Caldarchaeol

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Caldarchaeol
Caldarchaeol nostereochem.png
Caldarchaeol labeled.png
Names
Preferred IUPAC name
[(2R,7R,11R,15S,19S,22S,26S,30R,34R,38R,43R,47R,51S,55S,58S,62S,66R,70R)-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-Hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacontane-2,38-diyl]dimethanol
Other names
  • Dibiphytanyl diglycerol tetraether
  • GDGT-0
Identifiers
3D model (JSmol)
ChemSpider
PubChem CID
  • InChI=1S/C86H172O6/c1-69-29-17-33-73(5)41-25-49-81(13)57-61-89-67-85(65-87)91-63-59-83(15)52-28-44-76(8)36-20-32-72(4)40-24-48-80(12)56-54-78(10)46-22-38-70(2)30-18-34-74(6)42-26-50-82(14)58-62-90-68-86(66-88)92-64-60-84(16)51-27-43-75(7)35-19-31-71(3)39-23-47-79(11)55-53-77(9)45-21-37-69/h69-88H,17-68H2,1-16H3/t69-,70-,71-,72-,73+,74+,75+,76+,77-,78-,79-,80-,81+,82+,83+,84+,85+,86+/m0/s1 Yes check.svgY
    Key: VMHUDYKDOMRJOK-QUYWEVSVSA-N Yes check.svgY
  • CC1CCCC(CCCC(CCOCC(OCCC(CCCC(CCCC(CCCC(CCC(CCCC(CCCC(CCCC(CCOCC(OCCC(CCCC(CCCC(CCCC(CCC(CCC1)C)C)C)C)C)CO)C)C)C)C)C)C)C)C)CO)C)C
Properties
C86H172O6
Molar mass 1302.28 g/mol
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
Yes check.svgY  verify  (what is  Yes check.svgYX mark.svgN ?)
Molecular structures of iGDGTs containing 0 to 4 cyclopentane rings (GDGT-0 to GDGT-4). Isoprenoid GDGTs.jpg
Molecular structures of iGDGTs containing 0 to 4 cyclopentane rings (GDGT-0 to GDGT-4).

Caldarchaeol is a membrane-spanning lipid of the isoprenoid glycerol dialkyl glycerol tetraether (iGDGT) class, produced and used by archaea. [1] Membranes made up of caldarchaeol are more stable since the hydrophobic chains are linked together (as compared to lipid bilayer structures in eukaryotes and bacteria), allowing archaea to withstand extreme conditions.

Contents

Chemical Structure

Caldarchaeol is also known as dibiphytanyl diglycerol tetraether, or GDGT-0. Two glycerol units are linked together by two biphytanes, each of which consist of two phytanes linked together to form a linear chain of 32 carbon atoms (40 carbons including methyl branches).

The configuration of the macrocyclic tetraether has been determined by total synthesis of the C40-diol and comparison with a sample obtained by degradation of natural tetraether. [2] A synthesis of tetraether has also been carried out. [3]

Caldarchaeol is not currently described as having any hazards. Due to its high molecular weight, it is neither volatile nor flammable. Caldarchaeol and other GDGTs are present across environments at low concentrations, and no adverse affects or evidence of toxicity are known.

Nomenclature

Nomenclature for archaeal lipids is widely varied across history and fields, and caldarchaeol is no exception. It had originally been defined as dibiphytanyl diglycerol tetraether, [4] [5] a large lipid molecule with two biphytane chains, with or without cyclopentane rings, connected by ethers to glycerols on either end. It is used to describe the entire class of isoprenoid GDGTs in many papers, both historical and recent. [5] [6] [7] [8] However, as GDGTs began to be incorporated into paleoclimate investigations, many began defining caldarchaeol specifically as GDGT-0, the isoprenoid GDGT with no cyclopentane moieties, especially when this specific structure is used in the analysis. [9] [10] [11] [12] [13]

Biological Sources

Microscopy images of archaea, all of which make iGDGTs of various structures - see Archaea article for more information Archaea.png
Microscopy images of archaea, all of which make iGDGTs of various structures - see Archaea article for more information

Caldarchaeol is the most widely spread GDGT in the archaea domain, found in every major archaeal clade except halophiles. [7] Caldarchaeol, as well as other GDGTs, were previously thought to be specific to hot environments, partially due to the assumption that archaea are only found at these temperatures [14] . However, as archaea continue to be isolated from more environmental types, the discovery of caldarchaeol across temperature, chemical, and physical conditions continues as well [5] [12] [15] [16] [17] [18] [19] [20] .

Biosynthesis

Caldarchaeol (GDGT-0) synthesis from archaeol, image adapted from Zeng et al., 2022 Caldarchaeol synthesis.png
Caldarchaeol (GDGT-0) synthesis from archaeol, image adapted from Zeng et al., 2022

The biosynthesis of caldarchaeol and other iGDGTs has been the subject of investigation for decades, due both to the complexity of the pathway and the difficulty of culturing archaea in laboratory settings. Isoprenoid-based molecules are synthesized by all three domains of life using isopentyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), 5-carbon structural isomers. Archaea make archaeol from these building blocks [22] , which is then condensed into tetraether structures using a radical S-adenosylmethionine (SAM) protein called tetraether synthase (Tes) [21] .

Biomarker Applications

Hot springs such as the Grand Prismatic Spring in Yellowstone National Park, WY are home to many species of archaea. Grand Prismatic Spring 2013.jpg
Hot springs such as the Grand Prismatic Spring in Yellowstone National Park, WY are home to many species of archaea.

Caldarchaeol is a widely distributed lipid across archaea, making it a relatively poor biomarker for specific taxa within the domain. However, comparisons between caldarchaeol concentrations and other biomarkers are frequently used to reveal community composition and/or paleoclimate proxies.

Caldarchaeol to Crenarchaeol Ratio

Formula: Caldarchaeol/Crenarchaeol

A deep-ocean rock that contained methanotrophic archaea and their iGDGTs Archaea rock.jpg
A deep-ocean rock that contained methanotrophic archaea and their iGDGTs

Tetraether Index of 86 Carbon Atoms (TEX₈₆)

Formula: TEX₈₆ = ([GDGT-2] + [GDGT-3] + [Cren']) / ([GDGT-1] + [GDGT-2] + [GDGT-3] + [Cren'])

Archaeol and Caldarchaeol Ecometric (ACE)

Formula: ACE = 100 × ([archaeol] / ([archaeol] + [caldarchaeol]))

References

  1. ↑ Langworthy, Thomas A. (1977-04-26). "Long-chain diglycerol tetraethers from Thermoplasma acidophilum". Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism. 487 (1): 37–50. doi:10.1016/0005-2760(77)90042-X. ISSN   0005-2760. PMID   857900.
  2. ↑ C. H. Heathcock; B. L. Finkelstein; E. T. Jarvi; P. A. Radel; C. R. Hadley (1988). "Acyclic stereoselection. Part 42. 1,4- and 1,5-Stereoselection by sequential aldol addition to a .alpha.,.beta.-unsaturated aldehydes followed by Claisen rearrangement. Application to total synthesis of the vitamin E side chain and the archaebacterial C40 diol". J. Org. Chem. 53 (9): 1922–1942. doi:10.1021/jo00244a017.
  3. ↑ T. Eguchi; K. Ibaragi; K. Kakinuma (1998). "Total Synthesis of Archaeal 72-Membered Macrocyclic Tetraether Lipids". J. Org. Chem. 63 (8): 2689–2698. doi:10.1021/jo972328p. PMID   11672138.
  4. ↑ NISHIHARA, Masateru; MORII, Hiroyuki; KOGA, Yosuke (1987-01-01). "Structure Determination of a Quartet of Novel Tetraether Lipids from Methanobacterium thermoautotrophicum1". The Journal of Biochemistry. 101 (4): 1007–1015. doi:10.1093/oxfordjournals.jbchem.a121942. ISSN   0021-924X. PMID   3611039.
  5. 1 2 3 Koga, Y; Nishihara, M; Morii, H; Akagawa-Matsushita, M (March 1993). "Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses". Microbiological Reviews. 57 (1): 164–182. doi:10.1128/mr.57.1.164-182.1993. ISSN   0146-0749. PMC   372904 . PMID   8464404.
  6. ↑ Jahnke, L. L.; Orphan, V. J.; Embaye, T.; Turk, K. A.; Kubo, M. D.; Summons, R. E.; Des Marais, D. J. (2008). "Lipid biomarker and phylogenetic analyses to reveal archaeal biodiversity and distribution in hypersaline microbial mat and underlying sediment". Geobiology. 6 (4): 394–410. Bibcode:2008Gbio....6..394J. doi:10.1111/j.1472-4669.2008.00165.x. ISSN   1472-4669. PMID   18564188.
  7. 1 2 Schouten, Stefan; Hopmans, Ellen C.; Sinninghe Damsté, Jaap S. (January 2013). "The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: A review". Organic Geochemistry. 54: 19–61. Bibcode:2013OrGeo..54...19S. doi:10.1016/j.orggeochem.2012.09.006.
  8. ↑ Jain, Samta (2014). "Biosynthesis of archaeal membrane ether lipids". Frontiers in Microbiology. 5: 641. doi: 10.3389/fmicb.2014.00641 . PMC   4244643 . PMID   25505460.
  9. 1 2 Turich, Courtney; Freeman, Katherine H. (June 2011). "Archaeal lipids record paleosalinity in hypersaline systems". Organic Geochemistry. 42 (9): 1147. Bibcode:2011OrGeo..42.1147T. doi:10.1016/j.orggeochem.2011.06.002.
  10. 1 2 3 Wang, Huanye; Dong, Hailiang; Zhang, Chuanlun L.; Jiang, Hongchen; Liu, Zhonghui; Zhao, Meixun; Liu, Weiguo (January 2015). "Deglacial and Holocene Archaeal Lipid-Inferred Paleohydrology and Paleotemperature History of Lake Qinghai, Northeastern Qinghai–Tibetan Plateau". Quaternary Research. 83 (1): 116–126. Bibcode:2015QuRes..83..116W. doi:10.1016/j.yqres.2014.10.003. ISSN   0033-5894.
  11. 1 2 Feakins, Sarah J.; Wu, Mong Sin; Ponton, Camilo; Tierney, Jessica E. (June 2019). "Biomarkers reveal abrupt switches in hydroclimate during the last glacial in southern California". Earth and Planetary Science Letters. 515: 164–172. Bibcode:2019E&PSL.515..164F. doi:10.1016/j.epsl.2019.03.024.
  12. 1 2 3 Kou, Qiangqiang; Zhu, Liping; Ju, Jianting; Wang, Junbo; Xu, Teng; Li, Cunlin; Ma, Qingfeng (September 2022). "Influence of salinity on glycerol dialkyl glycerol tetraether-based indicators in Tibetan Plateau lakes: Implications for paleotemperature and paleosalinity reconstructions". Palaeogeography, Palaeoclimatology, Palaeoecology. 601: 111127. Bibcode:2022PPP...60111127K. doi:10.1016/j.palaeo.2022.111127.
  13. ↑ Řezanka, Tomáš; Kyselová, Lucie; Murphy, Denis J. (July 2023). "Archaeal lipids". Progress in Lipid Research. 91: 101237. doi:10.1016/j.plipres.2023.101237. PMID   37236370.
  14. ↑ Woese, C. R.; Magrum, L. J.; Fox, G. E. (1978-09-01). "Archaebacteria". Journal of Molecular Evolution. 11 (3): 245–252. Bibcode:1978JMolE..11..245W. doi:10.1007/BF01734485. ISSN   1432-1432.
  15. ↑ Pancost, R.D; Hopmans, E.C; Sinninghe Damsté, J.S (May 2001). "Archaeal lipids in Mediterranean cold seeps: molecular proxies for anaerobic methane oxidation". Geochimica et Cosmochimica Acta. 65 (10): 1611–1627. Bibcode:2001GeCoA..65.1611P. doi:10.1016/S0016-7037(00)00562-7.
  16. ↑ Schouten, Stefan; Wakeham, Stuart G; Damsté, Jaap S.Sinninghe (October 2001). "Evidence for anaerobic methane oxidation by archaea in euxinic waters of the Black Sea". Organic Geochemistry. 32 (10): 1277–1281. Bibcode:2001OrGeo..32.1277S. doi:10.1016/S0146-6380(01)00110-3.
  17. 1 2 3 Bechtel, Achim; Smittenberg, Rienk H.; Bernasconi, Stefano M.; Schubert, Carsten J. (2010-08-01). "Distribution of branched and isoprenoid tetraether lipids in an oligotrophic and a eutrophic Swiss lake: Insights into sources and GDGT-based proxies". Organic Geochemistry. 41 (8): 822–832. Bibcode:2010OrGeo..41..822B. doi:10.1016/j.orggeochem.2010.04.022. ISSN   0146-6380.
  18. ↑ Sinninghe Damsté, Jaap S.; Rijpstra, W. Irene C.; Hopmans, Ellen C.; Jung, Man-Young; Kim, Jong-Geol; Rhee, Sung-Keun; Stieglmeier, Michaela; Schleper, Christa (October 2012). "Intact Polar and Core Glycerol Dibiphytanyl Glycerol Tetraether Lipids of Group I.1a and I.1b Thaumarchaeota in Soil". Applied and Environmental Microbiology. 78 (19): 6866–6874. Bibcode:2012ApEnM..78.6866S. doi:10.1128/AEM.01681-12. ISSN   0099-2240. PMC   3457472 . PMID   22820324.
  19. ↑ Elling, Felix J.; Könneke, Martin; Nicol, Graeme W.; Stieglmeier, Michaela; Bayer, Barbara; Spieck, Eva; de la Torre, José R.; Becker, Kevin W.; Thomm, Michael; Prosser, James I.; Herndl, Gerhard J.; Schleper, Christa; Hinrichs, Kai-Uwe (July 2017). "Chemotaxonomic characterisation of the thaumarchaeal lipidome". Environmental Microbiology. 19 (7): 2681–2700. Bibcode:2017EnvMi..19.2681E. doi:10.1111/1462-2920.13759. ISSN   1462-2912. PMID   28419726.
  20. 1 2 3 Baxter, A.J.; van Bree, L.G.J.; Peterse, F.; Hopmans, E.C.; Villanueva, L.; Verschuren, D.; Sinninghe Damsté, J.S. (December 2021). "Seasonal and multi-annual variation in the abundance of isoprenoid GDGT membrane lipids and their producers in the water column of a meromictic equatorial crater lake (Lake Chala, East Africa)". Quaternary Science Reviews. 273: 107263. Bibcode:2021QSRv..27307263B. doi:10.1016/j.quascirev.2021.107263.
  21. 1 2 Zeng, Zhirui; Chen, Huahui; Yang, Huan; Chen, Yufei; Yang, Wei; Feng, Xi; Pei, Hongye; Welander, Paula V. (2022-03-22). "Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids". Nature Communications. 13 (1): 1545. Bibcode:2022NatCo..13.1545Z. doi:10.1038/s41467-022-29264-x. ISSN   2041-1723. PMID   35318330.
  22. ↑ Jain, Samta; Caforio, Antonella; Driessen, Arnold J. M. (2014-11-26). "Biosynthesis of archaeal membrane ether lipids". Frontiers in Microbiology. 5: 641. doi: 10.3389/fmicb.2014.00641 . ISSN   1664-302X. PMC   4244643 . PMID   25505460.
  23. 1 2 Blaga, Cornelia Iulia; Reichart, Gert-Jan; Heiri, Oliver; Sinninghe Damsté, Jaap S. (April 2009). "Tetraether membrane lipid distributions in water-column particulate matter and sediments: a study of 47 European lakes along a north–south transect". Journal of Paleolimnology. 41 (3): 523–540. Bibcode:2009JPall..41..523B. doi:10.1007/s10933-008-9242-2. ISSN   0921-2728.
  24. 1 2 Schouten, Stefan; Hopmans, Ellen C.; Schefuß, Enno; Sinninghe Damsté, Jaap S. (November 2002). "Distributional variations in marine crenarchaeotal membrane lipids: a new tool for reconstructing ancient sea water temperatures?". Earth and Planetary Science Letters. 204 (1–2): 265–274. Bibcode:2002E&PSL.204..265S. doi:10.1016/S0012-821X(02)00979-2.
  25. ↑ Guo, Jinqiang; Yuan, Huamao; Song, Jinming; Qu, Baoxiao; Xing, Jianwei; Wang, Qidong; Li, Xuegang; Duan, Liqin; Li, Ning; Wang, Yingxia (2021-08-18). "Variation of Isoprenoid GDGTs in the Stratified Marine Water Column: Implications for GDGT-Based TEX86 Paleothermometry". Frontiers in Marine Science. 8. doi: 10.3389/fmars.2021.715708 . ISSN   2296-7745.
  26. ↑ Kim, Jung-Hyun; van der Meer, Jaap; Schouten, Stefan; Helmke, Peer; Willmott, Veronica; Sangiorgi, Francesca; Koç, Nalân; Hopmans, Ellen C.; Damsté, Jaap S. Sinninghe (August 2010). "New indices and calibrations derived from the distribution of crenarchaeal isoprenoid tetraether lipids: Implications for past sea surface temperature reconstructions". Geochimica et Cosmochimica Acta. 74 (16): 4639–4654. Bibcode:2010GeCoA..74.4639K. doi:10.1016/j.gca.2010.05.027.
  27. ↑ Bale, Nicole J.; Palatinszky, Marton; Rijpstra, W. Irene C.; Herbold, Craig W.; Wagner, Michael; Sinninghe Damsté, Jaap S. (2019-10-15). Atomi, Haruyuki (ed.). "Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon " Candidatus Nitrosotenuis uzonensis" at Different Growth Temperatures". Applied and Environmental Microbiology. 85 (20). Bibcode:2019ApEnM..85E1332B. doi:10.1128/AEM.01332-19. ISSN   0099-2240. PMID   31420340.
  28. ↑ Hurley, Sarah J.; Elling, Felix J.; Könneke, Martin; Buchwald, Carolyn; Wankel, Scott D.; Santoro, Alyson E.; Lipp, Julius Sebastian; Hinrichs, Kai-Uwe; Pearson, Ann (2016-07-12). "Influence of ammonia oxidation rate on thaumarchaeal lipid composition and the TEX86 temperature proxy". Proceedings of the National Academy of Sciences. 113 (28): 7762–7767. doi:10.1073/pnas.1518534113. PMC   4948339 . PMID   27357675.
  29. ↑ Zhang, Yi Ge; Pagani, Mark; Wang, Zhengrong (2016). "Ring Index: A new strategy to evaluate the integrity of TEX86 paleothermometry". Paleoceanography. 31 (2): 220–232. doi:10.1002/2015PA002848. ISSN   1944-9186.

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