TitleAbstractYear(sorted ascending)
diversity of free-living prokaryotes from a deep-sea site at the antarctic polar contribute to the understanding of deep-sea planktonic communities, we explored the prokaryotic diversity of a 3000 m deep site at the antarctic polar front using molecular methods. bacterial 16s rdna-amplified sequences corresponded to the as yet uncultivated groups sar11, within the alpha-proteobacteria, and sar324, within the delta-proteobacteria, as well as to the gamma-proteobacteria, cytophagales, planctomyces, gram-positives, and the group of environmental sequences sar406. among them, ...200111451524
purification, crystallization, and preliminary x-ray diffraction analysis of the tricorn protease hexamer from thermoplasma acidophilum.tricorn protease from thermoplasma acidophilum is a hexameric enzyme; in vivo the hexamers assemble further to form large icosahedral capsids of 14.6 mda. recombinant tricorn protease was purified as an enzymatically active hexamer of 0.72 mda that formed crystals of octahedral morphology under low-ionic-strength conditions. these crystals belong to space group c2 with unit cell dimensions a = 307.5 a, b = 163.2 a, c = 220.9 a, beta = 105.5 degrees and diffract to 2.2-a resolution using high-bri ...200111469880
the chaperones of the archaeon thermoplasma acidophilum.chaperonesare an essential component of a cell's ability to respond to environmental challenges. chaperones have been studied primarily in bacteria, but in recent years it has become apparent that some classes of chaperones either are very divergent in bacteria relative to archaea and eukaryotes or are missing entirely. in contrast, a high degree of similarity was found between the chaperonins of archaea and those of the eukaryotic cytosol, which has led to the establishment of archaeal model sy ...200111580262
atp-induced structural change of the thermosome is temperature-dependent.protein folding by chaperonins is powered by atp binding and hydrolysis. atpase activity drives the folding machine through a series of conformational rearrangements, extensively described for the group i chaperonin groel from escherichia coli but still poorly understood for the group ii chaperonins. the latter--archaeal thermosome and eukaryotic tric/cct--function independently of a groes-like cochaperonin and are proposed to rely on protrusions of their own apical domains for opening and closu ...200111580263
review: nucleotide binding to the thermoplasma thermosome: implications for the functional cycle of group ii chaperonins.structural information on group ii chaperonins became available during recent years from electron microscopy and x-ray crystallography. three conformational states have been identified for both archaeal and eukaryotic group ii chaperonins: an open state, a spherical closed conformation, and an intermediate asymmetric bullet-shaped form. however, the functional cycle of group ii chaperonins appears less well understood, although major principles are conserved when compared to group i chaperonins: ...200111580264
gene duplication and the evolution of group ii chaperonins: implications for structure and function.chaperonins are multisubunit protein-folding assemblies. they are composed of two distinct structural classes, which also have a characteristic phylogenetic distribution. group i chaperonins (called groel/cpn60/hsp60) are present in bacteria and eukaryotic organelles while group ii chaperonins are found in archaea (called the thermosome or tf55) and the cytoplasm of eukaryotes (called cct or tric). gene duplication has been an important force in the evolution of group ii chaperonins: archaea pos ...200111580265
the hunt for living gold. the search for organisms in extreme environments yields useful enzymes for industry. 200111713183
crystal structure of the tricorn protease reveals a protein disassembly line.the degradation of cytosolic proteins is carried out predominantly by the proteasome, which generates peptides of 7-9 amino acids long. these products need further processing. recently, a proteolytic system was identified in the model organism thermoplasma acidophilum that performs this processing. the hexameric core protein of this modular system, referred to as tricorn protease, is a 720k protease that is able to assemble further into a giant icosahedral capsid, as determined by electron micro ...200111719810
hydration and molecular motions in synthetic phytanyl-chained glycolipid vesicle membranes.proton permeation rates across membranes of a synthetic branch-chained glycolipid, 1,3-di-o-phytanyl-2-o-(beta-d-maltotriosyl)glycerol (mal3(phyt)2) as well as a branch-chained phospholipid, diphytanoylphosphatidylcholine (dphpc) were lower than those of straight-chained lipids such as egg yolk phosphatidylcholine (epc) by a factor of approximately 4 at ph 7.0 and 25 degrees c. to examine whether degrees of water penetration and molecular motions in mal3(phyt)2 membranes can account for the lowe ...200111721000
the intein of the thermoplasma a-atpase a subunit: structure, evolution and expression in e. coli.inteins are selfish genetic elements that excise themselves from the host protein during post translational processing, and religate the host protein with a peptide bond. in addition to this splicing activity, most reported inteins also contain an endonuclease domain that is important in intein propagation.200111722801
mechanosensitive channel of thermoplasma, the cell wall-less archaea: cloning and molecular using a functional approach of reconstituting detergent-solubilized membrane proteins into liposomes and following their function in patch-clamp experiments, we identified a novel mechanosensitive (ms) channel in the thermophilic cell wall-less archaeon thermoplasma volcanium. sodium dodecyl sulfate polyacrylamide gel electrophoresis (sds-page) of the enriched protein fractions revealed a band of approx 15 kda comparable to mscl, the bacterial ms channel of large conductance. 20 n-terminal re ...200111898860
prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic comparing the gene order in the completely sequenced archaeal genomes complemented by sequence profile analysis, we predict the existence and protein composition of the archaeal counterpart of the eukaryotic exosome, a complex of rnases, rna-binding proteins, and helicases that mediates processing and 3'->5' degradation of a variety of rna species. the majority of the predicted archaeal exosome subunits are encoded in what appears to be a previously undetected superoperon. in methanobacterium ...200111157787
quinone profiles of thermoplasma acidophilum ho-62.quinones of thermoplasma acidophilum ho-62 were analyzed by high-performance liquid chromatography, mass spectrometry, and nuclear magnetic resonance. menaquinone, methionaquinone, and 2-trans and 2-cis forms of thermoplasmaquinone were identified. the relative amount of thermoplasmaquinone increased under anaerobic conditions, and those of menaquinone and methionaquinone increased under aerobic conditions.200111157962
the evolution of 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 ...200111803978
mobile elements in archaeal genomes.the recent availability of several archaeal genome sequences has provided a basis for detailed analyses of the frequency, location and phylogeny of archaeal mobile elements. all the known elements fall into two main types, autonomous insertion sequence (is) elements and the non-autonomous miniature inverted repeat element (mite)-like elements. both classes are considered to be mobilized via transposases that are encoded by the is elements, although mobility has only been demonstrated experimenta ...200211814653
effects of a squalene epoxidase inhibitor, terbinafine, on ether lipid biosyntheses in a thermoacidophilic archaeon, thermoplasma acidophilum.the archaeal plasma membrane consists mainly of diether lipids and tetraether lipids instead of the usual ester lipids found in other organisms. although a molecule of tetraether lipid is thought to be synthesized from two molecules of diether lipids, there is no direct information about the biosynthetic pathway(s) or intermediates of tetraether lipid biosynthesis. in this study, we examined the effects of the fungal squalene epoxidase inhibitor terbinafine on the growth and ether lipid biosynth ...200211844769
archaeal signal peptidases from the genus thermoplasma: structural and mechanistic hybrids of the bacterial and eukaryal enzymes. 200211847567
facile distinction of neutral and acidic tetraether lipids in archaea membrane by halogen atom adduct ions in electrospray ionization mass spectrometry.calditocaldarchaeol (neutral tetraether lipid) from sulfolobus acidocaldarius (acidothermophilic archaea) and intact total lipid from the thermoacidophilic archaea sulfolobus sp. was examined by electrospray ionization time-of-flight mass spectrometry in the negative-ion mode using high resolution. when the sample was injected as a solution in a 3:1 mixture of methanol (meoh) and chloroform (chcl(3)) using an infusion system, the total ether lipid afforded molecular-related ions as [m - h](-) fo ...200211857765
electron cryo-microscopy of vat, the archaeal p97/cdc48 homologue from thermoplasma acidophilum.vat (valosine containing protein-like atpase from thermoplasma acidophilum), an archaeal member of the aaa-family (atpases associated with a variety of cellular activities) that possesses foldase as well as unfoldase-activity, forms homo-hexameric rings like its eukaryotic homologues p97 and cdc48. the vat-monomer exhibits the tripartite domain architecture typical for type ii aaa-atpases: n-d1-d2, whereby n is the substrate binding n-terminal domain preceding domains d1 and d2, both containing ...200211955016
purifying and directional selection in overlapping prokaryotic overlapping genes, the same dna sequence codes for two proteins using different reading frames. analysis of overlapping genes can help in understanding the mode of evolution of a coding region from noncoding dna. we identified 71 pairs of convergent genes, with overlapping 3' ends longer than 15 nucleotides, that are conserved in at least two prokaryotic genomes. among the overlap regions, we observed a statistically significant bias towards the 123:132 phase (i.e. the second codon base in on ...200212047938
acidophiles of saline water at thermal vents of vulcano, italy.dna was extracted from samples taken from close to acidic hydrothermal vents on shore of the aeolian island of vulcano (italy). rna gene sequences were amplified by pcr, cloned, and sequenced. a sequence with an origin in samples at 35 degrees and 45 degrees c corresponded to that of a novel acidithiobacillus species that was isolated from water close to the vents. novel, iron-oxidizing mesophilic acidophiles were isolated through enrichment cultures with ferrous iron but were not represented in ...200212072955
specific orientation and two-dimensional crystallization of the proteasome at metal-chelating lipid interfaces.the potential of a protein-engineered his tag to immobilize macromolecules in a predictable orientation at metal-chelating lipid interfaces was investigated using recombinant 20 s proteasomes his-tagged in various positions. electron micrographs demonstrated that the orientation of proteasomes bound to chelating lipid films could be controlled via the location of their his tags: proteasomes his-tagged at their sides displayed exclusively side-on views, while proteasomes his-tagged at their ends ...200212114506
identification of the gene (bbs1) most commonly involved in bardet-biedl syndrome, a complex human obesity syndrome.bardet-biedl syndrome (bbs, omim 209900) is a genetic disorder with the primary features of obesity, pigmentary retinopathy, polydactyly, renal malformations, mental retardation and hypogenitalism. individuals with bbs are also at increased risk for diabetes mellitus, hypertension and congenital heart disease. what was once thought to be a homogeneous autosomal recessive disorder is now known to map to at least six loci: 11q13 (bbs1), 16q21 (bbs2), 3p13 p12 (bbs3), 15q22.3 q23 (bbs4), 2q31 (bbs5 ...200212118255
expression of long- and short-type fk506 binding proteins in hyperthermophilic has been reported that the hyperthermophilic archaeon, methanococcus jannaschii, possesses two fkbp (fk506 binding protein) genes in the genome, one being 26 kda fkbp (long-type fkbp) and the other, 18 kda fkbp (short-type fkbp). fkbp is a family of peptidyl-prolyl cis-trans isomerases (ppiases). in order to clarify the difference between their roles in archaeal cells, they were expressed in escherichia coli, and their ppiase and chaperone-like protein-folding activities were investigated. th ...200212119099
formation of metal nanoclusters on specific surface sites of protein molecules.during vacuum condensation of metals on frozen proteins, nanoclusters are preferentially formed at specific surface sites (decoration). understanding the nature of metal/protein interaction is of interest for structure analysis and is also important in the fields of biocompatibility and sensor development. studies on the interaction between metal and distinct areas on the protein which enhance or impede the probability for cluster formation require information on the structural details of the pr ...200212144790
structures of the tricorn-interacting aminopeptidase f1 with different ligands explain its catalytic mechanism.f1 is a 33.5 kda serine peptidase of the alpha/beta-hydrolase family from the archaeon thermoplasma acidophilum. subsequent to proteasomal protein degradation, tricorn generates small peptides, which are cleaved by f1 to yield single amino acids. we have solved the crystal structure of f1 with multiwavelength anomalous dispersion (mad) phasing at 1.8 a resolution. in addition to the conserved catalytic domain, the structure reveals a chiefly alpha-helical domain capping the catalytic triad. thus ...200212374735
structural basis for the processive protein degradation by tricorn protease.cell survival critically depends on the efficient use of available resources. this includes both the clearance and the recycling of those protein components that have become futile or defective. several proteins sequentially accomplish this complex task. the proteasome serves as an initial protein shredder and generates peptides of 7-12 amino acids in length. in general, these products are useless burden to the cell and need further processing. a few years ago, a proteolytic system was identifie ...200212437101
novel thermoactive glucoamylases from the thermoacidophilic archaea thermoplasma acidophilum, picrophilus torridus and picrophilus oshimae.the thermoacidophilic archaea thermoplasma acidophilum (optimal growth at 60 degrees c and ph 1-2), picrophilus torridus and picrophilus oshimae (optimal growth at 60 degrees c and ph 0.7) were able to utilize starch as sole carbon source. during growth these microorganisms secreted heat and acid-stable glucoamylases into the culture fluid. applying sds gel electrophoresis activity bands were detected with appearent molecular mass (mw) of 141.0, 95.0 kda for t. acidophilum, 133.0, 90.0 kda for p ...200212448707
recovery of novel bacterial diversity from a forested wetland impacted by reject coal.sulphide mineral mining together with improperly contained sulphur-rich coal represents a significant environmental problem caused by leaching of toxic material. the savannah river site's d-area harbours a 22-year-old exposed reject coal pile (rcp) from which acidic, metal rich, saline runoff has impacted an adjacent forested wetland. in order to assess the bacterial community composition of this region, composite sediment samples were collected at three points along a contamination gradient (hi ...200212460285
navigation inside a protease: substrate selection and product exit in the tricorn protease from thermoplasma acidophilum.the proposed pathway and mechanism of substrate entry and product egress in the hexameric d3 symmetric tricorn protease from thermoplasma acidophilum were explored by crystallographic studies of ligand complexes and by structure-based mutagenesis. obstruction of the pore within the 7-bladed beta-propeller (beta7) domain by alkylation or oxidation of an engineered double cysteine mutant strongly decreased enzymatic activities. in line herewith, the crystal structure of the tricorn protease in com ...200212470958
safety of archaeosome adjuvants evaluated in a mouse model.archaeosomes, liposomes prepared from the polar ether lipids extracted from archaea, demonstrate great potential as immunomodulating carriers of soluble antigens, promoting humoral and cell mediated immunity in the vaccinated host. the safety of unilamellar archaeosomes prepared from the total polar lipids (tpl) of halobacterium salinarum, methanobrevibacter smithii or thermoplasma acidophilum was evaluated in female balb/c mice using ovalbumin (ova) as the model antigen. groups of 6-8 mice were ...200212519630
complete polar lipid composition of thermoplasma acidophilum ho-62 determined by high-performance liquid chromatography with evaporative light-scattering detection.polar ether lipids of thermoplasma acidophilum ho-62 were purified by high-performance liquid chromatography with an evaporative light-scattering detector. structures of purified lipids were investigated by capillary gas chromatography, mass spectrometry, and nuclear magnetic resonance. three types of ether lipids were found: phospholipids, glycolipids, and phosphoglycolipids. the two phospholipids had glycerophosphate as the phosphoester moiety. the seven glycolipids had different combinations ...200211751835
a dna repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis.during a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most archaea (with the exception of thermoplasma acidophilum and halobacterium nrc-1) and some bacteria, including the hyperthermophiles thermotoga maritima and aquifex aeolicus. the gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conse ...200211788711
characterization of the precursor of tetraether lipid biosynthesis in the thermoacidophilic archaeon thermoplasma acidophilum.polar lipid biosynthesis in the thermoacidophilic archaeon thermoplasma acidophilum was analyzed using terbinafine, an inhibitor of tetraether lipid biosynthesis. cells of t. acidophilum were labeled with [(14)c]mevalonic acid, and their lipids were extracted and analyzed by two-dimensional thin-layer chromatography. lipids labeled with [(14)c]mevalonic acid, [(14)c]glycerol, and [(32)p]orthophosphoric acid were extracted and hydrolyzed under different conditions to determine the structure of po ...200312768455
purification and characterization of geranylgeranylglyceryl phosphate synthase from a thermoacidophilic archaeon, thermoplasma acidophilum.we purified a geranylgeranylglyceryl phosphate (gggp) synthase from thermoplasma acidophilum by several steps of chromatography. based on the proteinase-fragment-mass-pattern analysis of the sds-page band of the partially purified protein, the dna sequence encoding the protein was identified from the whole genome sequence database of the species. the gene encoding gggp synthase in t. acidophilum was cloned after pcr amplification of the gene from the genomic dna. the recombinant enzyme was expre ...200312801917
effect of temperature and pressure on the proteolytic specificity of the recombinant 20s proteasome from methanococcus jannaschii.the hydrolytic specificity of the recombinant 20s proteasome from the deep-sea thermophile methanococcus jannaschii was evaluated toward oxidized insulin b-chain across a range of temperatures (35 degrees, 55 degrees, 75 degrees, and 90 degrees c) and hydrostatic pressures (1, 250, 500, and 1,000 atm). of the four temperatures considered, the same maximum overall hydrolysis rate was observed at both 55 degrees and 75 degrees c, which are much lower than the t(opt) of 116 degrees c previously obs ...200312820035
proline- and arginine-rich peptides constitute a novel class of allosteric inhibitors of proteasome activity.substrate-specific inhibition of the proteasome has been unachievable despite great interest in proteasome inhibitors as drugs. recent studies demonstrated that pr39, a natural proline- and arginine-rich antibacterial peptide, stimulates angiogenesis and inhibits inflammatory responses by specifically blocking degradation of ikappabalpha and hif-1alpha by the proteasome. however, molecular events involved in the pr39-proteasome interaction have not been elucidated. here we show that pr39 is a no ...200312873125
proteasome-cytochrome c interactions: a model system for investigation of proteasome host-guest interactions.owing to its high thermal stability and structural simplicity, the archaebacterium thermoplasma acidophilum 20s proteasome was selected for mechanistic studies in this work. this oligomeric enzyme complex consists of a barrel-shaped 20s core (approximately 700kda) comprised of four stacked seven-membered rings with a alpha(7)beta(7)beta(7)alpha(7) subunit structure situated around a 7-fold symmetry axis. the hollow interior of the proteasome has three large interconnected chambers with narrow (1 ...200312873127
microbiology. biogeography for bacteria. 200312881575
microbial ecology of an extreme acidic environment, the tinto river.the tinto river (huelva, southwestern spain) is an extreme environment with a rather constant acidic ph along the entire river and a high concentration of heavy metals. the extreme conditions of the tinto ecosystem are generated by the metabolic activity of chemolithotrophic microorganisms thriving in the rich complex sulfides of the iberian pyrite belt. molecular ecology techniques were used to analyze the diversity of this microbial community. the community's composition was studied by denatur ...200312902280
the pore of activated 20s proteasomes has an ordered 7-fold symmetric conformation.the 20s proteasome is a large multisubunit assembly that performs most of the intracellular non-lysosomal proteolysis of eukaryotes. substrates access the proteasome active sites, which are sequestered in the interior of the barrel-shaped structure, through pores that are opened by binding of activator complexes. the crystal structure of yeast proteasome in complex with an 11s activator suggested that activation results from disordering of the proteasome gate residues. here we report further ana ...200312941688
perspectives on the origin of microfilaments, microtubules, the relevant chaperonin system and cytoskeletal motors--a commentary on the spirochaete origin of flagella.the origin of cytoskeleton and the origin of relevant intracellular transportation system are big problems for understanding the emergence of eukaryotic cells. the present article summarized relevant information of evidences and molecular traces on the origin of actin, tubulin, the chaperonin system for folding them, myosins, kinesins, axonemal dyneins and cytoplasmic dyneins. on this basis the authors proposed a series of works, which should be done in the future, and indicated the ways for rea ...200312974612
characterization of a novel intracellular endopeptidase of the alpha/beta hydrolase family from streptomyces coelicolor a3(2).in a proteasome-lacking mutant of streptomyces coelicolor a3(2), an intracellular enzyme with chymotrypsin-like activity, absent from the wild type, was detected. complementation that restored proteasome function did not suppress expression of the endopeptidase. since the enzyme was not found in two other s. coelicolor proteasome mutants, its expression probably resulted from a secondary mutation arisen in the proteasome mutant. purification of the endopeptidase revealed its identity to sco7095, ...200312511496
archaeosomes as self-adjuvanting delivery systems for cancer vaccines.archaeal ether glycerolipid vesicles (archaeosomes) efficiently deliver exogenous antigen for induction of humoral and cell-mediated immunity. because induction of cd8 cytotoxic t cells is critical for protective vaccination against tumors, we compared the ability of various archaeosome lipid compositions to evoke a strong cd8 ctl response to entrapped antigen. subcutaneous immunization of mice with ovalbumin (ova) entrapped in all archaeosome lipid compositions evoked a primary (day 10) splenic ...200315203920
characterization of methanogenic archaea in the leachate of a closed municipal solid waste landfill.cultivation-independent molecular approaches were used to investigate the phylogenetic composition of archaea and the relative abundance of phylogenetically defined groups of methanogens in the leachate of a closed municipal solid waste landfill. cloning and phylogenetic analysis of archaeal 16s rrna gene sequences (16s rdna) revealed that the landfill leachate harbored a diverse archaea community, with sequence types distributed within the two archaeal kingdoms of the euryarchaeota and the cren ...200319719570
protein-based biosensors for diabetic this article we show the recent progress in the field of glucose sensing based on the utilization of enzymes and proteins as probes for stable and non-consuming fluorescence biosensors. we developed a new methodology for glucose sensing using inactive forms of enzymes such as the glucose oxidase from aspergillus niger, the glucose dehydrogenase from the thermophilic microorganism thermoplasma acidophilum, and the glucokinase from the thermophilic eubacterium bacillus stearothermophilus. gluco ...200415617257
analysis of bacterial glucose dehydrogenase homologs from thermoacidophilic archaeon thermoplasma acidophilum: finding and characterization of aldohexose dehydrogenase.the nadp(+)-preferring glucose dehydrogenase from thermoacidophilic archaeon thermoplasma acidophilum has been characterized, and its crystal structure has been determined (structure, 2:385-393, 1994). its sequence and structure are not homologous to bacterial nad(p)(+)-dependent glucose dehydrogenases, and its molecular weight is also quite defferent. on the other hand, three functionally unknown genes with homologies to bacterial nad(p)(+)-dependent glucose dehydrogenases have been sequenced a ...200415618614
crystal structure of the hypothetical protein ta1238 from thermoplasma acidophilum: a new type of helical super-bundle.the crystal structure of the hypothetical protein ta1238 from thermoplasma acidophilum was solved with multiple-wavelength anomalous diffraction and refined at 2.0 a resolution. the molecule consists of a typical four-helix antiparallel bundle with overhand connection. however, its oligomerization into a trimer leads to a coiled "super-helix" which is novel for such bundles. its central feature, a six-stranded coiled coil, is also novel for proteins. ta1238 does not have strong sequence homologu ...200415704011
the persistence exponent of dna.using the complete genome of thermoplasma volcanium, as an example, we have examined the distribution functions for the amount of c or g in consecutive, non-overlapping blocks of m bases in this system. we find that these distributions are very much broader (by many factors) than those expected for a random distribution of bases. if we plot the widths of the c-g distributions relative to the widths expected for random distributions, as a function of the block size used, we obtain a power law wit ...200415223144
mutational analysis of conserved aaa+ residues in the archaeal lon protease from thermoplasma acidophilum.the lon protease from the archaeon thermoplasma acidophilum (talon) is composed of an n-terminal atpase associated with various cellular activities (aaa+) domain and a c-terminal lon protease domain. although related in sequence to the soluble lon proteases, talon was shown to be membrane-bound in its native host and also when expressed in escherichia coli. recombinant talon was purified as a functional high-molecular weight complex displaying atpase and proteolytic activity. mutagenesis of cons ...200415358558
crystal structure of a dodecameric tetrahedral-shaped aminopeptidase.protein turnover is an essential process in living cells. the degradation of cytosolic polypeptides is mainly carried out by the proteasome, resulting in 7-9-amino acid long peptides. further degradation is usually carried out by energy-independent proteases like the tricorn protease from thermoplasma acidophilum. recently, a novel tetrahedral-shaped dodecameric 480-kda aminopeptidase complex (tet) has been described in haloarcula marismortui that differs from the known ring- or barrel-shaped se ...200415375159
phylogenie: automated phylome generation and analysis.phylogenetic reconstruction is the method of choice to determine the homologous relationships between sequences. difficulties in producing high-quality alignments, which are the basis of good trees, and in automating the analysis of trees have unfortunately limited the use of phylogenetic reconstruction methods to individual genes or gene families. due to the large number of sequences involved, phylogenetic analyses of proteomes preclude manual steps and therefore require a high degree of automa ...200415459293
characterization of sac10a, a hyperthermophile dna-binding protein from sulfolobus acidocaldarius.sac10a is a member of a group of basic dna-binding proteins thought to be important in chromatin structure and regulation in the archaeon sulfolobus. we describe here the isolation, gene identification, and biophysical characterization of native sac10a. the protein exists as a 23.8 kda homodimer at ph 7 and unfolds with a t degrees of 122 degrees c. dissociation of the dimer into folded globular subunits is promoted by decreased ph and salt concentration. thermal unfolding of the monomeric subun ...200415476396
discovery of the catalytic function of a putative 2-oxoacid dehydrogenase multienzyme complex in the thermophilic archaeon thermoplasma acidophilum.those aerobic archaea whose genomes have been sequenced possess a single 4-gene operon that, by sequence comparisons with bacteria and eukarya, appears to encode the three component enzymes of a 2-oxoacid dehydrogenase multienzyme complex. however, no catalytic activity of any such complex has ever been detected in the archaea. in the current paper, we have cloned and expressed the first two genes of this operon from the thermophilic archaeon, thermoplasma acidophilum. we demonstrate that the pr ...200415556640
the thermoplasma acidophilum lon protease has a ser-lys dyad active site.a gene with significant similarity to bacterial lon proteases was identified during the sequencing of the genome of the thermoacidophilic archaeon thermoplasma acidophilum. protein sequence comparison revealed that thermoplasma lon protease (talon) is more similar to the lonb proteases restricted to gram-positive bacteria than to the widely distributed bacterial lona. however, the active site residues of the protease and atpase domain are highly conserved in all lon proteases. using site-directe ...200415560777
thermoplasma acidophilum taa43 is an archaeal member of the eukaryotic meiotic branch of aaa atpases.sequencing of the thermoplasma acidophilum genome revealed a new gene, taa43 , which codes for a 43-kda protein containing one aaa domain; we therefore termed it thermoplasma aaa atpase of 43 kda (taa43). close homologs of taa43 are found only in related thermoplasmales, e.g. t. volcanium and ferroplasma acidarmanus , but not in other archaea. a detailed phylogenetic analysis showed that taa43 and its homologs belong to the 'meiotic' branch of the aaa family. although aaa proteins usually assemb ...200415576333
bifunctional phosphoglucose/phosphomannose isomerases from the archaea aeropyrum pernix and thermoplasma acidophilum constitute a novel enzyme family within the phosphoglucose isomerase superfamily.the hyperthermophilic crenarchaeon aeropyrum pernix contains phosphoglucose isomerase (pgi) activity. however, obvious homologs with significant identity to known pgis could not be identified in the sequenced genome of this organism. the pgi activity from a. pernix was purified and characterized. kinetic analysis revealed that, unlike all known pgis, the enzyme catalyzed reversible isomerization not only of glucose 6-phosphate but also of epimeric mannose 6-phosphate at similar catalytic efficie ...200414551194
structure- and function-based characterization of a new phosphoglycolate phosphatase from thermoplasma acidophilum.the protein ta0175 has a large number of sequence homologues, most of which are annotated as unknown and a few as belonging to the haloacid dehalogenase superfamily, but has no known biological function. using a combination of amino acid sequence analysis, three-dimensional crystal structure information, and kinetic analysis, we have characterized ta0175 as phosphoglycolate phosphatase from thermoplasma acidophilum. the crystal structure of ta0175 revealed two distinct domains, a larger core dom ...200414555659
crystal structures of the rhodococcus proteasome with and without its pro-peptides: implications for the role of the pro-peptide in proteasome understand the role of the pro-peptide in proteasome assembly, we have determined structures of the rhodococcus proteasome and a mutant form that prevents the autocatalytic removal of its pro-peptides. the structures reveal that the pro-peptide acts as an assembly-promoting factor by linking its own beta-subunit to two adjacent alpha-subunits, thereby providing a molecular explanation for the observed kinetics of proteasome assembly. the rhodococcus proteasome has been found to have a substan ...200414659753
crystal structures of the group ii chaperonin from thermococcus strain ks-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms.the crystal structures of the group ii chaperonins consisting of the alpha subunit with amino acid substitutions of g65c and/or i125t from the hyperthermophilic archaeum thermococcus strain ks-1 were determined. these mutants have been shown to be active in atp hydrolysis but inactive in protein folding. the structures were shown to be double-ring hexadecamers in an extremely closed form, which was consistent with the crystal structure of native alpha8beta8-chaperonin from thermoplasma acidophil ...200414729342
solution structure of hypothetical protein ta1414 from thermoplasma acidophilum. 200414739641
a novel endonucleolytic mechanism to generate the cca 3' termini of trna molecules in thermotoga maritima.the trna 3'-terminal cca sequence is essential for aminoacylation of the trnas and for translation on the ribosome. the trnas are transcribed as larger precursor molecules containing 5' and 3' extra sequences. in the trnas that do not have the encoded cca, the 3' extra sequence after the discriminator nucleotide is usually cleaved off by the trna 3' processing endoribonuclease (3' trnase, or rnase z), and the 3'-terminal cca residues are added thereto. here we analyzed thermotoga maritima 3' trn ...200414749326
rapid and sensitive dot-matrix methods for genome analysis.motivation: dot-matrix plots are widely used for similarity analysis of biological sequences. many algorithms and computer software tools have been developed for this purpose. though some of these tools have been reported to handle sequences of a few 100 kb, analysis of genome sequences with a length of >10 mb on a microcomputer is still impractical due to long execution time and computer memory requirement. results: two dot-matrix comparison methods have been developed for analysis of large seq ...200414764561
highly robust lipid membranes on crystalline s-layer supports investigated by electrochemical impedance the present work, s-layer supported lipid membranes formed by a modified langmuir-blodgett technique were investigated by electrochemical impedance spectroscopy (eis). basically two intermediate hydrophilic supports for phospholipid- (dphypc) and bipolar tetraetherlipid- (mpl from thermoplasma acidophilum) membranes have been applied: first, the s-layer protein sbpa isolated from bacillus sphaericus ccm 2177 recrystallized onto a gold electrode; and second, as a reference support, an s-layer ...200415003878
the structural basis for methylmalonic aciduria. the crystal structure of archaeal atp:cobalamin adenosyltransferase.atp:cobalamin adenosyltransferase mmab was recently identified as the gene responsible for a disorder of cobalamin metabolism in humans (cblb complementation group). the crystal structure of the mmab sequence homologue from thermoplasma acidophilum (ta1434; genbank identification number gi|16082403) was determined to a resolution of 1.5 a. ta1434 was confirmed to be an atp:cobalamin adenosyltransferase, which depended absolutely on divalent metal ions (mg2+ > mn2+ > co2+) and only used atp or da ...200415044458
nmr studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion ii chaperonins close their cavity with the help of conserved, helical extensions, the so-called protrusions, which emanate from the apical or substrate-binding domains. a comparison of previously solved crystal structures of the apical domains of the thermosome from thermoplasma acidophilum showed structural plasticity in the protrusion parts induced by extensive packing interactions. in order to assess the influence of the crystal contacts we investigated both the alpha and beta-apical do ...200415095983
[proteases in archaea]. 200415168532
two-substrate association with the 20s proteasome at single-molecule level.the bipartite structure of the proteasome raises the question of functional significance. a rational design for unraveling mechanistic details of the highly symmetrical degradation machinery from thermoplasma acidophilum pursues orientated immobilization at metal-chelating interfaces via affinity tags fused either around the pore apertures or at the sides. end-on immobilization of the proteasome demonstrates that one pore is sufficient for substrate entry and product release. remarkably, a 'dead ...200415175655
a voyage to the inner space of cells. 200515608126
crystal structure of a predicted precorrin-8x methylmutase from thermoplasma acidophilum. 200515609338
crystal structure of a nicotinate phosphoribosyltransferase from thermoplasma acidophilum.we have determined the crystal structure of nicotinate phosphoribosyltransferase from themoplasma acidophilum (tanaprtase). the tanaprtase has three domains, an n-terminal domain, a central functional domain, and a unique c-terminal domain. the crystal structure revealed that the functional domain has a type ii phosphoribosyltransferase fold that may be a common architecture for both nicotinic acid and quinolinic acid (qa) phosphoribosyltransferases (prtase) despite low sequence similarity betwe ...200515753098
phylogenetic analysis of archaea in the deep-sea sediments of west pacific warm pool.archaea are known to play important roles in carbon cycling in marine sediments. the main compositions of archaeal community in five deep-sea sediment samples collected from west pacific warm pool area (wp-0, wp-1, wp-2, wp-3, wp-4), and in five sediment layers (1 cm-, 3 cm-, 6 cm-, 10 cm-, 12 cm- layer) of the 12 cm sediment core of wp-0 were checked and compared by denaturing gradient gel electrophoresis and 16 s rrna gene sequencing. it was revealed that all the deep-sea sediment samples chec ...200515761691
cooperativity in the thermosome.the thermosome from thermoplasma acidophilum is a type ii chaperonin composed of eight alpha and eight beta subunits. the genes encoding the two types of subunit were co-expressed in escherichia coli and the alpha8/beta8 complex purified from the cell extract. the isolated complex showed steady-state atpase properties characteristic of the thermosome purified from the native organism and was capable of enhancing the folding yield of a thermostable enzyme at elevated temperature (55 degrees c). t ...200515808850
biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes.a phylogenetic analysis of the genes encoding enzymes in the pentose phosphate pathway (ppp), the ribulose monophosphate (rump) pathway, and the chorismate pathway of aromatic amino acid biosynthesis, employing data from 13 complete archaeal genomes, provides a potential explanation for the enigmatic phylogenetic patterns of the ppp genes in archaea. genomic and biochemical evidence suggests that three archaeal species (methanocaldococcus jannaschii, thermoplasma acidophilum and thermoplasma vol ...200515876568
crystal structures of the tricorn interacting factor f3 from thermoplasma acidophilum, a zinc aminopeptidase in three different conformations.the tricorn interacting factor f3 is an 89 kda zinc aminopeptidase from the archaeon thermoplasma acidophilum. together with the tricorn interacting factors f1 and f2, f3 degrades the tricorn protease products and thus completes the proteasomal degradation pathway by generating free amino acids. here, we present the crystal structures of f3 in three different conformations at 2.3 a resolution. the zinc aminopeptidase is composed of four domains: an n-terminal saddle-like beta-structure domain; a ...200515893768
the 1.9 a structure of a proteasome-11s activator complex and implications for proteasome-pan/pa700 interactions.proteasomes are cylindrical structures that function in multiple cellular processes by degrading a wide variety of cytosolic and nuclear proteins. substrate access and product release from the enclosed catalytic chamber occurs through axial pores that are opened by activator complexes. here, we report high-resolution structures of wild-type and mutant archaeal proteasomes bound to the activator pa26. these structures support the proposal that an ordered open conformation is required for proteoly ...200515916965
cultivated anaerobic acidophilic/acidotolerant thermophiles from terrestrial and deep-sea hydrothermal habitats.metabolic and phylogenetic diversity of cultivated anaerobic microorganisms from acidic continental hot springs and deep-sea hydrothermal vents was studied by molecular and microbiological methods. anaerobic organotrophic enrichment cultures growing at ph 3.5-4.0 and 60 or 85 degrees c with organic energy sources were obtained from samples of acidic hot springs of kamchatka peninsula (pauzhetka, moutnovski volcano, uzon caldera) and kunashir island (south kurils) as well as from the samples of c ...200515970992
structuring of the genetic code took place at acidic ph.i have observed that in multiple regression the number of codons specifying amino acids in the genetic code is positively correlated with the isoelectric point of amino acids and their molecular weight. therefore basic amino acids are, on average, codified in the genetic code by a larger number of codons, which seems to imply that the genetic code originated in an acidic 'intracellular' environment. moreover, i compare the proteins from picrophilus torridus and thermoplasma volcanium, which have ...200515978625
microbial community in a geothermal aquifer associated with the subsurface of the great artesian basin, investigate the biomass and phylogenetic diversity of the microbial community inhabiting the deep aquifer of the great artesian basin (gab), geothermal groundwater gushing out from the aquifer was sampled and analyzed. microbial cells in the groundwater were stained with acridine orange and directly counted by epifluorescence microscopy. microbial cells were present at a density of 10(8)-10(9) cells per liter of groundwater. archaeal and bacterial small-subunit rrna genes (rdnas) were amplifi ...200515980939
x-ray snapshots of peptide processing in mutants of tricorn-interacting factor f1 from thermoplasma acidophilum.the tricorn-interacting factor f1 of the archaeon thermoplasma acidophilum cleaves small hydrophobic peptide products of the proteasome and tricorn protease. f1 mutants of the active site residues that are involved in substrate recognition and catalysis displayed distinct activity patterns toward fluorogenic test substrates. crystal structures of the mutant proteins complexed with peptides phe-leu, pro-pro, or pro-leu-gly-gly showed interaction of glutamates 213 and 245 with the n termini of the ...200515994304
crystal structure of lipoate-protein ligase a bound with the activated intermediate: insights into interaction with lipoyl domains.lipoic acid is the covalently attached cofactor of several multi-component enzyme complexes that catalyze key metabolic reactions. attachment of lipoic acid to the lipoyl-dependent enzymes is catalyzed by lipoate-protein ligases (lpls). in escherichia coli, two distinct enzymes lipoate-protein ligase a (lpla) and lipb-encoded lipoyltransferase (lipb) catalyze independent pathways for lipoylation of the target proteins. the reaction catalyzed by lpla occurs in two steps. first, lpla activates exo ...200516141198
studies on codon usage in thermoplasma acidophilum and its possible implications on the occurrences of lateral gene transfer.codon usage studies have been carried out on the coding sequences of thermoplasma acidophilum, which is an archaeon and grows at very low ph and high temperature. overall codon usage data analysis indicates that all the four bases are almost equifrequent at the third position of codons, which is expected (since genomic gc % of this genome is about 46%). however, multivariate statistical analysis indicates that there are two major trends in the codon usage variation among the genes in this organi ...200516187257
vat, the thermoplasma homolog of mammalian p97/vcp, is an n domain-regulated protein unfoldase.the thermoplasma vcp-like atpase from thermoplasma acidophilum (vat) atpase is a member of the two-domain aaa atpases and homologous to the mammalian p97/vcp and nsf proteins. we show here that the vat atpase complex unfolds green fluorescent protein (gfp) labeled with the ssra-degradation tag. increasing the mg2+ concentration derepresses the atpase activity and concomitantly stimulates the unfolding activity of vat. similarly, the vatdeltan complex, a mutant of vat deleted for the n domain, di ...200516236712
solution structure of archaeglobus fulgidis peptidyl-trna hydrolase (pth2) provides evidence for an extensive conserved family of pth2 enzymes in archea, bacteria, and eukaryotes.the solution structure of protein af2095 from the thermophilic archaea archaeglobus fulgidis, a 123-residue (13.6-kda) protein, has been determined by nmr methods. the structure of af2095 is comprised of four alpha-helices and a mixed beta-sheet consisting of four parallel and anti-parallel beta-strands, where the alpha-helices sandwich the beta-sheet. sequence and structural comparison of af2095 with proteins from homo sapiens, methanocaldococcus jannaschii, and sulfolobus solfataricus reveals ...200516251366
purification and analysis of recombinant 11s activators of the 20s proteasome: trypanosoma brucei pa26 and human pa28 alpha, pa28 beta, and pa28 gamma.proteasomes perform the bulk of nonlysosomal degradation of aberrant, damaged, misfolded, and naturally short-lived regulatory proteins in eukaryotic cells. they are approximately 700-kda assemblies whose hollow architecture sequesters the proteolytic sites inside a central chamber, thereby ensuring that the activity of isolated proteasomes is repressed. in vivo, proteasomes are activated by protein complexes, including the 11s activators (pa28 and pa26), which bind to one or both ends of the ba ...200516275338
characterization of the dna gyrase from the thermoacidophilic archaeon thermoplasma acidophilum.thermoplasma acidophilum is sensitive to the antibiotic drug novobiocin, which inhibits dna gyrase. we characterized dna gyrases from t. acidophilum strains in vitro. the dna gyrase from a novobiocin-resistant strain and an engineered mutant were less sensitive to novobiocin. the novobiocin-resistant gyrase genes might serve as t. acidophilum genetic markers.200516321962
photophysics of tryptophan fluorescence: link with the catalytic strategy of the citrate synthase from thermoplasma acidophilum.the formation of all major intermediates in the reaction catalyzed by the citrate synthase from thermoplasma acidophilum is accompanied by changes in tryptophan fluorescence. the largest change is the strong quenching observed on formation of the binary complex with substrate, oxaloacetate (oaa). the four tryptophan residues present in the enzyme have been changed to nonfluorescent ones in various combinations without major perturbations in protein stability, enzyme mechanism, or other physical ...200515683225
properties of the recombinant glucose/galactose dehydrogenase from the extreme thermoacidophile, picrophilus picrophilus torridus, a euryarchaeon that grows optimally at 60 degrees c and ph 0.7 and thus represents the most acidophilic thermophile known, glucose oxidation is the first proposed step of glucose catabolism via a nonphosphorylated variant of the entner-doudoroff pathway, as deduced from the recently completed genome sequence of this organism. the p. torridus gene for a glucose dehydrogenase was cloned and expressed in escherichia coli, and the recombinant enzyme, gdha, was purified and c ...200515691337
a molecular dynamics study of an archaeal tetraether lipid membrane: comparison with a dipalmitoylphosphatidylcholine lipid bilayer.molecular dynamics simulations of an archaeal membrane made up of bipolar tetraether lipids and a dipalmitoylphosphatidylcholine (dppc) lipid membrane were performed and compared for the first time. the simulated archaeal membrane consists of a pure monolayer of asymmetrical lipids, analogous to the main polar lipid [mpl; swain, m., brisson, j.-r., sprott, g.d., cooper, f.p., and patel, g.b., (1997) identification of beta-l-gulose as the sugar moiety of the main polar lipid of thermoplasma acido ...200516382574
structure of a putative lipoate protein ligase from thermoplasma acidophilum and the mechanism of target selection for post-translational modification.lipoyl-lysine swinging arms are crucial to the reactions catalysed by the 2-oxo acid dehydrogenase multienzyme complexes. a gene encoding a putative lipoate protein ligase (lpla) of thermoplasma acidophilum was cloned and expressed in escherichia coli. the recombinant protein, a monomer of molecular mass 29 kda, was catalytically inactive. crystal structures in the absence and presence of bound lipoic acid were solved at 2.1 a resolution. the protein was found to fall into the alpha/beta class a ...200616384580
thermoplasma polariton within scaling theory of single-layer graphene.the electrodynamics of single-layer graphene is studied in the scaling regime. at any finite temperature, there is a weakly damped collective thermoplasma polariton mode whose dispersion and wavelength-dependent damping is determined analytically. the electric and magnetic fields associated with this mode decay exponentially in the direction perpendicular to the graphene layer, but, unlike the surface plasma polariton modes of metals, the decay length and the mode frequency are strongly temperat ...200617280441
purification and characterization of an intracellular chymotrypsin-like serine protease from thermoplasma intracellular serine protease produced by thermoplasma (tp.) volcanium was purified using a combination of ammonium sulfate fractionation, ion exchange, and alpha-casein agarose affinity chromatography. this enzyme exhibited the highest activity and stability at ph 7.0, and at 50 degrees c. the purifed enzyme hydrolyzed synthetic peptides preferentially at the carboxy terminus of phenylalanine or leucine and was almost completely inhibited by pmsf, tpck, and chymostatin, similarly to a chymot ...200616428830
interaction analysis of the aaa atpase taa43 by the bacterial two-hybrid system.the taa43 atpase of thermoplasma acidophilum, an archaeal member of the aaa protein family, is known to have an atypical oligomeric state and a nonspecific association with high-molecular-weight protein complexes. we assessed the in vivo binding pattern of taa43 using the bacterial two-hybrid system. we found 36 positive isolates interacting with taa43. our analysis showed that taa43 interacts preferentially with nonribosomal proteins containing ribosomal domains and regions involved in rna meta ...200616445759
20s proteasomes have the potential to keep substrates in store for continual degradation.the 20s core of the proteasome, which together with the regulatory particle plays a major role in the degradation of proteins in eukaryotic cells, is traversed by an internal system of cavities, namely two antechambers and one central proteolytic chamber. little is known about the mechanisms underlying substrate binding and translocation of polypeptide chains into the interior of 20s proteasomes. specifically, the role of the antechambers is not fully understood, and the number of substrate mole ...200616446364
glyceraldehyde dehydrogenases from the thermoacidophilic euryarchaeota picrophilus torridus and thermoplasma acidophilum, key enzymes of the non-phosphorylative entner-doudoroff pathway, constitute a novel enzyme family within the aldehyde dehydrogenase superfamily.cells of picrophilus torridus, grown on glucose, contained all enzyme activities of a non-phosphorylative entner-doudoroff pathway, including glucose dehydrogenase, gluconate dehydratase, 2-keto-3-deoxygluconate aldolase, glyceraldehyde dehydrogenase (gadh), glycerate kinase (2-phosphoglycerate forming), enolase and pyruvate kinase. gadh was purified to homogeneity. the 115-kda homodimeric protein catalyzed the oxidation of glyceraldehyde with nadp+ at highest catalytic efficiency. nad+ was not ...200616458304
structural analysis of the plasmid pta1 isolated from the thermoacidophilic archaeon thermoplasma acidophilum.thermoplasma acidophilum is a thermoacidophilic archaeon that grows optimally at ph1.8 and 56 degrees c and has no cell wall. plasmid pta1 was found in some strains of the species. we sequenced plasmid pta1 and analyzed the open reading frames (orfs). pta1 was found to be a circular dna molecule of 15,723 bp. eighteen orfs were found; none of the gene products except orf1 had sequence similarity to known proteins. orf1 showed similarity to cdc6, which is involved in genome-replication initiation ...200616493526
crystal structure of an archaeal actin homolog.prokaryotic homologs of the eukaryotic structural protein actin, such as mreb and parm, have been implicated in determination of bacterial cell shape, and in the segregation of genomic and plasmid dna. in contrast to these bacterial actin homologs, little is known about the archaeal counterparts. as a first step, we expressed a predicted actin homolog of the thermophilic archaeon thermoplasma acidophilum, ta0583, and determined its crystal structure at 2.1a resolution. ta0583 is expressed as a s ...200616500678
thermophilic lifestyle for an uncultured archaeon from hydrothermal vents: evidence from environmental genomics.we present a comparative analysis of two genome fragments isolated from a diverse and widely distributed group of uncultured euryarchaea from deep-sea hydrothermal vents. the optimal activity and thermostability of a dna polymerase predicted in one fragment were close to that of the thermophilic archaeon thermoplasma acidophilum, providing evidence for a thermophilic way of life of this group of uncultured archaea.200616517686
dna unwinding assay using streptavidin-bound oligonucleotides.helicases play essential roles in many cellular processes including replication, transcription and translation. most helicases translocate along one strand of the duplex while displacing the complementary strand (of either dna or rna). thus, helicases have directionality. they move along nucleic acids in either the 3'--> 5' or 5'--> 3' direction. the directionality of helicases with low activity or of those that cannot initiate duplex unwinding from a substrate that contains only one single-stra ...200617132162
nmr structure of the conserved novel-fold protein ta0743 from thermoplasma acidophilum. 200616374782
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