geochemistry.

    CAS  Article  Google Scholar 

  11. Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990).

    CAS  Article  Google Scholar 

  12. Gribaldo, S. & Brochier-Armanet, C. The origin and evolution of Archaea: a state of the art. Phil. Trans. R. Soc. B 361, 1007–1022 (2006).

    CAS  Article  Google Scholar 

  13. Stetter, K. O., Fiala, G., Huber, G., Huber, R. & Segerer, A. Hyperthemophilic microorganisms. FEMS Microbiol. Rev. 75, 117–124 (1990).

    Article  Google Scholar 

  14. Madsen, E. L. Environmental Microbiology: From Genomes to Biogeochemistry. (Wiley-Blackwell, 2008).

    Google Scholar 

  15. Nelson-Sathi, S. et al. Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc. Natl Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1209119109 (2012).

  16. Ruepp, A. et al. The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508–5139 (2000).

    CAS  Article  Google Scholar 

  17. Brochier-Armanet, C., Forterre, P. & Gribaldo, S. Phylogeny and evolution of the Archaea: one hundred genomes later. Curr. Opin. Microbiol. 14, 274–281 (2011).

    Article  Google Scholar 

  18. Elkins, J. G. et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl Acad. Sci. USA 105, 8102–8107 (2008).

    CAS  Article  Google Scholar 

  19. Huber, H., Hohn, M. J., Stetter, K. O. & Rachel, R. The phylum Nanoarchaeota: present knowledge and future perspectives of a unique form of life. Res. Microbiol. 154, 165–171 (2003).

    CAS  Article  Google Scholar 

  20. Brochier-Armanet, C., Boussau, B., Gribaldo, S. & Forterre, P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nature Rev. Microbiol. 6, 245–252 (2008). Analysis article proposing the classification of Thaumarchaeota as a separate phylum of the Archaea.

    CAS  Article  Google Scholar 

  21. Nunoura, T. et al. Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res. 39, 3204–3223 (2011).

    CAS  Article  Google Scholar 

  22. Pester, M., Schleper, C. & Wagner, M. The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology. Curr. Opin. Microbiol. 14, 300–306 (2011).

    CAS  Article  Google Scholar 

  23. Koga, Y. & Morii, H. Recent advances in structural research on ether lipids from Archaea including comparative and physiological aspects. Biosci. Biotechnol. Biochem. 69, 2019–2034 (2005).

    CAS  Article  Google Scholar 

  24. Koga, Y., Akagawa-Matsushita, M., Ohga, M. & Nishihara, M. Taxonomic significance of the distribution of component parts of polar ether lipids in methanogens. Syst. Appl. Microbiol. 16, 342–351 (1993).

    CAS  Article  Google Scholar 

  25. Langworthy, T. A. in The Bacteria (eds Woese, C. R. & Wolfe, R. S.) 459–497 (Academic Press,1985).

    Google Scholar 

  26. Uda, I., Sugai, A., Itoh, Y. H. & Itoh, T. Variation in molecular species of polar lipids from Thermoplasma acidophilum depends on growth temperature. Lipids 36, 103–105 (2001).

    CAS  Article  Google Scholar 

  27. Chong, P. L. G. Archaebacterial bipolar tetraether lipids: physico-chemical and membrane properties. Chem. Phys. Lip. 163, 253–265 (2010).

    CAS  Article  Google Scholar 

  28. Macalady, J. L. et al. Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid. Extremophiles 8, 411–419 (2004).

    CAS  Article  Google Scholar 

  29. Pitcher, A. et al. Core and intact polar glycerol dibiphytanyl glycerol tetraether lipids of ammonia-oxidizing archaea enriched from marine and estuarine sediments. Appl. Environ. Microbiol. 77, 3468–3477 (2011).

    CAS  Article  Google Scholar 

  30. Reysenbach, A. L. et al. Isolation of a ubiquitous obligate thermoacidophilic archaeon from deep-sea hydrothermal vents. Nature 442, 444–447 (2006).

    CAS  Article  Google Scholar 

  31. De Rosa, M. et al. An asymmetric archaebacterial diether lipid from alkaliphilic halophiles. J. Gen. Microbiol. 128, 343–348 (1982).

    CAS  Google Scholar 

  32. Matsumi, R., Atomi, H., Driessen, A. J. & van der Oost, J. Isoprenoid biosynthesis in archaea — biochemical and evolutionary implications. Res. Microbiol. 162, 39–52 (2011).

    CAS  Article  Google Scholar 

  33. Lai, D. Isoprenoid Ether Lipid Biosynthesis in the Extremophile, Archaeoglobus fulgidus. Thesis, Univ. California Los Angeles (2009).

    Google Scholar 

  34. Langworthy, T. A. Turnover of di-O-phytanylglycerol in Thermoplasma. Rev. Infect. Dis. 4, S266 (1982).

    Google Scholar 

  35. Nemoto, N., Shida, Y., Shimada, H., Oshima, T. & Yamagishi, A. Characterization of the precursor of tetraether lipid biosynthesis in the thermoacidophilic archaeon Thermoplasma acidophilum. Extremophiles 7, 235–243 (2003).

    CAS  Article  Google Scholar 

  36. Poulter, C. D., Aoki, T. & Daniels, L. Biosynthesis of isoprenoid membranes in the methanogenic archaebacterium Methanospirillum hungatei. J. Am. Chem. Soc. 110, 2620–2624 (1988).

    CAS  Article  Google Scholar 

  37. Eguchi, T., Takyo, H., Morita, M., Kakinuma, K. & Koga, Y. Unusual double-bond migration as plausible key reaction on the synthesis of the isoprenoid membrane lipids of methanogenic archaea. J. Chem. Soc. Chem. Commun. 2000, 1545–1546 (2000).

    Article  Google Scholar 

  38. Eguchi, T. Nishimura, Y. & Kakinuma, K. Importance of the isopropylene terminal of geranylgeranyl group for the formation of tetraether lipid in methanogenic archaea. Tetrahedron Lett. 44, 3275–3279 (2003).

    CAS  Article  Google Scholar 

  39. Wang, K. C. & Ohnuma, S.-I. Isoprenyl diphosphate synthases. Biochim. Biophys. Acta. 1529, 33–48 (2000). A review of the classification, catalytic mechanism and chain-length determination of IPP synthases.

    CAS  Article  Google Scholar 

  40. Wang, K. & Ohnuma, S. Chain-length determination mechanism of isoprenyl diphosphate synthases and implications for molecular evolution. Trends Biochem. Sci. 24, 445–451 (1999).

    CAS  Article  Google Scholar 

  41. Chen, A. & Poulter, C. D. Purification and characterization of farnesyl diphosphate/geranylgeranyl diphosphate synthase. A thermostable bifunctional enzyme from Methanobacterium thermoautotrophicum. J. Biol. Chem. 268, 11002–11007 (1993).

    CAS  PubMed  Google Scholar 

  42. Ogawa, T., Yoshimura, T. & Hemmi, H. Geranylfarnesyl diphosphate synthase from Methanosarcina mazei: different role, different evolution. Biochem. Biophys. Res. Commun. 393, 16e20 (2010).

    Article  Google Scholar 

  43. Peters, K. E., Wlaters, C. C. & Moldowan, J. M. The biomarker guide: Biomarkers and Isotopes in Petroleum Exploration and Earth History 2nd edn (Cambridge University Press, 2007).

    Google Scholar 

  44. Zhang, D. & Poulter, C. D. Biosynthesis of archaebacterial ether lipids. Formation of ether linkages by prenyltransferases. J. Am. Chem. Soc. 115, 1270–1277 (1993).

    CAS  Article  Google Scholar 

  45. Payadeh, J., Fujihashi, M., Gillon, W. & Pai, E. F. The crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase reveals an ancient fold for an ancient enzyme. J. Biol. Chem. 281, 6070–6078 (2006). First report of the crystal structure of an archaeal GGGP synthase.

    Article  Google Scholar 

  46. Guldan, H., Matysik, F.-M., Bocola, M., Sterner, R. & Babinger, P. Functional assignment of an enzyme that catalyzes the synthesis of an Archaea-type ether lipid in Bacteria. Angew. Chem. Int. Ed. 50, 8188–8191 (2011).

    CAS  Article  Google Scholar 

  47. Ren, F. et al. Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus. ChemBioChem. 14, 195–199 (2013).

    CAS  Article  Google Scholar 

  48. Hemmi, H., Shibuya, K., Takahashi, Y., Nakayama, T. & Nishino, T. J. (S)-2,3-Di-O-geranylgeranylglyceryl phosphate synthase from the thermoacidophilic archaeon Sulfolobus solfataricus. Molecular cloning and characterization of a membrane-intrinsic prenyltransferase involved in the biosynthesis of archaeal ether-linked membrane lipids. Biol. Chem. 279, 50197–50203 (2004).

    CAS  Article  Google Scholar 

  49. Klassen, J. L. Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics. PLoS ONE 5, e11257 (2010).

    Article  Google Scholar 

  50. Knappy, C. S. & Keely, B. J. Novel glycerol dialkanol triols in sediments: transformation products of glycerol diphytanyl glycerol tetraether lipids or biosynthetic intermediates? Chem. Commun. 48, 841–843 (2012).

    CAS  Article  Google Scholar 

  51. Liu, X. -L., Lipp, J. S., Schröder, J. M., Summons, R. E. & Hinrichs, K. -U. Isoprenoid glycerol dialkanol diethers: a series of novel archaeal lipids in marine sediments. Org. Geochem. 43, 50–55 (2012).

    Article  Google Scholar 

  52. Schouten, S., Hoefs, M. J. L., Koopmans, M. P., Bosch, H.-J. & Sinninghe Damsté, J. S. Structural characterization, ocurrence and fate of archaeal ether-bound acyclic and cyclic biphytanes and corresponding diols in sediments. Org. Geochem. 29, 1305–1319 (1998).

    CAS  Article  Google Scholar 

  53. Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 113 (2004).

    Article  Google Scholar 

  54. Cole, C., Barber, J. D. & Barton, G. J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 35, W197–W201 (2008).

    Article  Google Scholar 

  55. Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).

    CAS  Article  Google Scholar 

  56. Abascal, F., Zardoya, R. & Posada, D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104–2105 (2005).

    CAS  Article  Google Scholar 

  57. Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).

    CAS  Article  Google Scholar 

  58. Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).

    CAS  Article  Google Scholar 

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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)

Glossary

Hyperthermophiles

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

Thermoacidophiles

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

Halophilic

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

Methanogenic

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).

Isoprenoid

(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.

Prenyltransferases

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.

Squalene

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

Phytol

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

Geranylgeraniol

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

Isopropylidene

An isopropyl moiety with a terminal double bond.

Allylic

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

Biphytanyl

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

Phytoene

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). https://doi.org/10.1038/nrmicro3260

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