Novel Intact Polar and Core Lipid Compositions in the Pyrococcus Model Species, P. furiosus and P. yayanosii, Reveal the Largest Lipid Diversity Amongst Thermococcales

Elucidating the lipidome of Archaea is essential to understand their tolerance to extreme environmental conditions. Previous characterizations of the lipid composition of Pyrococcus species, a model genus of hyperthermophilic archaea belonging to the Thermococcales order, led to conflicting results, which hindered the comprehension of their membrane structure and the putative adaptive role of their lipids. In an effort to clarify the lipid composition data of the Pyrococcus genus, we thoroughly investigated the distribution of both the core lipids (CL) and intact polar lipids (IPL) of the model Pyrococcus furiosus and, for the first time, of Pyrococcus yayanosii, the sole obligate piezophilic hyperthermophilic archaeon known to date. We showed a low diversity of IPL in the lipid extract of P. furiosus, which nonetheless allowed the first report of phosphatidyl inositol-based glycerol mono- and trialkyl glycerol tetraethers. With up to 13 different CL structures identified, the acid methanolysis of Pyrococcus furiosus revealed an unprecedented CL diversity and showed strong discrepancies with the IPL compositions reported here and in previous studies. By contrast, P. yayanosii displayed fewer CL structures but a much wider variety of polar heads. Our results showed severe inconsistencies between IPL and CL relative abundances. Such differences highlight the diversity and complexity of the Pyrococcus plasma membrane composition and demonstrate that a large part of its lipids remains uncharacterized. Reassessing the lipid composition of model archaea should lead to a better understanding of the structural diversity of their lipidome and of their physiological and adaptive functions.

Gene deletions leading to a reduction in the number of cyclopentane rings in Sulfolobus acidocaldarius tetraether lipids

The cell membrane of (hyper)thermophilic archaea, including the thermoacidophile Sulfolobus acidocaldarius, incorporates dibiphytanylglycerol tetraether lipids. The hydrophobic cores of such tetraether lipids can include up to eight cyclopentane rings. Presently, nothing is known of the biosynthesis of these rings. In this study, a series of S. acidocaldarius mutants deleted of genes currently annotated as encoding proteins involved in sugar/polysaccharide processing were generated and their glycolipids were considered. Whereas the glycerol-dialkyl-glycerol tetraether core of a S. acidocaldarius tetraether glycolipid considered here mostly includes four cyclopentane rings, in cells where the Saci_0421 or Saci_1201 genes had been deleted, species containing zero, two or four cyclopentane rings were observed. At the same time, in cells lacking Saci_0201, Saci_0275, Saci_1101, Saci_1249 or Saci_1706, lipids containing mostly four cyclopentane rings were detected. Although Saci_0421 and Saci_1201 are not found in proximity to other genes putatively involved in lipid biosynthesis, homologs of these sequences exist in other Archaea containing cyclopentane-containing tetraether lipids. Thus, Saci_0421 and Saci_1201 represent the first proteins described that somehow contribute to the appearance of cyclopentane rings in the core moiety of the S. acidocaldarius glycolipid considered here.

Distribution of tetraether lipids in sulfide chimneys at the Deyin hydrothermal field, southern Mid-Atlantic Ridge: Implication to chimney growing stage

This study presents analysis of four chimney samples in terms of glycerol dialkyl glycerol tetraether lipids (GDGTs), representing different growing stages of sulfide chimneys at the Deyin hydrothermal field, the southern mid-Atlantic ridge. The modified Bligh-Dyer method was used for lipid extraction and purification. GDGTs were analyzed with an Agilent 1200 series liquid chromatograph and 6460A triple quadrupole mass spectrometer. Our results showed that the intact polar GDGTs were more abundant than the core GDGTs in the 4 samples. The intact polar isoprenoidal GDGT-0 was the dominant composition (>70% of isoprenoidal GDGTs), indicating input of thermophilic Euryarchaeota. Most branched GDGTs were likely originated from the in situ thermophilic bacteria. However, the intact polar GDGTs in the sample at the late growing stage was similar to that in normal marine sediments, suggesting that the archaea mainly came from the planktonic Thaumarchaeota input. Our results suggested that the ratio of H-GDGTs to iGDGTs could be considered as a proxy to differentiated growing stages of a chimney. This study shed light on how to assess hydrothermal venting and sulfide chimneys in deep marine environments with a biomarker method in terms of different groups of GDGTs.

Homeoviscous Adaptation of Membranes in Archaea

Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Membrane adaptation is achieved by a modification of the membrane lipid composition, a strategy termed homeoviscous adaptation. Homeoviscous adaptation in archaea involves strategies similar to that observed in bacteria and eucarya, such as the regulation of lipid chain length or saturation levels, as well as strategies specific to archaea, such as the regulation of the number of cycles along the isoprenoid chains or the regulation of the ratio between mono and bipolar lipids. Although not described yet described in hyperthermophilic bacteria, it is possible that these two strategies also apply to these latter organisms.

Membrane homeoviscous adaptation in the piezo-hyperthermophilic archaeon Thermococcus barophilus

The archaeon Thermococcus barophilus, one of the most extreme members of hyperthermophilic piezophiles known thus far, is able to grow at temperatures up to 103°C and pressures up to 80 MPa. We analyzed the membrane lipids of T. barophilus by high performance liquid chromatography–mass spectrometry as a function of pressure and temperature. In contrast to previous reports, we show that under optimal growth conditions (40 MPa, 85°C) the membrane spanning tetraether lipid GDGT-0 (sometimes called caldarchaeol) is a major membrane lipid of T. barophilus together with archaeol. Increasing pressure and decreasing temperature lead to an increase of the proportion of archaeol. Reversely, a higher proportion of GDGT-0 is observed under low pressure and high temperature conditions. Noticeably, pressure and temperature fluctuations also impact the level of unsaturation of apolar lipids having an irregular polyisoprenoid carbon skeleton (unsaturated lycopane derivatives), suggesting a structural role for these neutral lipids in the membrane of T. barophilus. Whether these apolar lipids insert in the membrane or not remains to be addressed. However, our results raise questions about the structure of the membrane in this archaeon and other Archaea harboring a mixture of di- and tetraether lipids.

Adaptation of the membrane in Archaea

Microbes often face contrasted and fluctuating environmental conditions, to which they need to adapt or die. Because membranes play a central role in regulating fluxes inward and outward from the cells, maintaining the appropriate structure of the membrane is crucial to maintain cellular integrity and functions. This is achieved in bacteria and eucarya by a modification of the membrane lipid compositions, a strategy termed homeoviscous adaptation. We review here evidence for homeoviscous adaptation in Archaea, and discuss the limits of this strategy and our knowledge in this very peculiar domain of life.

Archaebacterial bipolar tetraether lipids: Physico-chemical and membrane properties

Bipolar tetraether lipids (BTL) are abundant in archaea and can be chemically synthesized. The structures of BTL are distinctly different from the lipids found in bacteria and eukaryotes. In aqueous solution, BTL can form extraordinarily stable liposomes with different sizes, lamellarities and membrane packing densities. BTL liposomes can serve as membrane models for understanding the structure-function relationship of the plasma membrane in thermoacidophiles and can be used for technological applications. This article reviews the separation, characterization and structures of BTL as well as the physical properties and technological applications of BTL liposomes. One of the structural features of BTL is the presence of cyclopentane rings in the lipid hydrocarbon core. Archaea use the cyclopentane ring as an adaptation strategy to cope with high growth temperature. Special attention of this article is focused on how the number of cyclopentane rings varies with environmental factors and affects membrane properties.

Effect of growth temperature and growth phase on the lipid composition of the archaeal membrane from Thermococcus kodakaraensis

Archaea have unique membrane lipids typified by ether linkages of the glycerol-to-isoprenoid chains with sn-2,3 stereochemistry that runs against the naturally occurring sn-1,2 stereochemistry of the glycerophospholipids of Bacteria and Eukarya. Membrane lipids were extracted and analyzed from the hyperthermophilic archaeon, Thermococcus kodakaraensis, cultivated at various temperatures. At all growth temperatures examined, both the diphytanylglycerol diether (archaeol, C(20)) and diphytanyldiglycerol tetraether (caldarchaeol, C(40)) were identified as saturated forms, and no other lipids could be identified. The ratio of caldarchaeol to archaeol increased with increasing growth temperature, particularly at 93 degrees C. A larger amount of archaeol was detected from cells in the logarithmic phase than from those in the stationary phase at all temperatures examined. These results indicate that T. kodakaraensis modulated the membrane lipid composition depending on both the growth phase and the growth temperature, and suggest that the membrane fluidity to environmental change was maintained by altering the length of the hydrocarbon chains, and not by side-chain saturation such as double-bond hydrogenation nor by such a modification as cyclopentane ring formation.

Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent

A fast-growing and cell-fusing hyperthermophilic archaeon was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. Strain TS2T is an irregular, motile coccus that is generally 0.7–1.5 μm in diameter and possesses a polar tuft of flagella. In the mid-exponential phase of growth, cells that appeared black under phase-contrast microscopy fused at room temperature in the presence of a DNA-intercalating dye, as previously observed in Thermococcus coalescens. Cell fusion was not observed in later growth phases. Transmission electron microscopy revealed that the cells in the mid-exponential phase had a 5 nm-thick, electron-dense cell envelope that appeared to associate loosely with the cytoplasmic membrane. As the growth stage progressed, a surface layer developed on the membrane under the envelope and the envelope eventually peeled off. These observations suggest that the surface layer prevents the fusion of cells. Cells of strain TS2T grew at 50–85 °C, pH 5.6–8.3 and at NaCl concentrations of 1.0 to 4.5 %, with optimal growth occurring at 80 °C, pH 7.0 and 3.0 % NaCl. Under optimal growth conditions, strain TS2T grew very fast with an apparent doubling time of 20 min. It is suggested that the biosynthesis of the surface layer cannot catch up with cell multiplication in the mid-exponential phase and thus cells without the surface layer are generated. Strain TS2T was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 54.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belongs to the genus Thermococcus. However, no significant DNA–DNA hybridization was observed between the genomic DNA of strain TS2T and phylogenetically related Thermococcus species. On the basis of this evidence, strain TS2T is proposed to represent a novel species, Thermococcus celericrescens sp. nov., a name chosen to reflect the fast growth of the strain. The type strain is TS2T (=NBRC 101555T=JCM 13640T=DSM 17994T).

Structure elucidation of C80, C81 and C82 isoprenoid tetraacids responsible for naphthenate deposition in crude oil production

A series of C(80) isoprenoid 20-bis-16,16'-biphytanyl tetraacids has previously been found to be responsible for calcium naphthenate scaling in crude oil processing. This paper describes the structure elucidation by high-field NMR spectroscopy of the structures of the series of homologous C(80) tetraacids containing 4-8 five-membered rings. In addition, the structures of methyl-substituted C(81) and C(82) analogues containing 7 and 8 five-membered rings have been determined for the first time. The biosynthetic implications are discussed.

Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount

A cell-fusing hyperthermophilic archaeon was isolated from hydrothermal fluid obtained from Suiyo Seamount of the Izu-Bonin Arc. The isolate, TS1(T), is an irregular coccus, usually 0.5-2 microm in diameter and motile with a polar tuft of flagella. Cells in the exponential phase of growth fused at room temperature in the presence of DNA-intercalating dye to become as large as 5 microm in diameter. Fused cells showed dark spots that moved along in the cytoplasm. Large cells with a similar appearance were also observed upon culture at 87 degrees C, suggesting the occurrence of similar cell fusions during growth. Transmission electron microscopy revealed that cells in the exponential phase possessed a thin and electron-lucent cell envelope that could be lost subsequently during culture. The fragile cell envelope must be related to cell fusion. The cells grew at 57-90 degrees C, pH 5.2-8.7 and at NaCl concentrations of 1.5-4.5 %, with the optima being 87 degrees C, pH 6.5 and 2.5 % NaCl. The isolate was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 53.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate was closely related to Thermococcus species. However, no significant DNA-DNA hybridization was observed between genomic DNA of strain TS1(T) and phylogenetically related Thermococcus species. We propose that isolate TS1(T) represents a novel species, Thermococcus coalescens sp. nov., with the name reflecting the cell fusion activity observed in the strain. The type strain is TS1(T) (=JCM 12540T=DSM 16538T).

Archaeal C80 isoprenoid tetraacids responsible for naphthenate deposition in crude oil processing

The structure of a novel class of octaterpene tetracarboxylic acids which is responsible for naphthenate deposition in crude oil processing has been determined by NMR and mass spectroscopy.

The evolution of lipids

Living organisms on the Earth which are divided into three major domains--Archaea, Bacteria, and Eucarya, probably came from a common ancestral cell. Because there are many thermophilic microorganisms near the root of the universal phylogenetic tree, the common ancestral cell should be considered to be a thermophilic microorganism. The existence of a cell is necessary for the living organisms; the cell membrane is the essential structural component of a cell, so its amphiphilic property is vital for the molecule of lipids for cell membranes. Tetraether type glycerophospholipids with C40 isoprenoid chains are major membrane lipids widely distributed in archaeal cells. Cyclization number of C40 isoprenoid chains in thermophilic archaea influences the fluidity of lipids whereas the number of carbons and degree of unsaturation in fatty acids do so in bacteria and eucarya. In addition to the cyclization of the tetraether lipids, covalent bonding of two C40 isoprenoid chains was found in hyperthermophiles. These characteristic structures of the lipids seem to contribute to their fundamental physiological roles in hyperthermophiles. Stereochemical differences between G-1-P archaeal lipids and G-3-P bacterial and eucaryal lipids might have occurred by the function of some proteins long after the first cell was developed by the reactions of small organic molecules. We propose that the structure of lipids of the common ancestral cell may have been similar to those of hyperthermophilic archaea.