Importance of the isopropylidene terminal of geranylgeranyl group for the formation of tetraether lipid in methanogenic archaea

Labeling experiments using several deuterated lipids were pursued to study the biosynthesis of macrocyclic isoprenoidal lipids of thermophilic methanogenic archaea, Methanothermobacter thermautotrophicus. The isopropylidene terminal of geranylgeranyl group of monomeric precursor appeared to be important for the CC bond formation at the hydrophobic end in the macrocyclic lipids. A mechanism involving a radical trigger at the allylic methyl group is proposed for this CC bond formation.     

Effect of Headgroups on Small‐Ion Permeability across Archaea‐Inspired Tetraether Lipid Membranes

This paper examines the effects of four different polar headgroups on small‐ion membrane permeability from liposomes comprised of Archaea‐inspired glycerolmonoalkyl glycerol tetraether (GMGT) lipids. We found that the membrane‐leakage rate across GMGT lipid membranes varied by a factor of ≤1.6 as a function of headgroup structure. However, the leakage rates of small ions across membranes comprised of commercial bilayer‐forming 1‐palmitoyl‐2‐oleoyl‐sn‐glycerol (PO) lipids varied by as much as 32‐fold within the same series of headgroups. These results demonstrate that membrane leakage from GMGT lipids is less influenced by headgroup structure, making it possible to tailor the structure of the polar headgroups on GMGT lipids while retaining predictable leakage properties of membranes comprised of these tethered lipids.     

Physiological aspects involved in production of xylanolytic enzymes by deep-sea hyperthermophilic archaeon Pyrodictium abyssi

Xylanases (EC3.2.1.8) catalyze the hydrolysis of xylan, the major constituent of hemicellulose. The use of these enzymes could greatly improve the overall economics of processing lignocellulosic materials for the generation of liquid fuels and chemicals. The hyperthermophilic archaeon Pyrodictium abyssi, which was originally isolated from marine hot abyssal sites, grows optimally at 97°C and is a prospective source of highly thermostable xylanase. Its endoxylanase was shown to be highly thermostable (over 100 m in at 105°C) and active even at 110°C. The growth of the deep-sea archaeon P. abyssi was investigated using different culture techniques. Among the carbohydrates used, beech wood xylan, birch wood glucuronoxylan and the arabinoxylan from oats pelt appeared to be good inducers for endoxylanase and β-xylosidase production. The highest production of arabinofuranosidase, however, was detected in the cell extracts after growth on xylose and pyruvate, indicating that the intermediate of the tricarboxylic acid cycle acted as a nonrepressing carbon source for the production of thi enzyme. Electron microscopic studies did not show a significant difference in the cell surface (e.g., xylanosomes) when P. abyssi cells were grown on different carbohydrates. The main kinetic parameters of the organism have been determined. The cell yield was shown to be very low owing to incomplete substrate utilization, but a very high maximal specific growth rate was determined (μ_max=0.0195) at 90°C and pH 6.0. We also give information on the problems that arise during the fermentation of this hyperthermophilic archaeon at elevated temperatures.     

Mono‐, di‐ and trimethylated homologues of isoprenoid tetraether lipid cores in archaea and environmental samples: mass spectrometric identification and significance

Higher homologues of widely reported C₈₆ isoprenoid diglycerol tetraether lipid cores, containing 0–6 cyclopentyl rings, have been identified in (hyper)thermophilic archaea, representing up to 21% of total tetraether lipids in the cells. Liquid chromatography‐tandem mass spectrometry confirms that the additional carbon atoms in the C_87‐88 homologues are located in the etherified chains. Structures identified include dialkyl and monoalkyl (‘H‐shaped’) tetraethers containing C_40‐42 or C_81‐82 hydrocarbons, respectively, many representing novel compounds. Gas chromatography‐mass spectrometric analysis of hydrocarbons released from the lipid cores by ether cleavage suggests that the C₄₀ chains are biphytanes and the C₄₁ chains 13‐methylbiphytanes. Multiple isomers, having different chain combinations, were recognised among the dialkyl lipids. Methylated tetraethers are produced by Methanothermobacter thermautotrophicus in varying proportions depending on growth conditions, suggesting that methylation may be an adaptive mechanism to regulate cellular function. The detection of methylated lipids in Pyrobaculum sp. AQ1.S2 and Sulfolobus acidocaldarius represents the first reported occurrences in Crenarchaeota. Soils and aquatic sediments from geographically distinct mesotemperate environments that were screened for homologues contained monomethylated tetraethers, with di‐ and trimethylated structures being detected occasionally. The structural diversity and range of occurrences of the C_87‐89 tetraethers highlight their potential as complementary biomarkers for archaea in natural environments. Copyright © 2015 John Wiley & Sons, Ltd.     

互花米草定植的养殖尾水处理人工湿地中古菌群落的组成与分布

为探究凡纳滨对虾养殖尾水处理过程中互花米草湿地的净化效果和沉积物古菌群落的组成与分布,基于16S rRNA基因的高通量测序技术,从沉积物环境因子、古菌群落结构和多样性、环境因子与古菌群落间的相互关系进行分析.结果表明:互花米草人工湿地深层沉积物的古菌群落多样性显著高于表层和根际沉积物;门水平上,互花米草人工湿地优势古菌为泉古菌门、广古菌门和奇古菌门;纲水平上,优势古菌为深古菌纲、甲烷微菌纲和热源体纲;目水平上,互花米草人工湿地中含3种氨氧化古菌和7种产甲烷古菌.非度量多维尺度分析(NMDS)表明,互花米草根际沉积物与深层沉积物古菌群落差异显著(P<0.05),与表层更为相似.冗余分析(RDA)及Mantel检验表明,影响古菌群落的主要环境因子包括p H、铵氮(NH₄⁺-N)、总有机碳(TOC)和总磷(TP).相关性热图表明奇古菌门和其中的亚硝基菌纲与环境因子的相关性最强.氨氧化古菌群落与pH、NH₄⁺-N、总氮(TN)和TP呈显著相关(P<0.01),产甲烷古菌与环境因子则无显著相关性....     

The chaperonin of the archaeonSulfolobus solfataricus

The chaperonin of the hyperthermophilic archaeonSulfolobus solfataricus, briefly Ssocpn, was purified by a fast and high-yield procedure. Ssocpn, a 920 kDa-complex of two different subunits, displays a potassium-dependent ATPase activity with a temperature optimum at 80°C. The ability of Ssocpn to function in vitro was investigated using different protein substrates. Ssocpn promotes correct refolding of thermophilic and mesophilic enzymes from their chemically unfolded state; moreover, Ssocpn prevents the irreversible inactivation of native proteins by suppressing their precipitation upon heating. Both the activity in assisting refolding of unfolded proteins and that in preventing heat denaturation of native proteins require the hydrolysis of ATP. The chaperone-based strategies in different technological fields are discussed, and the advantages in using archaeal chaperonins are underlined.     

Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism

Methanol is a valuable raw material used in the manufacture of useful chemicals as well as a potential source of energy to replace coal and petroleum. Biotechnological interest in the microbial utilization of methanol has increased because it is an ideal carbon source and can be produced from renewable biomass. Formaldehyde, a cytotoxic compound, is a central metabolic intermediate in methanol metabolism. Therefore, microorganisms utilizing methanol have adopted several metabolic strategies to cope with the toxicity of formaldehyde. Formaldehyde is initially detoxified through trapping by some cofactors, such as glutathione, mycothiol, tetrahydrofolate, and tetrahydromethanopterin, before being oxidized to CO2. Alternatively, free formaldehyde can be trapped by sugar phosphates as the first reaction in the C1 assimilation pathways: the xylulose monophosphate pathway for yeasts and the ribulose monophosphate (RuMP) pathway for bacteria. In yeasts, although formaldehyde generation and consumption takes place in the peroxisome, the cytosolic formaldehyde oxidation pathway also plays a role in formaldehyde detoxification as well as energy formation. The key enzymes of the RuMP pathway are found in a variety of microorganisms including bacteria and archaea. Regulation of the genes encoding these enzymes and their catalytic mechanisms depend on the physiological traits of these organisms during evolution.     

First Isolation and Structure Elucidation of GDNT-β-Glu – Tetraether Lipid Fragment from Archaeal Sulfolobus Strains

Due to their special chemical structure, tetraether lipids (TEL) represent essential elements of archaeal membranes, providing these organisms with extraordinary properties. Here we describe the characterization of a newly isolated structural element of the main lipids. The TEL fragment GDNT-β-Glu was isolated from Sulfolobus metallicus and characterized in terms of its chemical structure by NMR- and MS-investigations. The obtained data are dissimilar to analogically derived established structures – in essence, the binding relationships in the polar head group are re-determined and verified. With this work, we provide an important contribution to the structure elucidation of intact TEL also contained in other Sulfolobus strains such as Solfulobus acidocaldarius and Sulfolobus solfataricus.     

Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea

We reflect on some of our studies on the hyperthermophilic archaeon, Thermococcus kodakaraensis KOD1 and its enzymes. The strain can grow at temperatures up to the boiling point and also represents one of the simplest forms of life. As expected, all enzymes displayed remarkable thermostability, and we have determined some of the basic principles that govern this feature. To our delight, many of the enzymes exhibited unique biochemical properties and novel structures not found in mesophilic proteins. Here, we focus on a few enzymes that are useful in application, and whose three-dimensional structures are characteristic of thermostable enzymes.