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Caldarchaeol

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Caldarchaeol
Linear structure of caldarchaeol
Linear structure of caldarchaeol with regions of molecule labeled
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
  • 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 checkY
    Key: VMHUDYKDOMRJOK-QUYWEVSVSA-N checkY
  • 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).
checkY verify (what is checkY☒N ?)
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.

Chemical Structure

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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

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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

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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 in hot environments[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][21](and many more publications).

Biosynthesis

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Caldarchaeol (GDGT-0) synthesis from archaeol, image adapted from Zeng et al., 2022[22]

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 moelcules 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[23], which is then condensed into tetraether structures using a radical S-adenosylmethionine (SAM) protein called tetraether synthase (Tes)[22].

Biomarker Applications

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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.

These include:

Caldarchaeol to Crenarchaeol Ratio

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Formula: Caldarchaeol/Crenarchaeol

  • Methanogenic archaea have not been found to synthesize crenarchaeol, but they do produce caldarchaeol[24]
  • Used to estimate contribution to iGDGT pool by methanogens[17][20] (first used in 2009[24])
A deep-ocean rock that contained methanotrophic archaea and their iGDGTs

Tetraether Index of 86 Carbon Atoms (TEX₈₆)

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

  • The number of rings in iGDGT structures has been correlated to mean annual sea surface temperature[25]
  • Used frequently since originally described [10][17][20][21][26][27] (first defined in 2002[25])
  • Rather than temperature, the iGDGT ring number has since been found to actually be a function of NH3 oxidation rates, yet it still empirically aligns with temperature [citation needed]
  • This metric does not include a term for caldarchaeol due its synthesis by methanogens as well as the crenarchaeota that are meant to be impacting this proxy; however, methanogen growth (and therefore caldarchaeol concentrations) are still affected by temperature. To clarify this consideration and quantify the contribution of caldarchaeol to the iGDGT pool, some studies have compared TEX86 to the Ring Index (RI)[28]
    • RI = 0*[GDGT-0] + 1*[GDGT-1] + 2*[GDGT-2] + 3*[GDGT-3] + 4*[Cren] + 4*[Cren']
    • While the caldarchaeol term is multiplied by 0, it impacts the RI value through its impact on the total iGDGT pool and calculations of relative concentrations for other structures

Archaeol and Caldarchaeol Ecometric (ACE)

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

  • Halophilic archaea do not synthesize caldarchaeol, but they do make archaeol
  • Measures contribution of halophilic archaea to samples [10][11][12] (first defined in 2011[9])

References

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  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. ^ a b c 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. ^ a b 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. ^ a b 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. ^ a b c 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. ^ a b 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. ^ a b c 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. ^ a b c 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. ^ a b c 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. ^ a b 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.
  22. ^ a b 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.
  23. ^ 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.
  24. ^ a b 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.
  25. ^ a b 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.
  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. ^ 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.

Additional resources

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  • Focus of research, University of Occupational and Environmental Health, Kitakyushu, Japan
  • Monolayer properties of archaeol and caldarchaeol polar lipids of a methanogenic archaebacterium, Methanospirillum hungatei, at the air/water interface. Tomoaia-Cotisel M, Chifu E, Zsako J, Mocanu A, Quinn PJ, Kates M. Chem Phys Lipids. 1992 Nov;63(1-2):131-8
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