Names | |
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IUPAC name 2,3-Bis(3,7,11,15-tetramethylhexadecoxy)propan-1-ol | |
Other names Archaeol lipid; 2,3-Di-O-phytanyl-sn-glycerol; 2,3-Bis[(3,7,11,15-tetramethylhexadecyl)oxy]-1-propanol | |
Identifiers | |
3D model (JSmol) | |
MeSH | archaeol+lipid |
PubChem CID | |
CompTox Dashboard (EPA) | |
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Properties | |
C43H88O3 | |
Molar mass | 653.174 g·mol−1 |
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). |
Archaeol is a diether composed of two phytanyl chains linked to the sn-2 and sn-3 positions of glycerol. As its phosphate ester, it is a common component of the membranes of archaea. [1]
The 2,3-sn-glycerol structure and ether bond linkage are two key differences between lipids found in archaea vs those of bacteria and eukarya. The latter use 1,2-sn-glycerol, and mostly, ester bonds. [2] Natural archaeol has 3R, 7R, 11R configurations for the three chiral centers in the isoprenoid chains. There are four structural variations, contributing to the complexity of the membrane lipids in function and properties. The two phytanyl chains can form a 36-member ring to yield macrocyclic archaeol. Hydroxylated archaeol has phytanyl chains hydroxylated at the first tertiary carbon atom, while sesterterpanyl archaeol have the phytanyl side chains with C25 sesterterpanyl chains, substituting at C2 of glycerol or at both carbons. Unsaturated archaeol, with the same carbon skeleton as standard archaeol but one or multiple double bonds in the phytanyl side chains is also discovered. [3]
Two archaeol molecules can undergo head-to-head linkage to form caldarchaeol (one typical glycerol dialkyl glycerol tetraether, GDGT), one of the most common tetraether lipid in archaea.
This section is missing information about archaetidylethanolamine (AE) and archaetidylglycerol (AG).(December 2023) |
Archaeol has been found in all archaea so far, at least in trace amounts. It represents 100% of the diether core lipids in most neutrophilic halophiles [3] and sulfur-dependent thermophiles (though their most core lipids are tetraether lipids). Methanogens contain hydroxyarchaeol and macrocyclic other than the standard archaeol, and sesterterpanyl-chain-containing archaeol is characteristic of alkaliphilic extreme halophiles. It is noteworthy that tetraether lipids are also widely present in archaea. [2]
Liposomes (a spherical vesicle having at least at least one lipid bilayer) of lipids from archaea typically demonstrate extremely low permeability for molecules and ions, even including protons. The ion permeability induced by ionophores (ion transporters across the membranes) are also quite low, and only comparable to that of egg phosphatidylcholine (a very common biological membrane component) at 37˚C when the temperature rises up to c.a. 70˚C. [4] [5] Compared to bacteria and eukarya, the isoprenoid side chains of archaeol are highly branched. This structural difference is believed lower the permeability of archaea over the whole growth temperature range which enables archaea to adapt to extreme environments. [6]
Archaeol's biosynthesis proceeds by a multistep process mediated by several enzymes. In simplified terms, glycerol 1-phosphate is etherified to two geranylgeranyl substituents contributed by geranylgeranyl pyrophosphate. The double bonds are reduced by nicotinamide and flavins. The phosphate group is subject to modification. [7] [8]
Archaea utilize biosynthetic pathways of isoprenoids that is distinct compared to bacteria and eukarya. The C5 precursors to the geranylgeranyl chains are isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), which are produced by modified mevalonic acid pathway. [8]
Though archaeol, featuring the ether linkage between isoprenoid chain to glycerol, has been considered as a biomarker for archaea, ether membrane lipids have also been discovered in some aerobic and anaerobic bacteria, including lipids with one ester bond and one ether bond to alkyl chains. Many strictly anoxic bacteria and a few aerobic species contain plasmalogens (Pla), which has an alkyl chain bound to sn-1 position of the glycerol via a vinyl-ether bond. Similar to archaea, these lipids are thought to increase the resistivity of bacteria to adverse environments. More stunning is the discovery of nonisoprenoid dialkyl glycerol diether lipids(DGD) and branched dialkyl glycerol tetraether lipids (brGDGT), which are formed, in the similar way to archaeol, by binding alkyls chains (but not isoprenoid chains) to glycerol molecules via ether linkage. It's highly notable that these lipids are only different from archaea ether lipids in the side chains and binding positions on the glycerol. DGD is reported in thermophilic bacteria, a few mesophilic bacteria and aggregating myxobacteria. [9] [10]
In 2018, a group from the University of Groningen managed to produce a large amount (30% of total phospholipids) of true archaeol-based phospholipid in transgenic E. coli. They found that the modified cells show higher tolerance to heat and cold. The result builds on top of their earlier 2015 attempt, which produced only a minuscule amount. [11]
Archaeol in the sediments typically originates from the hydrolysis of archaea membrane phospholipids during diagenesis. Due to its high preservation potential, it is often detected and used by organic geochemists as a biomarker for archaea activity, especially for methanogen biomass and activity. As a methanogen proxy, it is used by Michinari Sunamura et al. to directly measure the methanogens in the sediments of Tokyo Bay, [12] and also used by Katie L. H. Lim et al. as an indicator of methanogenesis in water-saturated soils. [13] C. A. McCartney et al. used it as a proxy for methane production in cattle. [14]
In the meantime, it's also used to help understand ancient biogeochemistry. It was used as a biomarker by Richard D. Pancost et al. in order to reconstruct the Holocene biogeochemistry in ombrotrophic peatlands. [15] A pilot study led by Ian D. Bull et al. also used archaeol as a biomarker to reveal the differences between fermenting digestive systems in foregut and hindgut of ancient herbivorous mammals. [16]
Additionally, because of different degradation kinetics of intact archaeol and caldarchaeol, the ratio of archaeol to caldarchaeol was proposed as a salinity proxy in highland lakes, providing a tool for paleosalinity studies. [17]
Archaeol can also get hydrolyzed in some cases, with its side chains preserved as phytane or pristane, depending on the redox conditions. [18]
To analyze archaeol, lipids are commonly extracted via the traditional Bligh-Dyer procedure, [19] usually followed by fractionation (by thin layer or column chromatography) and derivatization. Kazuhiro Demizu et al. [20] and Sadami Ohtsubo et al. [21] proposed similar processes involving acid Bligh and Dyer extraction, acid treatment and derivatization, with the core lipids finally being subjected to chromatography.
To determine the concentration of archaeol present in a sample, chromatography technologies are commonly employed, including high-performance liquid chromatography (HPLC), [20] [21] [22] gas chromatography (GC), [23] and supercritical fluid chromatography (SFC), [24] [25] with mass spectrometry (MS) often applied to aid the identification.
Glycerophospholipids or phosphoglycerides are glycerol-based phospholipids. They are the main component of biological membranes in eukaryotic cells. They are a type of lipid, of which its composition affects membrane structure and properties. Two major classes are known: those for bacteria and eukaryotes and a separate family for archaea.
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. In contrast, conventional glycerophospholipids and triglycerides are triesters. Structural types include:
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.
γ-Carotene (gamma-carotene) is a carotenoid, and is a biosynthetic intermediate for cyclized carotenoid synthesis in plants. It is formed from cyclization of lycopene by lycopene cyclase epsilon. Along with several other carotenoids, γ-carotene is a vitamer of vitamin A in herbivores and omnivores. Carotenoids with a cyclized, beta-ionone ring can be converted to vitamin A, also known as retinol, by the enzyme beta-carotene 15,15'-dioxygenase; however, the bioconversion of γ-carotene to retinol has not been well-characterized. γ-Carotene has tentatively been identified as a biomarker for green and purple sulfur bacteria in a sample from the 1.640 ± 0.003-Gyr-old Barney Creek Formation in Northern Australia which comprises marine sediments. Tentative discovery of γ-carotene in marine sediments implies a past euxinic environment, where water columns were anoxic and sulfidic. This is significant for reconstructing past oceanic conditions, but so far γ-carotene has only been potentially identified in the one measured sample.
Methanobacterium is a genus of the Methanobacteria class in the Archaea kingdom, which produce methane as a metabolic byproduct. Despite the name, this genus belongs not to the bacterial domain but the archaeal domain. Methanobacterium are nonmotile and live without oxygen, which is toxic to them, and they only inhabit anoxic environments.
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.
Methanobrevibacter smithii is the predominant methanogenic archaeon in the microbiota of the human gut. M. smithii has a coccobacillus shape. It plays an important role in the efficient digestion of polysaccharides (complex sugars) by consuming the end products of bacterial fermentation (H2, acetate, formate to some extant). M. smithii is a hydrogenotrophic methanogen that utilizes hydrogen by combining it with carbon dioxide to form methane. The removal of hydrogen by M. smithii is thought to allow an increase in the extraction of energy from nutrients by shifting bacterial fermentation to more oxidized end products.
Archaea is a domain of organisms. Traditionally, Archaea only included its prokaryotic members, but this sense has been found to be paraphyletic, as eukaryotes are now known to have evolved from archaea. Even though the domain Archaea includes eukaryotes, the term "archaea" in English still generally refers specifically to prokaryotic members of Archaea. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
sn-Glycerol 1-phosphate is the conjugate base of a phosphoric ester of glycerol. It is a component of ether lipids, which are common for archaea.
Thermococcus celer is a Gram-negative, spherical-shaped archaeon of the genus Thermococcus. The discovery of T. celer played an important role in rerooting the tree of life when T. celer was found to be more closely related to methanogenic Archaea than to other phenotypically similar thermophilic species. T. celer was the first archaeon discovered to house a circularized genome. Several type strains of T. celer have been identified: Vu13, ATCC 35543, and DSM 2476.
CDP-archaeol synthase is an enzyme with systematic name CTP:2,3-bis-O-(geranylgeranyl)-sn-glycero-1-phosphate cytidylyltransferase. This enzyme catalyses the following chemical reaction
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.
Methanococcoides burtonii is a methylotrophic methanogenic archaeon first isolated from Ace Lake, Antarctica. Its type strain is DSM 6242.
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
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.
Lycopane (C40H82; 2,6,10,14,19,23,27,31-octamethyldotriacontane), a 40 carbon alkane isoprenoid, is a widely present biomarker that is often found in anoxic settings. It has been identified in anoxically deposited lacustrine sediments (such as the Messel formation and the Condor oil shale deposit). It has been found in sulfidic and anoxic hypersaline environments (such as the Sdom Formation). It has been widely identified in modern marine sediments, including the Peru upwelling zone, the Black Sea, and the Cariaco Trench. It has been found only rarely in crude oils.
Hydroxyarchaeol is a core lipid unique to archaea, similar to archaeol, with a hydroxide functional group at the carbon-3 position of one of its ether side chains. It is found exclusively in certain taxa of methanogenic archaea, and is a common biomarker for methanogenesis and methane-oxidation. Isotopic analysis of hydroxyarchaeol can be informative about the environment and substrates for methanogenesis.
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. Some structural forms of GDGT form the basis for the TEX86 paleothermometer. Isoprenoid GDGTs, now known to be synthesized by many archaeal classes, were first discovered in extremophilic archaea cultures. Branched GDGTs, likely synthesized by acidobacteriota, were first discovered in a natural Dutch peat sample in 2000.
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.
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