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At least 19 recordsLinked to original sources

PubMed2024

The Lrs14 family of DNA-binding proteins as nucleoid-associated proteins in the Crenarchaeal order Sulfolobales.

Organization of archaeal chromatin combines bacterial, eukaryotic, and unique characteristics. Many archaeal lineages harbor a wide diversity of small and highly expressed nucleoid-associated proteins, which are involved in DNA structuring. In Sulfolobales, representing model organisms within the Crenarchaeota, Sul7d, Cren7, Sul10a, and Sul12a are well-characterized nucleoid-associated proteins. Here, we combine evidence that the Lrs14 family of DNA binders is part of the repertoire of nucleoid-associated proteins in Sulfolobales. Lrs14-encoding genes are widespread within genomes of different members of the Sulfolobales, typically encoded as four to nine homologs per genome. The Lrs14 proteins harbor a winged helix-turn-helix DNA-binding domain and are typified by a coiled-coil dimerization. They are characterized by distinct sequence- and structure-based features, including redox-sensitive motifs and residues targeted for posttranslational modification, allowing a further classification of the family into five conserved clusters. Lrs14-like proteins have unique DNA-organizing properties. By binding to the DNA nonsequence specifically and in a highly cooperative manner, with a slight preference for AT-rich promoter regions, they introduce DNA kinks and are able to affect transcription of adjacent transcription units either positively or negatively. Genes encoding Lrs14-type proteins display considerable differential expression themselves in response to various stress conditions, with certain homologs being specific to a particular stressor. Taken together, we postulate that members of the Lrs14 family can be considered nucleoid-associated proteins in Sulfolobales, combining a DNA-structuring role with a global gene expression role in response to stress conditions.

DNA-Binding Proteins↗

PubMed1994

Using protein synthesis inhibitors to establish the phylogenetic relationships of the Sulfolobales order.

The sensitivity of the cell-free protein synthesis systems from Acidanus brierleyi, Acidianus infernus, and Metallosphaera sedula, members of the archaeal order Sulfolobales, to 40 antibiotics with different specificities has been studied. The sensitivity patterns were compared to those of Sulfolobus solfataricus and other archaeal, bacterial, and eukaryotic systems. The comparative analysis shows that ribosomes from the sulfolobales are the most refractory to inhibitors of protein synthesis described so far. The sensitivity results have been used to ascertain in phylogenetic relationships among the members of the order Sulfolobales. The evolutionary significance of these results are analyzed in the context of the phylogenetic position of this group of extreme thermophilic microorganisms.

Anti-Bacterial Agents↗

PubMed1996

Gene analysis of trehalose-producing enzymes from hyperthermophilic archaea in Sulfolobales.

The genes encoding new trehalose-producing enzymes from S. acidocaldarius ATCC33909 were cloned to analyze the distribution of these genes in Sulfolobales. Comparison of the amino acid sequences with S. solfataricus KM1 showed approximately 50% similarity. Southern analysis suggest that homologues of the trehalose-producing enzyme genes exist widely in sulfolobales and strains in Sulfolobales were classified into three kinds of genotypes.

Amino Acid Sequence↗

PubMed2005

The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79.

The Judicial Commission of the International Committee on Systematics of Prokaryotes has corrected the nomenclatural types of 12 orders: Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales.

Archaea↗

PubMed2002

Total synthesis of calditol: structural clarification of this typical component of Archaea order Sulfolobales.

The original structure of calditol--that is, an open-chain branched nonitol--has recently been questioned by various research groups and cyclopentane-based structures have been proposed. To unambiguously clear up this confusion, four isomeric cyclopentane candidates 26-29 have been synthesized. Of these, compound 27 was found to be fully identical to the natural product present in Sulfolobus solfataricus (A.T.C.C. 49155). The synthesis of 27 uses a samarium-diiodide-induced pinacolization reaction of the ketoaldehyde 15 as the critical step.

Acetates↗

PubMed1998

Sulfurisphaera ohwakuensis gen. nov., sp. nov., a novel extremely thermophilic acidophile of the order Sulfolobales.

Three spherical thermoacidophilic archaea (strains TA-1T, TA-13, TA-14) were obtained from acidic hot springs located in Ohwaku Valley, Hakone, Japan. All the isolates are facultatively anaerobic, and grew optimally at around 85 degrees C, pH 2.0. Isolate TA-1T was characterized further. The G + C content of DNA from TA-1T is 33 mol%. Although these properties resemble those of the genus Acidianus, the sequence of the 16S rRNA gene from strain TA-1T was more similar to that of species of Stygiolobus than of Acidianus. DNA-DNA hybridization experiments also indicated that strain TA-1T is clearly distinguished phylogenetically from the members of Acidianus, Sulfolobus and Metallosphaera. On the basis of the distinct physiological and molecular properties, we describe the new strains as members of the new genus Sulfurisphaera. The type species of the genus is Sulfurisphaera ohwakuensis, and the type strain of the species is TA-1T (= IFO 15161T).

Base Composition↗

PubMed1999

The alcohol dehydrogenase gene: distribution among Sulfolobales and regulation in Sulfolobus solfataricus.

The distribution of the alcohol dehydrogenase gene (adh) among different Archaea was investigated by Southern blot analysis revealing the potentiality of the adh gene as a specific marker for the genus Sulfolobus. Moreover, the in vivo expression of the adh gene from a new isolate of Sulfolobus solfataricus, G theta, was studied to investigate gene regulation in Archaea. Primer extension analysis allowed the identification of a single initiation site and the TATA box element. Comparison of the G theta adh promoter with the corresponding Ssadh (adh from S. solfataricus) and RC3adh (adh from Sulfolobus RC3) also revealed the presence of two putative regulatory inverted repeats at the 5' of the TATA element. Northern blot analysis and enzymatic assays demonstrated that the transcription and expression of the G theta adh gene is regulated by different carbon and energy sources or by the natural substrate of the ADH enzyme.

Alcohol Dehydrogenase↗

PubMed1997

DNA topology in hyperthermophilic archaea: reference states and their variation with growth phase, growth temperature, and temperature stresses.

In order to address the dynamics of DNA topology in hyperthermophilic archaea, we analysed the topological state of several plasmids recently discovered in Thermococcales and Sulfolobales. All of these plasmids were from relaxed to highly positively supercoiled in vitro, i.e. they exhibited a significant linking excess compared to the negatively supercoiled plasmids from mesophilic organisms (both Archaea and Bacteria). In the two archaeal orders, plasmid linking number (Lk) decreased as growth temperature was lowered from its optimal value, i.e. positively supercoiled plasmids were relaxed whereas relaxed plasmids became negatively supercoiled. Growth temperatures above the optimum correlated with higher positive supercoiling in Sulfolobales (Lk increase) but with relaxation of positive supercoils in Thermococcus sp. GE31. The topological variation of plasmid DNA isolated from cells at different growth phases were found to be species specific in both archaeal orders. In contrast, the direction of topological variation under temperature stress was the same, i.e. a heat shock correlated with an increase in plasmid positive supercoiling, whilst a cold shock induced negative supercoiling. The kinetics of these effects were analysed in Sulfolobales. In both temperature upshift (from 80 to 85 degrees C) and downshift (from 80 to 65 degrees C), a transient sharp variation of Lk occurred first, and then DNA supercoiling progressively reached levels typical of steady-state growth at the final temperature. These results indicate that DNA topology can change with physiological states and environmental modifications in hyperthermophilic archaea.

Archaea↗

PubMed1998

Estimation of genome sizes of hyperthermophiles.

Genomes of various hyperthermophilic and extremely thermophilic prokaryotes were analyzed with respect to size, physical organization, and 16S rDNA copy number. Our results show that all the genomes are circular, and they are in the size range of 1.6-1.8 Mb for Pyrodictium abyssi, Methanococcus igneus, Pyrobaculum aerophilum, Archaeoglobus fulgidus, Archaeoglobus lithotrophicus, and Archaeoglobus profundus (the two bacteria Fervidobacterium islandicum and Thermosipho africanus possess genomes of 1.5-Mb size). A systematic study of all validly described species of the order Sulfolobales revealed the existence of two classes of genome size for these archaea, correlating with phylogenetic analyses. The Metallosphaera-Acidianus group, plus Sulfolobus metallicus, have genomes of ca. 1.9 Mb; the other members of the order Sulfolobales group possess genome > 2.7 Mb. The special case of stygiolobus azoricus is discussed.

Archaea↗

PubMed2001

Metallosphaera sedula TA-2, a calditoglycerocaldarchaeol deletion strain of a thermoacidophilic archaeon.

A spherical thermoacidophilic archaeon, strain TA-2, was obtained from acidic hot springs located in Ohwaku Valley, Hakone, Japan. This isolate is an obligate aerobic chemoorganoheterotroph that grows optimally at about 75 degrees C, pH 2.8. The G + C content of DNA from TA-2 is 47 mol%. The 16S rRNA gene from TA-2 showed more than 99% similarity with those of Metallosphaera sedula and Metallosphaera prunae and less than 92% similarity with other members of the order Sulfolobales. DNA-DNA hybridization experiments showed more than 93% genomic DNA homology among TA-2, M. sedula DSM5348T, and M. prunae DSM10039T. However, TA-2 lacks calditoglycerocaldarchaeol derivatives, which are usually found in the membrane lipids of members of the order Sulfolobales. Therefore, calditoglycerocaldarchaeol may not be essential for survival in thermophilic and acidophilic environments. The isolate was deposited as Metallosphaera sedula TA-2 (JCM 9064, IFO 15160).

Adaptation, Biological↗

PubMed2002

An archaeal b-type cytochrome containing a nonfunctional carbonic anhydrase-like domain.

A new type of cytochrome b was isolated from the cytoplasmatic fraction of the archaeon Acidianus ambivalens, which is the first soluble cytochrome found in this member of the thermoacidophilic order of the Sulfolobales. The protein is a monomeric and monohemic cytochrome b with a molecular mass of 22 kDa. Visible spectroscopy of the as-purified protein shows a Soret peak at 405 nm and a broad band at 625 nm, indicating the presence of a high-spin ferric heme. Upon reduction, the Soret band shifts to 422 nm and a broad band at 560 nm develops, again characteristic of high-spin ferrous heme. The reduced form can bind carbon monoxide, with visible absorption bands arising at 411 and 566 nm. EPR spectroscopy of the oxidized protein shows a spectrum typical of a high-spin heme, with major g values at 6.56 and 5.85. The reduction potential of the heme cofactor was determined to be -16+/-10 mV, at pH 6.5. Analysis of the protein amino acid sequence shows that it consists of a novel arrangement of domains. The first domain, at the N-terminus, has a remarkable similarity towards beta class carbonic anhydrases, whereas the second region comprises a putative cytochrome domain. The latter presumably consists of a novel fold, as it bears no sequence similarities towards other known cytochromes, or towards known domains. Strikingly, the first module contains the C-X (n)-H-X(2)-C motif that accounts for the binding of the catalytic zinc in carbonic anhydrases, but lacks several other critical residues required for substrate binding and proper active site geometry. In agreement with this finding, the isolated cytochrome contains one bound zinc atom, but has no carbonic anhydrase activity. Inspection of the sequences available from the genomic sequencing project of the close relative archaeon Sulfolobus solfataricus shows the presence of an identical protein, suggesting its dissemination among the Sulfolobales. The role of zinc as a key element for the intrinsic thermal stability of these proteins is discussed.

Amino Acid Sequence↗

PubMed2005

Assaying for the 3-hydroxypropionate cycle of carbon fixation.

The 3-hydroxypropionate cycle is a novel pathway for autotrophic CO2 fixation, which has been demonstrated in the thermophilic phototrophic bacterium Chloroflexus aurantiacus; a yet to be defined variant of this pathway occurs in autotrophic members of the Sulfolobales (Crenarchaeota). The 3-hydroxypropionate cycle consists of the conversion of acetyl-CoA to succinyl-CoA, via malonyl-CoA, 3-hydroxypropionate, propionyl-CoA, and methylmalonyl-CoA. Carboxylation of acetyl-CoA and propionyl-CoA by acetyl-CoA/propionyl-CoA carboxylase are the CO2 fixation reactions. Succinyl-CoA serves as a precursor of cell carbon and also as a precursor of the starting compound acetyl-CoA. In C. aurantiacus, the cycle is completed by converting succinyl-CoA to malyl-CoA and cleaving malyl-CoA to acetyl-CoA and glyoxylate. Glyoxylate is then converted in a second cyclic pathway to pyruvate, which serves as a universal cell carbon precursor. The fate of succinyl-CoA in Sulfolobales is at issue. Assays used to study the characteristic enzymes of this novel pathway in C. aurantiacus are reported.

Acetyl-CoA Carboxylase↗

PubMed2004

Design of 16S rRNA-targeted oligonucleotide probes for detecting cultured and uncultured archaeal lineages in high-temperature environments.

In order to facilitate the evaluation of archaeal community diversity and distribution in high-temperature environments, 14 16S rRNA oligonucleotide probes were designed. Adequate hybridization and wash conditions of the probes encompassing most known hyperthermophilic Archaea, members of the orders Thermococcales, Desulfurococcales and Sulfolobales, of the families Methanocaldococcaceae, Pyrodictiaceae and Thermoproteaceae, of the genera Archaeoglobus, Methanopyrus and Ignicoccus, and of the as yet uncultured lineages Korarchaeota, Crenarchaeota marine group I, deep-sea hydrothermal vent euryarchaeotic group 2 (DHVE 2), and deep-sea hydrothermal vent euryarchaeotic group 8 (DHVE 8) were determined by dot-blot hybridization from target and non-target reference organisms and environmental clones. The oligonucleotide probes were also used to evaluate the archaeal community composition in nine deep-sea hydrothermal vent samples. All probes, except those targeting members of Sulfolobales, Thermoproteaceae, Pyrodictiaceae and Korarchaeota, gave positive hybridization signals when hybridized against 16S rDNA amplification products obtained from hydrothermal DNA extracts. The results confirmed the widespread occurrence of Thermococcales, Desulfurococcales, Methanocaldococcaceae and Archaeoglobus in deep-sea hydrothermal vents, and extended the known ecological habitats of uncultured lineages. Despite their wide coverage, the probes were unable to resolve the archaeal communities associated with hydrothermally influenced sediments, suggesting that these samples may contain novel lineages. This suite of oligonucleotide probes may represent an efficient tool for rapid qualitative and quantitative characterization of archaeal communities. Their application would help to provide new insights in the future into the composition, distribution and abundance of Archaea in high-temperature environments.

Archaea↗

PubMed1990

Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides.

The hyperthermophilic peptide-fermenting sulfur archaebacterium Hyperthermus butylicus was isolated from the sea floor of a solfataric habitat with temperatures of up to 112 degrees C on the coast of the island of São Miguel, Azores. The organism grows at up to 108 degrees C, grows optimally between 95 and 106 degrees C at 17 g of NaCl per liter and pH 7.0, utilizes peptide mixtures as carbon and energy sources, and forms H2S from elemental sulfur and molecular hydrogen as a growth-stimulating accessory energy source but not by sulfur respiration. The same fermentation products, CO2, 1-butanol, acetic acid, phenylacetic acid, and a trace of hydroxyphenylacetic acid, are formed both with and without of S0 and H2. Its ether lipids, the absence of a mureine sacculus, the nature of the DNA-dependent RNA polymerase, and phylogenetic classification by DNA-rRNA cross-hybridization characterize H. butylicus as part of a novel genus of the major branch of archaebacteria comprising the orders Thermoproteales and Sulfolobales, representing a particularly long lineage bifurcating with the order Sulfolobales above the branching off of the genus Thermoproteus and distinct from the genera Desulfurococcus and Pyrodictium.

Archaea↗

PubMed2004

Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry--new biomarkers for biogeochemistry and microbial ecology.

Lipids from prokaryotic cell membranes can serve as sources of information on the biogeochemistry and microbial ecology of natural ecosystems. Traditionally, apolar derivatives of the intact polar membrane molecules, e.g., fatty acids, have been the major target of lipid-based biogeochemical studies. However, when still intact, i.e., as glycerol esters and ethers with attached polar headgroups, membrane lipids are diagnostic for living prokaryotes, which makes them excellent biomarkers for the study of in situ microbial processes in geological systems such as sediments or soils. Intact polar lipids (IPLs) are attractive analytical targets because they are taxonomically more specific than their apolar derivatives and avoid exclusion of signals from prokaryotes that primarily build their membranes with ether-bound lipids such as archaea and some bacteria. Here we report results from analyses of IPLs in pure cultures of biogeochemically relevant prokaryotes and marine sediments by high-performance liquid chromatography/electrospray ionization ion-trap mass spectrometry (HPLC/ESI-IT-MSn). This technique is suitable for screening of biomass and environmental samples for distinctive taxonomic structural features such as distribution of polar lipid headgroups, types of bonds between alkyl moiety and glycerol backbone, and the chain length and degree of unsaturation in the alkyl moieties. We present analytical protocols to decipher structural information from mass spectral data. The IPL contents in selected archaeal and bacterial species are diverse and qualify as molecular fingerprints. Applied to marine sediments, the approach provided detailed information on the dominant microbial groups. The IPLs from bacterial members of anaerobic methanotrophic communities in surface sediments at Hydrate Ridge resemble those found in Desulfosarcina variabilis. The presence of dietherglycerophospholipids, however, suggests the presence of other bacteria possibly affiliated with the deepest phylogenetic branches in the tree of life. Sediments from approximately 90 m below the seafloor on the Peruvian continental margin are dominated by intact archaeal tetraethers with glycosidically bound hexoses as headgroups, consistent with a significant fraction of the community being archaea. Additional calditol-based tetraethers imply that the sedimentary archaea are taxonomically linked to the crenarchaeal Sulfolobales.

Biomarkers↗

PubMed2006

Archaeal diversity in two thermophilic chalcopyrite bioleaching reactors.

This study used a culture-independent molecular approach to investigate the archaeal community composition of thermophilic bioleaching reactors. Two culture samples, MTC-A and MTC-B, grown with different concentrations of chalcopyrite (CuFeS2), a copper sulfidic ore, at a temperature of 78 degrees C and pH 1.6 were studied. Phylogenetic analysis of the 16S rRNA genes revealed that both cultures consisted of Archaea belonging to the Sulfolobales. The 16S rRNA gene clone library of MTC-A grown with 4% (w/v) chalcopyrite was dominated by a unique phylotype related to Sulfolobus shibatae (69% of total clones). The remaining clones were affiliated with Stygiolobus azoricus (11%), Metallosphaera sp. J1 (8%), Acidianus infernus (2%), and a novel phylotype related to Sulfurisphaera ohwakuensis (10%). In contrast, the clones from MTC-B grown with 12% (w/v) chalcopyrite did not appear to contain Sulfolobus shibatae-like organisms. Instead the bioleaching consortium was dominated by clones related to Sulfurisphaera ohwakuensis (73.9% of total clones). The remaining microorganisms detected were similar to those found in MTC-A.

Biodiversity↗

PubMed2004

Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox.

BACKGROUND: Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively). RESULTS: Important relationships were confirmed, notably the dichotomy of the archaeal domain as represented by the Crenarchaeota and Euryarchaeota, the sister grouping of Sulfolobales and Aeropyrum pernix, and the monophyly of a large group comprising Thermoplasmatales, Archaeoglobus fulgidus, Methanosarcinales and Halobacteriales, with the latter two orders forming a robust cluster. The main difference concerned the position of Methanopyrus kandleri, which grouped with Methanococcales and Methanobacteriales in the translation tree, whereas it emerged at the base of the euryarchaeotes in the transcription tree. The incongruent placement of M. kandleri is likely to be the result of a reconstruction artifact due to the high evolutionary rates displayed by the components of its transcription apparatus. CONCLUSIONS: We show that two informational systems, transcription and translation, provide a largely congruent signal for archaeal phylogeny. In particular, our analyses support the appearance of methanogenesis after the divergence of the Thermococcales and a late emergence of aerobic respiration from within methanogenic ancestors. We discuss the possible link between the evolutionary acceleration of the transcription machinery in M. kandleri and several unique features of this archaeon, in particular the absence of the elongation transcription factor TFS.

Archaea↗

PubMed1995

The structure of the core polyol of the ether lipids from Sulfolobus acidocaldarius.

The major ether-type lipid structures of Sulfolobus acidocaldarius (ATCC33909) were composed of caldarchaeol and calditoglycerocaldarchaeol. However, the characterization by nuclear magnetic resonance spectroscopy and mass spectrometry showed that the structure of calditol in calditoglycerocaldarchaeol is not nonitol, 2-(1',2',3'-trihydroxypropyl)1,2,3,4,5,6-hexahydroxyhexane, but 2-hydroxymethyl-1-(2,3-dihydroxypropoxy)2,3,4,5-cyclopentanetet raol with an ether linkage in the molecule. Such an intermolecular ether linkage was resistant to BCl3 treatment, but nonresistant to 57% HI degradation treatment conducted at 100 degrees C for 60 h, producing 2-hydroxymethyl-1,2,3,4,5-cyclopentanepentaol from calditol as reaction product. Further, it was confirmed that the structure of calditol is essentially a derivative of glycerol, and hydrocarbon chains were conjugated to the glycerol-like site in the structure. The calditol with an ether linkage in the molecule suggested an important role regarding the properties of heat-resistance and acid-resistance observed in Sulfolobales.

Acetylation↗