Glycerol dialkyl glycerol tetraether

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Chemical structure of caldarchaeol, a prototypical GDGT Caldarchaeol linear.png
Chemical structure of caldarchaeol, a prototypical GDGT

Glycerol dialkyl glycerol tetraether lipids (GDGTs) are a class of membrane lipids synthesized by archaea and some bacteria, making them useful biomarkers for these organisms in the geological record. Their presence, structure, and relative abundances in natural materials can be useful as proxies for temperature, terrestrial organic matter input, and soil pH for past periods in Earth history. [1] Some structural forms of GDGT form the basis for the TEX86 paleothermometer. [1] Isoprenoid GDGTs, now known to be synthesized by many archaeal classes, were first discovered in extremophilic archaea cultures. [2] Branched GDGTs, likely synthesized by acidobacteriota, [3] were first discovered in a natural Dutch peat sample in 2000. [4]

Contents

Chemical structure

Chemical structures of representative isoprenoid GDGTs Isoprenoid GDGTs.jpg
Chemical structures of representative isoprenoid GDGTs

The chemical nature of GDGTs is succinctly described by its name: they consist of two glycerol molecules connected via two alkyl chains, being held together at four ether linkages. In the living microbe, they are attached to two phosphate head groups that allow them to work as membrane phospholipids. [1] Compared to the typical lipid bilayer in eukaryotes and most bacteria, GDGT-diphosphates differ by having two headgroups, which allow one molecule to do the job of two typical phospholipids (allowing monolayers in water) and resist heat better. They are also connected by ether, instead of ester, bonds. [5]

The two primary structural classes of GDGTs are isoprenoid (isoGDGT) and branched (brGDGT), which refer to differences in the carbon skeleton structures. [1]

Biological origin

Isoprenoid GDGTs originate as archaeal membrane lipids, whose fatty acids are converted to glycerol via esterification (ether lipid). [1] They were first recognized as being associated with extremophilic archaea, [2] but research in recent decades has discovered the compounds in a wide range of mesophilic environments as well, including soils, lake sediment, and marine deposits. [1] Archaeal phylogenetic classes Nitrososphaerota (formerly Thaumarchaeota), Thermoproteota (formerly Crenarchaeota), "Euryarchaeota", and "Korarchaeota" produce GDGTs. [1]

Branched GDGTs are most commonly detected in peats and soils and are most associated with terrestrial settings. To date, no direct evidence for an unequivocal source organism has been reported, but the structural similarity of acidobacterial lipid to brGDGT alkyl chains strongly suggests that acidobacteriota synthesize brGDGT. [3] The stereochemistry strongly hints at a non-archaeal origin. [6]

GDGT-0

GDGT-0 has zero cyclopentane moieties and is the most ubiquitous isoGDGT synthesized by archaea. Halophilic archaea are the only group of archaea not known to produce GDGT-0. [1] Carbon isotope analyses and association with sites of anaerobic methane oxidation suggest that GDGT-0 is produced via methanotrophs. [1] In microbiology literature not dealing with the geological record, GDGT-0 is sometimes referred to as caldarchaeol. [1]

GDGT-1 – GDGT-4

GDGT-1, GDGT-2, and GDGT-3 have one, two, and three cyclopentane rings respectively within their isoprenoid biphytane carbon structures, respectively. Nitrososphaerota are the largest producers of these groups in marine and lacustrine environments. [1] Methanogens are not thought to be large synthesizers of these molecules, with the exception of Methanopyrus kandleri , which does produce them. [1] These classes are lower in abundance than GDGT-0 and GDGRT-4. They are used in the TEX86 paleothermometer. [1]

GDGT-4 refers to the version with four cyclopentane rings. It is quite abundant (although not easy to differentiate from crenarchaeol on GC/MS, see below). Nitrososphaerota also makes GDGT-4. [7]

Crenarchaeol

Crenarchaeol is mainly attributed to ammonium-oxidizing Nitrososphaerota and has four cyclopentane rings plus one cyclohexane ring, which distinguishes it from GDGT-4 and is unique to the Nitrososphaerota phylum. [1] The evolution of the cyclohexane ring was likely to adjust the density of the membrane packing to more optimally function at the cooler ocean temperatures to which Nitrososphaerota adapted. [8] Due to their structural similarities, crenarchaeol and GDGT-4 have similar GC/MS elution times. [1] They are similar in prevalence to GDGT-0 and therefore are not included in the TEX86 paleothermometer because their abundance overwhelms the less abundant GDGT groups. [9]

A crenarchaeol regioisomer, however, is a part of the TEX86 paleothermometer. This isomer likely differs by having a cis configuration on the cyclopentane ring neighboring the additional cyclohexane ring. It is presumed to be also made by Nitrososphaerota. [9]

GDGT-5 – GDGT-8

GDGTs -5 through -8 are nearly exclusive to extreme high-temperature environments such as hot springs. The larger number of cyclopentane moieties facilitates a more densely packed membrane lipid structure, which better inhibits trans-membrane passage of protons and ions. Doing so increases the molecules' thermal stability, which is necessary to survive at extreme temperatures. [10] [8]

Two proteins responsible for making these GDGTs were identified in Sulfolobus acidocaldarius , a thermoacidophile. grsA is responsible for producing the four cyclopentane rings at the C7 position (also seen in less ring-rich GDGTs), while grsB cyclizes at the unique C3 position. Homologs of the two genes are found throughout Nitrososphaerota. [11]

brGDGT

The building blocks of brGDGT, specifically the long alkyl groups (iso-diabolic acid), are detected in acidobacteria subdivisions 1, 3, 4, and 6. [3] [12] [13] Small amounts of brGDGT-I was detected in Acidobacteriaceae strain A2-4c by full mass spectrum and tentatively in Acidobacteriaceae strain 307 by single-ion monitoring MS; [3] none has been detected in the 44 other strains tested as of 2018. [13] More complex brGDGTs known from nature have not yet been detected in any cell culture. [12]

GDGT-based proxies

Molecular structures and HPLC detection of GDGTs. Retrieved from Tierney and Tingley (2015). Molecular structures and HPLC detection of GDGTs.jpg
Molecular structures and HPLC detection of GDGTs. Retrieved from Tierney and Tingley (2015).

TEX86

Because the number of cyclopentane moieties in a GDGT compound is related to the temperature of the growth environment, with increasing numbers of cyclopentane rings resulting in increased thermal stability and allowing for survival at higher temperatures, GDGT distribution and abundance can be employed as paleoclimate proxies. [1] TEX86 is one such paleothermometer which relates distribution and relative abundance of GDGT-1, GDGT-2, GDGT-3, and crenarchaeol isomer to past sea surface temperature (SST) (see TEX86). [1] GDGT-0, GDGT-4, and crenarchaeol are excluded from consideration for this proxy due to their very high abundances relative to isoGDGTs 1–3. [1] The relationship between isoGDGT distribution and temperature is not linear, and some studies have demonstrated its distinctive bias towards unrealistically cold temperatures in the lower latitudes. [15] Current research suggests TEX86 works best in the temperature range 15-34 degrees Celsius. [1] Seasonal variability in archaeal productivity and depth in the water column at which the archaea grow should be considered prior to employing this proxy. [1]

BIT Index

The branched:isoprenoid tetraether (BIT) index relates the relative abundances of brGDGTs in a natural sample to the relative abundance of soil organic matter in that sample. It is calculated by ratioing a sum of bacterially-produced brGDGT abundances over a sum of archaeal isoGDGT abundances and is based on the fundamental idea that brGDGTs are produced most commonly in terrestrial environments (most ubiquitous in soils and peats) while archaeal isoGDGTs (particularly crenarchaeol) are produced in marine environments. [1] While caveats and analytical uncertainties remain an issue, the BIT index is a potentially useful proxy for assessing the amount of fluvially transported soil organic matter compared to marine organic matter. [1]

MBT/CBT index

The methylation of branched tetraethers (MBT) and cyclization of branched tetraethers (CBT) indices relate abundances and distributions of bacterially-produced brGDGTs to relative changes in soil pH and mean annual air temperature. [1] Further research is needed to assess seasonal bias, appropriate calibration protocols, and whether the brGDGT distributions record air or soil temperature. [1]

Measurement techniques

GDGTs are identified via organic geochemical analysis as the polar head groups of the membrane lipids. High-precision liquid chromatography mass spectrometry (HPLC-MS) is the primary means by which GDGTs are analyzed due to this method's tolerance for high temperatures. [1]

Related Research Articles

<span class="mw-page-title-main">Nitrification</span> Biological oxidation of ammonia/ammonium to nitrate

Nitrification is the biological oxidation of ammonia to nitrate via the intermediary nitrite. Nitrification is an important step in the nitrogen cycle in soil. The process of complete nitrification may occur through separate organisms or entirely within one organism, as in comammox bacteria. The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.

<span class="mw-page-title-main">Ether lipid</span>

In biochemistry, an ether lipid refers to any lipid in which the lipid "tail" group is attached to the glycerol backbone via an ether bond at any position. This is in contrast to the more common ester linkage found in conventional glycerophospholipids and triglycerides. Structural types include:

TEX<sub>86</sub>

TEX86 is an organic paleothermometer based upon the membrane lipids of mesophilic marine Nitrososphaerota (formerly "Thaumarchaeota", "Marine Group 1 Crenarchaeota").

Phytane is the isoprenoid alkane formed when phytol, a chemical substituent of chlorophyll, loses its hydroxyl group. When phytol loses one carbon atom, it yields pristane. Other sources of phytane and pristane have also been proposed than phytol.

<span class="mw-page-title-main">Membrane lipid</span> Lipid molecules on cell membrane

Membrane lipids are a group of compounds which form the lipid bilayer of the cell membrane. The three major classes of membrane lipids are phospholipids, glycolipids, and cholesterol. Lipids are amphiphilic: they have one end that is soluble in water ('polar') and an ending that is soluble in fat ('nonpolar'). By forming a double layer with the polar ends pointing outwards and the nonpolar ends pointing inwards membrane lipids can form a 'lipid bilayer' which keeps the watery interior of the cell separate from the watery exterior. The arrangements of lipids and various proteins, acting as receptors and channel pores in the membrane, control the entry and exit of other molecules and ions as part of the cell's metabolism. In order to perform physiological functions, membrane proteins are facilitated to rotate and diffuse laterally in two dimensional expanse of lipid bilayer by the presence of a shell of lipids closely attached to protein surface, called annular lipid shell.

<i>Nitrosopumilus</i> Genus of archaea

Nitrosopumilus maritimus is an extremely common archaeon living in seawater. It is the first member of the Group 1a Nitrososphaerota to be isolated in pure culture. Gene sequences suggest that the Group 1a Nitrososphaerota are ubiquitous with the oligotrophic surface ocean and can be found in most non-coastal marine waters around the planet. It is one of the smallest living organisms at 0.2 micrometers in diameter. Cells in the species N. maritimus are shaped like peanuts and can be found both as individuals and in loose aggregates. They oxidize ammonia to nitrite and members of N. maritimus can oxidize ammonia at levels as low as 10 nanomolar, near the limit to sustain its life. Archaea in the species N. maritimus live in oxygen-depleted habitats. Oxygen needed for ammonia oxidation might be produced by novel pathway which generates oxygen and dinitrogen. N. maritimus is thus among organisms which are able to produce oxygen in dark.

<span class="mw-page-title-main">Caldarchaeol</span> Chemical compound

Caldarchaeol is a membrane-spanning lipid of the glycerol dialkyl glycerol tetraether class. It is found in hyperthermophilic archaea. Membranes made up of caldarchaeol are more stable since the hydrophobic chains are linked together, allowing the microorganisms to withstand high temperatures. It is also known as dibiphytanyldiglycerol tetraether. Two glycerol units are linked together by two strains which consist of two phytanes linked together to form a linear chain of 32 carbon atoms.

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<span class="mw-page-title-main">Archaea</span> Domain of single-celled organisms

Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.

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<span class="mw-page-title-main">Nitrososphaerota</span> Phylum of archaea

The Nitrososphaerota are a phylum of the Archaea proposed in 2008 after the genome of Cenarchaeum symbiosum was sequenced and found to differ significantly from other members of the hyperthermophilic phylum Thermoproteota. Three described species in addition to C. symbiosum are Nitrosopumilus maritimus, Nitrososphaera viennensis, and Nitrososphaera gargensis. The phylum was proposed in 2008 based on phylogenetic data, such as the sequences of these organisms' ribosomal RNA genes, and the presence of a form of type I topoisomerase that was previously thought to be unique to the eukaryotes. This assignment was confirmed by further analysis published in 2010 that examined the genomes of the ammonia-oxidizing archaea Nitrosopumilus maritimus and Nitrososphaera gargensis, concluding that these species form a distinct lineage that includes Cenarchaeum symbiosum. The lipid crenarchaeol has been found only in Nitrososphaerota, making it a potential biomarker for the phylum. Most organisms of this lineage thus far identified are chemolithoautotrophic ammonia-oxidizers and may play important roles in biogeochemical cycles, such as the nitrogen cycle and the carbon cycle. Metagenomic sequencing indicates that they constitute ~1% of the sea surface metagenome across many sites.

Nitrososphaera is a mesophilic genus of ammonia-oxidizing Crenarchaeota. The first Nitrososphaera organism was discovered in garden soils at the University of Vienna leading to the categorization of a new genus, family, order and class of Archaea. This genus is contains three distinct species: N. viennensis, Ca. N. gargensis, and Ca N. evergladensis. Nitrososphaera are chemolithoautotrophs and have important biogeochemical roles as nitrifying organisms.

This article discusses the Unique properties of hyperthermophilic archaea. Hyperthermophiles are organisms that can live at temperatures ranging between 70 and 125 °C. They have been the subject of intense study since their discovery in 1977 in the Galapagos Rift. It was thought impossible for life to exist at temperatures as great as 100 °C until Pyrolobus fumarii was discovered in 1997. P. fumarii is a unicellular organism from the domain Archaea living in the hydrothermal vents in black smokers along the Mid-Atlantic Ridge. These organisms can live at 106 °C at a pH of 5.5. To get energy from their environment these organisms are facultatively aerobic obligate chemolithoautotrophs, meaning these organisms build biomolecules by harvesting carbon dioxide (CO2) from their environment by using hydrogen (H2) as the primary electron donor and nitrate (NO3−) as the primary electron acceptor. These organisms can even survive the autoclave, which is a machine designed to kill organisms through high temperature and pressure. Because hyperthermophiles live in such hot environments, they must have DNA, membrane, and enzyme modifications that help them withstand intense thermal energy. Such modifications are currently being studied to better understand what allows an organism or protein to survive such harsh conditions. By learning what lets these organisms survive such harsh conditions, researchers can better synthesize molecules for industry that are harder to denature.

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Crenarchaeol is a glycerol biphytanes glycerol tetraether (GDGT) biological membrane lipid. Together with archaeol, crenarcheol comprises a major component of archaeal membranes. Archaeal membranes are distinct from those of bacteria and eukaryotes because they contain isoprenoid GDGTs instead of diacyl lipids, which are found in the other domains. It has been proposed that GDGT membrane lipids are an adaptation to the high temperatures present in the environments that are home to extremophile archaea

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Paula Veronica Welander is a microbiologist and professor at Stanford University who is known for her research using lipid biomarkers to investigate how life evolved on Earth.

Biphytane (or bisphytane) is a C40 isoprenoid produced from glycerol dialkyl glycerol tetraether (GDGT) degradation. As a common lipid membrane component, biphytane is widely used as a biomarker for archaea. In particular, given its association with sites of active anaerobic oxidation of methane (AOM), it is considered a biomarker of methanotrophic archaea. It has been found in both marine and terrestrial environments.

References

  1. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 Schouten, Stefan; Hopmans, Ellen C.; Sinninghe Damsté, Jaap S. (2013-01-01). "The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: A review". Organic Geochemistry. 54: 19–61. doi:10.1016/j.orggeochem.2012.09.006. ISSN   0146-6380.
  2. 1 2 De Rosa, Mario; De Rosa, Salvatore; Gambacorta, Agata; Minale, Luigi; Bu'Lock, John D. (1977-01-01). "Chemical structure of the ether lipids of thermophilic acidophilic bacteria of the Caldariella group". Phytochemistry. 16 (12): 1961–1965. doi:10.1016/0031-9422(77)80105-2. ISSN   0031-9422.
  3. 1 2 3 4 Sinninghe Damsté, Jaap S.; Rijpstra, W. Irene C.; Hopmans, Ellen C.; Weijers, Johan W. H.; Foesel, Bärbel U.; Overmann, Jörg; Dedysh, Svetlana N. (2011-06-15). "13,16-Dimethyl Octacosanedioic Acid ( iso -Diabolic Acid), a Common Membrane-Spanning Lipid of Acidobacteria Subdivisions 1 and 3". Applied and Environmental Microbiology. 77 (12): 4147–4154. doi:10.1128/AEM.00466-11. ISSN   0099-2240. PMC   3131667 . PMID   21515715.
  4. ↑ Damsté, Jaap S. Sinninghe; Hopmans, Ellen C.; Pancost, Richard D.; Schouten, Stefan; Geenevasen, Jan A. J. (2000). "Newly discovered non-isoprenoid glycerol dialkyl glycerol tetraether lipids in sediments". Chemical Communications (17): 1683–1684. doi:10.1039/b004517i.
  5. ↑ Schouten, Stefan; van der Meer, Marcel T. J.; Hopmans, Ellen C.; Rijpstra, W. Irene C.; Reysenbach, Anna-Louise; Ward, David M.; Sinninghe Damsté, Jaap S. (2007-10-01). "Archaeal and Bacterial Glycerol Dialkyl Glycerol Tetraether Lipids in Hot Springs of Yellowstone National Park". Applied and Environmental Microbiology. 73 (19): 6181–6191. doi:10.1128/AEM.00630-07. ISSN   0099-2240. PMC   2074994 . PMID   17693566.
  6. ↑ Weijers, JW; Schouten, S; Hopmans, EC; Geenevasen, JA; David, OR; Coleman, JM; Pancost, RD; Sinninghe Damsté, JS (April 2006). "Membrane lipids of mesophilic anaerobic bacteria thriving in peats have typical archaeal traits". Environmental microbiology. 8 (4): 648–57. doi:10.1111/j.1462-2920.2005.00941.x. PMID   16584476.
  7. ↑ Damsté, JS; Rijpstra, WI; Hopmans, EC; Jung, MY; Kim, JG; Rhee, SK; Stieglmeier, M; Schleper, C (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): 6866–74. doi:10.1128/AEM.01681-12. PMC   3457472 . PMID   22820324.
  8. 1 2 Damsté, Jaap S.Sinninghe; Schouten, Stefan; Hopmans, Ellen C.; van Duin, Adri C.T.; Geenevasen, Jan A.J. (October 2002). "Crenarchaeol". Journal of Lipid Research. 43 (10): 1641–1651. doi: 10.1194/jlr.M200148-JLR200 . PMID   12364548. S2CID   219230652.
  9. 1 2 Sinninghe Damsté, Jaap S.; Rijpstra, W. Irene C.; Hopmans, Ellen C.; Den Uijl, Mimi J.; Weijers, Johan W.H.; Schouten, Stefan (2018-10-01). "The enigmatic structure of the crenarchaeol isomer". Organic Geochemistry. 124: 22–28. doi: 10.1016/j.orggeochem.2018.06.005 . ISSN   0146-6380. S2CID   102862633.
  10. ↑ Rattray, Jayne E.; Smittenberg, Rienk H. (2020). "Separation of Branched and Isoprenoid Glycerol Dialkyl Glycerol Tetraether (GDGT) Isomers in Peat Soils and Marine Sediments Using Reverse Phase Chromatography". Frontiers in Marine Science. 7. doi: 10.3389/fmars.2020.539601 . hdl: 20.500.11850/455576 . ISSN   2296-7745.
  11. ↑ Zeng, Z; Liu, XL; Farley, KR; Wei, JH; Metcalf, WW; Summons, RE; Welander, PV (5 November 2019). "GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean". Proceedings of the National Academy of Sciences of the United States of America. 116 (45): 22505–22511. doi:10.1073/pnas.1909306116. PMC   6842593 . PMID   31591189.
  12. 1 2 Sinninghe Damsté, JS; Rijpstra, WI; Hopmans, EC; Foesel, BU; Wüst, PK; Overmann, J; Tank, M; Bryant, DA; Dunfield, PF; Houghton, K; Stott, MB (September 2014). "Ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4". Applied and environmental microbiology. 80 (17): 5207–18. doi:10.1128/AEM.01066-14. PMC   4136120 . PMID   24928878.
  13. 1 2 Sinninghe Damsté, Jaap S.; Rijpstra, W. Irene C.; Foesel, Bärbel U.; Huber, Katharina J.; Overmann, Jörg; Nakagawa, Satoshi; Kim, Joong Jae; Dunfield, Peter F.; Dedysh, Svetlana N.; Villanueva, Laura (October 2018). "An overview of the occurrence of ether- and ester-linked iso-diabolic acid membrane lipids in microbial cultures of the Acidobacteria: Implications for brGDGT paleoproxies for temperature and pH". Organic Geochemistry. 124: 63–76. doi: 10.1016/j.orggeochem.2018.07.006 .
  14. ↑ Tierney, Jessica E.; Tingley, Martin P. (2015-06-23). "A TEX86 surface sediment database and extended Bayesian calibration". Scientific Data. 2 (1): 150029. doi:10.1038/sdata.2015.29. ISSN   2052-4463. PMC   4477698 .
  15. ↑ Zhang, Yi Ge; Pagani, Mark; Liu, Zhonghui (2014-04-04). "A 12-Million-Year Temperature History of the Tropical Pacific Ocean". Science. 344 (6179): 84–87. Bibcode:2014Sci...344...84Z. doi:10.1126/science.1246172. ISSN   0036-8075. PMID   24700856. S2CID   206552476.
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