View source for Chemistry:Glycerol dialkyl glycerol tetraether

[[File:Caldarchaeol linear.png|thumb|right|Chemical structure of caldarchaeol, a prototypical GDGT]]
'''Glycerol dialkyl glycerol tetraether''' lipids (GDGTs) are a class of [[Biology:Membrane lipid|membrane lipid]]s synthesized by [[Biology:Archaea|archaea]] and some [[Biology:Bacteria|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.<ref name="Schouten13.rev" /> Some structural forms of GDGT form the basis for the [[Earth:TEX86|TEX86]] [[Earth:Paleothermometer|paleothermometer]].<ref name="Schouten13.rev">{{Cite journal|date=2013-01-01|title=The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: A review|url=https://www.sciencedirect.com/science/article/abs/pii/S0146638012001982|journal=Organic Geochemistry|language=en|volume=54|pages=19–61|doi=10.1016/j.orggeochem.2012.09.006|issn=0146-6380|last1=Schouten|first1=Stefan|last2=Hopmans|first2=Ellen C.|last3=Sinninghe Damsté|first3=Jaap S.|bibcode=2013OrGeo..54...19S }}</ref> Isoprenoid GDGTs, now known to be synthesized by many archaeal classes, were first discovered in [[Earth:Extremophile|extremophilic]] archaea cultures.<ref name="MarioLuigi77">{{Cite journal|date=1977-01-01|title=Chemical structure of the ether lipids of thermophilic acidophilic bacteria of the Caldariella group|url=https://www.sciencedirect.com/science/article/abs/pii/0031942277801052|journal=Phytochemistry|language=en|volume=16|issue=12|pages=1961–1965|doi=10.1016/0031-9422(77)80105-2|issn=0031-9422|last1=De Rosa|first1=Mario|last2=De Rosa|first2=Salvatore|last3=Gambacorta|first3=Agata|last4=Minale|first4=Luigi|last5=Bu'Lock|first5=John D.|bibcode=1977PChem..16.1961D }}</ref> Branched GDGTs, likely synthesized by [[Biology:Acidobacteriota|acidobacteriota]],<ref name="Sinninghe11.acido1,3">{{Cite journal|last1=Sinninghe Damsté|first1=Jaap S.|last2=Rijpstra|first2=W. Irene C.|last3=Hopmans|first3=Ellen C.|last4=Weijers|first4=Johan W. H.|last5=Foesel|first5=Bärbel U.|last6=Overmann|first6=Jörg|last7=Dedysh|first7=Svetlana N.|date=2011-06-15|title=13,16-Dimethyl Octacosanedioic Acid ( iso -Diabolic Acid), a Common Membrane-Spanning Lipid of Acidobacteria Subdivisions 1 and 3|journal=Applied and Environmental Microbiology|language=en|volume=77|issue=12|pages=4147–4154|doi=10.1128/AEM.00466-11|issn=0099-2240|pmc=3131667|pmid=21515715|bibcode=2011ApEnM..77.4147S }}</ref> were first discovered in a natural Dutch peat sample in 2000.<ref>{{Cite journal|last1=Damsté|first1=Jaap S. Sinninghe|last2=Hopmans|first2=Ellen C.|last3=Pancost|first3=Richard D.|last4=Schouten|first4=Stefan|last5=Geenevasen|first5=Jan A. J.|date=2000|title=Newly discovered non-isoprenoid glycerol dialkyl glycerol tetraether lipids in sediments|url=http://xlink.rsc.org/?DOI=b004517i|journal=Chemical Communications|issue=17|pages=1683–1684|doi=10.1039/b004517i}}</ref>

== Chemical structure ==
[[File:Isoprenoid GDGTs.jpg|thumb|right|Chemical structures of representative isoprenoid GDGTs]]
The chemical nature of GDGTs is succinctly described by its name: they consist of two [[Chemistry:Glycerol|glycerol]] molecules connected via two [[Chemistry:Alkyl|alkyl]] chains, being held together at four [[Chemistry:Ether|ether]] linkages. In the living microbe, they are attached to two phosphate head groups that allow them to work as membrane [[Chemistry:Phospholipid|phospholipid]]s.<ref name="Schouten13.rev" /> Compared to the typical [[Biology:Lipid bilayer|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.<ref>{{Cite journal|last1=Schouten|first1=Stefan|last2=van der Meer|first2=Marcel T. J.|last3=Hopmans|first3=Ellen C.|last4=Rijpstra|first4=W. Irene C.|last5=Reysenbach|first5=Anna-Louise|last6=Ward|first6=David M.|last7=Sinninghe Damsté|first7=Jaap S.|date=2007-10-01|title=Archaeal and Bacterial Glycerol Dialkyl Glycerol Tetraether Lipids in Hot Springs of Yellowstone National Park|url=https://aem.asm.org/content/73/19/6181|journal=Applied and Environmental Microbiology|language=en|volume=73|issue=19|pages=6181–6191|doi=10.1128/AEM.00630-07|issn=0099-2240|pmc=2074994|pmid=17693566|bibcode=2007ApEnM..73.6181S }}</ref>

The two primary structural classes of GDGTs are isoprenoid (isoGDGT) and branched (brGDGT), which refer to differences in the carbon skeleton structures.<ref name="Schouten13.rev" /> 
* Isoprenoid compounds are numbered -0 through -8, with the numeral representing the number of cyclopentane rings present within the carbon skeleton structure. The exception is [[Chemistry:Crenarchaeol|crenarchaeol]], a [[Biology:Nitrososphaerota|Nitrososphaerota]] product with one cyclohexane ring moiety in addition to four cyclopentane rings.<ref name="Schouten13.rev" />
* Branched GDGTs have zero, one, or two cyclopentane moieties and are further classified based the positioning of their branches.<ref name="Schouten13.rev" /> They are numbered with roman numerals and letters.
** The roman numeral describes the total amount of modifications, summing branches and cyclopentane moieties. "I" indicates 4, "II" indicates 5, and "III" indicates 6. The simplest brGDGT is GDGT-I, with four methyls.<ref name="Schouten13.rev" />
** A lowercase suffix means that some modifications are cyclopentanes instead of methyl branches. a means one cyclopentane, b means two, and vice versa. For example, GDGT-IIb is a compound with three branches and two cyclopentane moieties (a total of five modifications).<ref name="Schouten13.rev" />

== Biological origin ==

Isoprenoid GDGTs originate as archaeal [[Biology:Membrane lipid|membrane lipid]]s, whose [[Chemistry:Fatty acid|fatty acid]]s are converted to [[Chemistry:Glycerol|glycerol]] via [[Chemistry:Esterification|esterification]] ([[Chemistry:Ether lipid|ether lipid]]).<ref name="Schouten13.rev" /> They were first recognized as being associated with [[Earth:Extremophile|extremophilic]] archaea,<ref name="MarioLuigi77" /> 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.<ref name="Schouten13.rev" /> Archaeal phylogenetic classes [[Biology:Nitrososphaerota|Nitrososphaerota]] (formerly Thaumarchaeota), [[Biology:Thermoproteota|Thermoproteota]] (formerly Crenarchaeota), "[[Biology:Euryarchaeota|Euryarchaeota]]", and "Korarchaeota" produce GDGTs.<ref name="Schouten13.rev" />

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 [[Biology:Acidobacteriota|acidobacteriota]] synthesize brGDGT.<ref name="Sinninghe11.acido1,3" /> The stereochemistry strongly hints at a non-archaeal origin.<ref>{{cite journal |last1=Weijers |first1=JW |last2=Schouten |first2=S |last3=Hopmans |first3=EC |last4=Geenevasen |first4=JA |last5=David |first5=OR |last6=Coleman |first6=JM |last7=Pancost |first7=RD |last8=Sinninghe Damsté |first8=JS |title=Membrane lipids of mesophilic anaerobic bacteria thriving in peats have typical archaeal traits. |journal=Environmental Microbiology |date=April 2006 |volume=8 |issue=4 |pages=648–57 |doi=10.1111/j.1462-2920.2005.00941.x |pmid=16584476|bibcode=2006EnvMi...8..648W |hdl=1874/22590 |s2cid=40067691 |hdl-access=free }}</ref>

=== 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.<ref name="Schouten13.rev" /> Carbon isotope analyses and association with sites of anaerobic methane oxidation suggest that GDGT-0 is produced via [[Biology:Methanotroph|methanotroph]]s.<ref name="Schouten13.rev" /> In microbiology literature not dealing with the geological record, GDGT-0 is sometimes referred to as [[Chemistry:Caldarchaeol|caldarchaeol]].<ref name="Schouten13.rev" />

=== 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.<ref name="Schouten13.rev" /> Methanogens are not thought to be large synthesizers of these molecules, with the exception of ''Methanopyrus kandleri'', which does produce them.<ref name="Schouten13.rev" /> These classes are lower in abundance than GDGT-0 and GDGRT-4. They are used in the [[Earth:TEX86|TEX86 paleothermometer]].<ref name="Schouten13.rev" />

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). [[Biology:Nitrososphaerota|Nitrososphaerota]] also makes GDGT-4.<ref>{{cite journal |last1=Damsté |first1=JS |last2=Rijpstra |first2=WI |last3=Hopmans |first3=EC |last4=Jung |first4=MY |last5=Kim |first5=JG |last6=Rhee |first6=SK |last7=Stieglmeier |first7=M |last8=Schleper |first8=C |title=Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids of group I.1a and I.1b thaumarchaeota in soil. |journal=Applied and Environmental Microbiology |date=October 2012 |volume=78 |issue=19 |pages=6866–74 |doi=10.1128/AEM.01681-12 |pmid=22820324 |pmc=3457472|bibcode=2012ApEnM..78.6866S }}</ref>

=== Crenarchaeol ===
{{main|Chemistry:Crenarchaeol}}
Crenarchaeol is mainly attributed to ammonium-oxidizing [[Biology:Nitrososphaerota|Nitrososphaerota]] and has four cyclopentane rings plus one cyclohexane ring, which distinguishes it from GDGT-4 and is unique to the Nitrososphaerota phylum.<ref name="Schouten13.rev" /> 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.<ref name=":3" /> Due to their structural similarities, crenarchaeol and GDGT-4 have similar GC/MS elution times.<ref name="Schouten13.rev" /> They are similar in prevalence to GDGT-0 and therefore are not included in the TEX<sub>86</sub> paleothermometer because their abundance overwhelms the less abundant GDGT groups.<ref name=cren.isomer/>

A crenarchaeol regioisomer, however, is a part of the [[Earth:TEX86|TEX<sub>86</sub> 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.<ref name=cren.isomer>{{Cite journal|date=2018-10-01|title=The enigmatic structure of the crenarchaeol isomer|journal=Organic Geochemistry|language=en|volume=124|pages=22–28|doi=10.1016/j.orggeochem.2018.06.005|issn=0146-6380|last1=Sinninghe Damsté|first1=Jaap S.|last2=Rijpstra|first2=W. Irene C.|last3=Hopmans|first3=Ellen C.|last4=Den Uijl|first4=Mimi J.|last5=Weijers|first5=Johan W.H.|last6=Schouten|first6=Stefan|bibcode=2018OrGeo.124...22S |s2cid=102862633 |doi-access=free}}</ref>

=== 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.<ref>{{Cite journal|last1=Rattray|first1=Jayne E.|last2=Smittenberg|first2=Rienk H.|date=2020|title=Separation of Branched and Isoprenoid Glycerol Dialkyl Glycerol Tetraether (GDGT) Isomers in Peat Soils and Marine Sediments Using Reverse Phase Chromatography|journal=Frontiers in Marine Science|language=English|volume=7|doi=10.3389/fmars.2020.539601|issn=2296-7745|hdl=20.500.11850/455576|hdl-access=free|doi-access=free}}</ref><ref name=":3">{{Cite journal|last1=Damsté|first1=Jaap S.Sinninghe|last2=Schouten|first2=Stefan|last3=Hopmans|first3=Ellen C.|last4=van Duin|first4=Adri C.T.|last5=Geenevasen|first5=Jan A.J.|date=October 2002|title=Crenarchaeol|journal=Journal of Lipid Research|language=en|volume=43|issue=10|pages=1641–1651|doi=10.1194/jlr.M200148-JLR200|pmid=12364548|s2cid=219230652 |doi-access=free}}</ref>

Two proteins responsible for making these GDGTs were identified in ''[[Biology:Sulfolobus acidocaldarius|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 [[Biology:Nitrososphaerota|Nitrososphaerota]].<ref>{{cite journal |last1=Zeng |first1=Z |last2=Liu |first2=XL |last3=Farley |first3=KR |last4=Wei |first4=JH |last5=Metcalf |first5=WW |last6=Summons |first6=RE |last7=Welander |first7=PV |title=GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=5 November 2019 |volume=116 |issue=45 |pages=22505–22511 |doi=10.1073/pnas.1909306116 |pmid=31591189 |pmc=6842593 |bibcode=2019PNAS..11622505Z |doi-access=free }}</ref>

=== brGDGT ===
The building blocks of brGDGT, specifically the long alkyl groups (iso-diabolic acid), are detected in [[Biology:Acidobacteria|acidobacteria]] subdivisions 1, 3, 4, and 6.<ref name="Sinninghe11.acido1,3" /><ref name=Sinninghe14>{{cite journal |last1=Sinninghe Damsté |first1=JS |last2=Rijpstra |first2=WI |last3=Hopmans |first3=EC |last4=Foesel |first4=BU |last5=Wüst |first5=PK |last6=Overmann |first6=J |last7=Tank |first7=M |last8=Bryant |first8=DA |last9=Dunfield |first9=PF |last10=Houghton |first10=K |last11=Stott |first11=MB |title=Ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4. |journal=Applied and Environmental Microbiology |date=September 2014 |volume=80 |issue=17 |pages=5207–18 |doi=10.1128/AEM.01066-14 |pmid=24928878|pmc=4136120|bibcode=2014ApEnM..80.5207S }}</ref><ref name=Sinninghe18/> Small amounts of brGDGT-I was detected in [[Biology:Acidobacteriaceae|Acidobacteriaceae]] strain A2-4c by full mass spectrum and tentatively in Acidobacteriaceae strain 307 by single-ion monitoring MS;<ref name="Sinninghe11.acido1,3" /> none has been detected in the 44 other strains tested as of 2018.<ref name=Sinninghe18>{{cite journal |last1=Sinninghe Damsté |first1=Jaap S. |last2=Rijpstra |first2=W. Irene C. |last3=Foesel |first3=Bärbel U. |last4=Huber |first4=Katharina J. |last5=Overmann |first5=Jörg |last6=Nakagawa |first6=Satoshi |last7=Kim |first7=Joong Jae |last8=Dunfield |first8=Peter F. |last9=Dedysh |first9=Svetlana N. |last10=Villanueva |first10=Laura |title=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 |journal=Organic Geochemistry |date=October 2018 |volume=124 |pages=63–76 |doi=10.1016/j.orggeochem.2018.07.006|bibcode=2018OrGeo.124...63S |doi-access=free }}</ref> More complex brGDGTs known from nature have not yet been detected in any cell culture.<ref name=Sinninghe14/>

== GDGT-based proxies ==
[[File:Molecular structures and HPLC detection of GDGTs.jpg|thumb|Molecular structures and [[High-performance liquid chromatography|HPLC detection]] of GDGTs. Retrieved from Tierney and Tingley (2015).<ref>{{Cite journal |last1=Tierney |first1=Jessica E. |last2=Tingley |first2=Martin P. |date=2015-06-23 |title=A TEX86 surface sediment database and extended Bayesian calibration |journal=Scientific Data |language=en |volume=2 |issue=1 |pages=150029 |doi=10.1038/sdata.2015.29 |pmid=26110065 |issn=2052-4463|pmc=4477698 }}</ref>|433x433px]]

=== 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 [[Earth:Proxy (climate)|proxies]].<ref name="Schouten13.rev" /> [[Earth:TEX86|TEX86]] is one such [[Earth:Paleothermometer|paleothermometer]] which relates distribution and relative abundance of GDGT-1, GDGT-2, GDGT-3, and crenarchaeol isomer to past [[Physics:Sea surface temperature|sea surface temperature]] (SST) (see [[Earth:TEX86|TEX86]]).<ref name="Schouten13.rev" /> GDGT-0, GDGT-4, and crenarchaeol are excluded from consideration for this proxy due to their very high abundances relative to isoGDGTs 1–3.<ref name="Schouten13.rev" /> 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.<ref>{{Cite journal|last1=Zhang|first1=Yi Ge|last2=Pagani|first2=Mark|last3=Liu|first3=Zhonghui|date=2014-04-04|title=A 12-Million-Year Temperature History of the Tropical Pacific Ocean|url=https://www.science.org/doi/10.1126/science.1246172|journal=Science|language=en|volume=344|issue=6179|pages=84–87|doi=10.1126/science.1246172|pmid=24700856|bibcode=2014Sci...344...84Z|s2cid=206552476|issn=0036-8075}}</ref> Current research suggests TEX86 works best in the temperature range 15-34 degrees Celsius.<ref name="Schouten13.rev" /> Seasonal variability in archaeal productivity and depth in the water column at which the archaea grow should be considered prior to employing this proxy.<ref name="Schouten13.rev" />

=== 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.<ref name="Schouten13.rev" /> 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.<ref name="Schouten13.rev" />

=== 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.<ref name="Schouten13.rev" /> Further research is needed to assess seasonal bias, appropriate calibration protocols, and whether the brGDGT distributions record air or soil temperature.<ref name="Schouten13.rev" />

== Measurement techniques ==

GDGTs are identified via organic geochemical analysis as the polar head groups of the membrane lipids. High-precision [[Physics:Liquid chromatography–mass spectrometry|liquid chromatography mass spectrometry]] (HPLC-MS) is the primary means by which GDGTs are analyzed due to this method's tolerance for high temperatures.<ref name="Schouten13.rev" />

== References ==
{{Reflist}}

[[Category:Lipids]]
[[Category:Ethers]]

{{Sourceattribution|Glycerol dialkyl glycerol tetraether}}