substrate recognition ability differs among various prokaryotic trnase zs.there exists a significant difference in pre-trna preference among prokaryotic trnase zs. this is an enigma, because pre-trnas should form the common l-shaped structure and trnase zs should form the common structure based on the alphabeta/betaalpha-fold. to address this issue, we examined six different eubacterial and archaeal trnase zs including two newly isolated trnase zs for cleavage of 18 different pre-trna substrates. two thermotoga maritima, one thermus thermophilus, one bacillus subtilis ...200616681995
characterization of glycerate kinase (2-phosphoglycerate forming), a key enzyme of the nonphosphorylative entner-doudoroff pathway, from the thermoacidophilic euryarchaeon picrophilus torridus.picrophilus torridus has been shown to degrade glucose via a nonphosphorylative entner-doudoroff (ed) pathway. here we report the characterization of a key enzyme of this pathway, glycerate kinase (2-phosphoglycerate forming). the enzyme was purified 5,100-fold to homogeneity. the 95 kda homodimeric protein catalyzed the atp-dependent phosphorylation of glycerate specifically to 2-phosphoglycerate. the enzyme showed highest activity at 60 degrees c and ph 7.3, with atp as phosphoryl donor and mg ...200616684110
resonance assignments for the hypothetical protein ta0938 from thermoplasma acidophilum. 200616703419
ferroplasma cupricumulans sp. nov., a novel moderately thermophilic, acidophilic archaeon isolated from an industrial-scale chalcocite bioleach heap.a new species of archaea was isolated from an industrial mineral sulphide bioleach heap. strain bh2, a non-motile pleomorphic coccus, was capable of chemomixotrophic growth on ferrous sulphate and yeast extract. growth was not supported in the absence of yeast extract. phylogenetic analysis based on the 16s rrna gene showed that strain bh2 was most closely related to the species ferroplasma acidiphilum; however, it showed only 95% sequence similarity with this species. strain bh2 had a temperatu ...200616721487
crystallization and preliminary crystallographic analysis of nad+-preferring aldohexose dehydrogenase from the thermoacidophilic archaeon thermoplasma acidophilum.the aldohexose dehydrogenase from the thermoacidophilic archaeon thermoplasma acidophilum (aldt) is a 28 kda molecular-weight enzyme that catalyzes the oxidation of various aldohexoses, with a preference for nad+ rather than nadp+ as a cofactor. the recombinant aldt was crystallized using the hanging-drop vapour-diffusion technique at 293 k under several acidic conditions with polyethylene glycol (peg) and ammonium sulfate as precipitants. optimization of the initial crystallizations conditions ...200616754989
molecular identification of methanogenic archaea from sheep in queensland, australia reveal more uncultured novel archaea.molecular diversity of rumen methanogens in sheep in queensland, australia was investigated using 16s rrna gene libraries prepared from pooled rumen contents from nine merino sheep. a total of 78 clones were identified revealing 26 different sequences. of these 26 sequences, eight sequences (15 clones) were 95-100% similar to cultivated methanogens belonging to the orders methanobacteriales and methanomicrobiales, and the remaining 18 phylotypes (63 clones) were 72-75% similar to thermoplasma ac ...200616765859
characterization of a thermophilic sulfur oxidizing enrichment culture dominated by a sulfolobus sp. obtained from an underground hot spring for use in extreme bioleaching conditions.a thermoacidophilic elemental sulfur and chalcopyrite oxidizing enrichment culture vs2 was obtained from hot spring run-off sediments of an underground mine. it contained only archaeal species, namely a sulfolobus metallicus-related organism (96% similarity in partial 16s rrna gene) and thermoplasma acidophilum (98% similarity in partial 16s rrna gene). the vs2 culture grew in a temperature range of 35-76 degrees c. sulfur oxidation by vs2 was optimal at 70 degrees c, with the highest oxidation ...200616767461
genome annotation transfer utility (gatu): rapid annotation of viral genomes using a closely related reference genome.since dna sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. however, many of these have been deposited in genbank without annotations, severely limiting their value to researchers. while maintaining comprehensive genomic databases for a set of virus families at the viral bioinformatics resource center and viral bioinformatics - canada, we found that researchers were unnecessarily spe ...200616772042
solution structure of ta1092, a ribosomal protein s24e from thermoplasma acidophilum. 200616786596
biosynthesis of archaeal membrane lipids: digeranylgeranylglycerophospholipid reductase of the thermoacidophilic archaeon thermoplasma acidophilum.the basic core structure of archaeal membrane lipids is 2,3-di-o-phytanyl-sn-glyceryl phosphate (archaetidic acid), which is formed by the reduction of 2,3-di-o-geranylgeranylglyceryl phosphate. the reductase activity for the key enzyme in membrane lipid biosynthesis, 2,3-digeranylgeranylglycerophospholipid reductase, was detected in a cell free extract of the thermoacidophilic archaeon thermoplasma acidophilum. the reduction activity was found in the membrane fraction, and fad and nadh were req ...200616788058
gauss-function-based model of hydrophobicity density in proteins.the model adopting the three-dimensional gauss function to express the hydrophobicity distribution in proteins is presented in this paper. the tendency to create the hydrophobic center during protein folding is expressed in form of an external force field of the form of three-dimensional gauss function which directs the folding polypeptide to locate the hydrophobic residues in a central part of the molecule and hydrophilic ones exposed toward the molecular surface. the decrease of the difference ...200616789910
crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications.we report here the crystal structure of a trehalose-6-phosphate phosphatase-related protein (t6pp) from thermoplasma acidophilum, ta1209, determined by the dual-wavelength anomalous diffraction (dad) method. t6pp is a member of the haloacid dehalogenase (had) superfamily with significant sequence homology with trehalose-6-phosphate phosphatase, phosphoserine phosphatase, p-type atpases and other members of the family. t6pp possesses a core domain of known alpha/beta-hydrolase fold, characteristi ...200616815921
inter-domain orientation and motions in vat-n explored by residual dipolar couplings and 15n backbone relaxation.the n-terminal domain of vat (valosine-containing protein-like atpase of thermoplasma acidophilum), vat-n (20.5 kda), is considered to be the primary substrate-recognition site of the complex. the solution structure of vat-n derived in our laboratory using conventionally obtained nmr restraints shows the existence of two equally sized sub-domains, vat-nn and vat-nc, together forming a kidney-shaped overall structure. the putative substrate-binding site of vat-n involves free loops and a highly c ...200616826545
controlling the activity of the 20s proteasome complex by synthetic gatekeepers. 200616858705
[structural biology of proteasome]. 200616922377
the asymmetric atpase cycle of the thermosome: elucidation of the binding, hydrolysis and product-release steps.using a combination of intrinsic fluorescence to report atp-induced rearrangements, quenched-flow to measure atp hydrolysis "on-enzyme" and optical methods to probe the kinetics of product release, we have begun to dissect the process of energy transduction in the thermosome, a type ii chaperonin from thermoplasma acidophilum. stoichiometric measurements of atp binding reveal the tight association of eight nucleotide molecules per hexa-decamer, implying the filling of only one ring owing to stro ...200616942780
characterization of the ap endonucleases from thermoplasma volcanium and lactobacillus plantarum: contributions of two important tryptophan residues to ap site recognition.escherichia coli ap endonuclease (exoiii) and its human homolog (ape1) have the sole tryptophan residue for ap site recognition (ap site recognizer) but these residues are at different positions near the catalytic sites. on the other hand, many bacterial ap endonucleases have two tryptophan residues at the same positions of both exoiii and ape1. to elucidate whether these residues are involved in ap site recognition, the exoiii homologs of thermoplasma volcanium and lactobacillus plantarum were ...200616960376
rare codon clusters at 5'-end influence heterologous expression of archaeal gene in escherichia coli.proteins from hyperthermophilic microorganisms are attractive candidates for novel biocatalysts because of their high resistance to temperature extremes. however, archaeal genes are usually poorly expressed in escherichia coli because of differences in codon usage. genes from the thermoacidophilic archaea sulfolobus solfataricus and thermoplasma acidophilum contain high proportions of rare codons for arginine, isoleucine, and leucine, which are recognized by the trnas encoded by the argu, iley, ...200616962338
solution structure of ta0895, a moad homologue from thermoplasma acidophilum. 200617019685
expression, crystallization and preliminary x-ray crystallographic analyses of two n-terminal acetyltransferase-related proteins from thermoplasma acidophilum.n-terminal acetylation is one of the most common protein modifications in eukaryotes, occurring in approximately 80-90% of cytosolic mammalian proteins and about 50% of yeast proteins. ard1 (arrest-defective protein 1), together with nat1 (n-acetyltransferase protein 1) and possibly nat5, is responsible for the nata activity in saccharomyces cerevisiae. in mammals, ard1 is involved in cell proliferation, neuronal development and cancer. interestingly, it has been reported that mouse ard1 (mard1( ...200617077495
overexpression, crystallization and preliminary x-ray crystallographic analysis of a putative transposase from thermoplasma acidophilum encoded by the ta0474 gene.is200 transposases, originally identified in salmonella typhimurium lt2, are present in many bacteria and archaea and are distinct from other groups of transposases. to facilitate further structural comparisons among is200-like transposases, structural analysis has been initiated of a putative transposase from thermoplasma acidophilum encoded by the ta0474 gene. its 137-residue polypeptide shows high levels of sequence similarity to other members of the is200 transposase family. the protein was ...200617077501
stimulation of mcm helicase activity by a cdc6 protein in the archaeon thermoplasma acidophilum.replicative dna helicases are ring-shaped hexamers that play an essential role in chromosomal dna replication. they unwind the two strands of the duplex dna and provide the single-stranded (ss) dna substrate for the polymerase. the minichromosome maintenance (mcm) proteins are thought to function as the replicative helicases in eukarya and archaea. the proteins of only a few archaeal organisms have been studied and revealed that although all have similar amino acid sequences and overall structur ...200617108356
thermal stability and biochemical properties of isocitrate dehydrogenase from the thermoacidophilic archaeon thermoplasma acidophilum.isocitrate dehydrogenase [idh; ec] from the thermoacidophilic archaeon thermoplasma acidophilum (taidh) showed high thermal stability with an apparent melting temperature, t(m), of 82.2 and 84.5 degrees c at ph 7.5 and 5.8, respectively. based on structural alignment of taidh with idh from aeropyrum pernix (apidh) and archaeoglobus fulgidus (afidh) residues forming an aromatic cluster in the clasp-domain thought to strengthen the dimer interface in apidh and afidh were identified in the ...200717123127
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
proteomics analysis of thermoplasma acidophilum with a focus on protein complexes.two-dimensional gel electrophoresis (2de) and maldi-tof ms were used to obtain a global view of the cytoplasmic proteins expressed by thermoplasma acidophilum. in addition, glycerol gradient ultracentrifugation coupled to 2de-maldi-tof ms analysis was used to identify subunits of macromolecular complexes. with the 2de proteomics approach, over 900 spots were resolved of which 271 proteins were identified. a significant number of these form macromolecular complexes, among them the ribosome, prote ...200717151018
an actin homolog of the archaeon thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin.actin, a central component of the eukaryotic cytoskeleton, plays a crucial role in determining cell shape in addition to several other functions. recently, the structure of the archaeal actin homolog ta0583, isolated from the archaeon thermoplasma acidophilum, which lacks a cell wall, was reported by roeben et al. (j. mol. biol. 358:145-156, 2006). here we show that ta0583 assembles into bundles of filaments similar to those formed by eukaryotic actin. specifically, ta0583 forms a helix with a f ...200717189356
quantitative dynamics and binding studies of the 20s proteasome by nmr.the machinery used by the cell to perform essential biological processes is made up of large molecular assemblies. one such complex, the proteasome, is the central molecular machine for removal of damaged and misfolded proteins from the cell. here we show that for the 670-kilodalton 20s proteasome core particle it is possible to overcome the molecular weight limitations that have traditionally hampered quantitative nuclear magnetic resonance (nmr) spectroscopy studies of such large systems. this ...200717237764
proteins from extremophiles as stable tools for advanced biotechnological applications of high social interest.extremophiles are micro-organisms adapted to survive in ecological niches defined as 'extreme' for humans and characterized by the presence of adverse environmental conditions, such as high or low temperatures, extreme values of ph, high salt concentrations or high pressure. biomolecules isolated from extremophiles possess extraordinary properties and, in particular, proteins isolated from extremophiles represent unique biomolecules that function under severe conditions, comparable to those prev ...200717251151
stereochemistry of reduction in digeranylgeranylglycerophospholipid reductase involved in the biosynthesis of archaeal membrane lipids from thermoplasma acidophilum.the basic core structure of archaeal membrane lipids is 2,3-di-o-phytanylglyceryl phosphate, which is formed by reduction of 2,3-di-o-geranylgeranylglyceryl phosphate. this reaction is the final committed step in the biosynthesis of archaeal membrane lipids and is catalyzed by digeranylgeranylglycerophospholipid reductase (dgggpl reductase). the putative dgggpl reductase gene (ta0516m) of thermoplasma acidophilum was cloned and expressed. the purified recombinant enzyme appeared to catalyze the ...200717275067
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
structural insights into unique substrate selectivity of thermoplasma acidophilum d-aldohexose dehydrogenase.the d-aldohexose dehydrogenase from the thermoacidophilic archaea thermoplasma acidophilum (aldt) belongs to the short-chain dehydrogenase/reductase (sdr) superfamily and catalyzes the oxidation of several monosaccharides with a preference for nad(+) rather than nadp(+) as a cofactor. it has been found that aldt is a unique enzyme that exhibits the highest dehydrogenase activity against d-mannose. here, we describe the crystal structures of aldt in ligand-free form, in complex with nadh, and in ...200717300803
nmr structure of hypothetical protein ta0938 from thermoplasma acidophilum. 200717377985
phylogenomic analysis of proteins that are distinctive of archaea and its main subgroups and the origin of methanogenesis.the archaea are highly diverse in terms of their physiology, metabolism and ecology. presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. the evolutionary relationships among different groups within the euryarchaeota branch are also not clearly understood.200717394648
the n-terminal region is important for the nuclease activity and thermostability of the flap endonuclease-1 from sulfolobus tokodaii.this paper reports the biochemical properties of two types of recombinant flap endonuclease-1 (fen-1) proteins obtained from the thermophilic crenarchaeon, sulfolobus tokodaii strain 7. one of the two fen-1 proteins is a product of the gene with aug as the translational start codon (stos-fen-1), which is originally assigned in the database. the other is a product of the gene with a new aug start codon (stol-fen-1), which is inserted at 153 bases upstream of the original aug codon. although stol- ...200717420588
lateral diffusion coefficients of an eicosanyl-based bisglycerophosphocholine determined by pfg-nmr and frap.we report the lateral diffusion properties of 2,2'-di-o-decyl-3,3'-di-o-(eicosanyl)-bis-(rac-glycero)-1,1'-diphosphocholine (c20bas) using pulsed-field gradient nmr (pfg-nmr) and fluorescence recovery after photobleaching (frap). c20bas membranes display a melting transition at tm = 15.7 degrees c, as determined by differential scanning calorimetry and 31p nmr chemical shift anisotropy. the lateral diffusion coefficient of c20bas, as determined by pfg-nmr and frap, at 25 degrees c, were dpfg-nmr ...200717465580
molecular cloning and biochemical characterization of the first archaeal maltogenic amylase from the hyperthermophilic archaeon thermoplasma volcanium gss1.maltogenic amylases (maases), a subclass of cyclodextrin (cd)-hydrolyzing enzymes belonging to glycoside hydrolase family 13, have been studied extensively, but their physiological roles in microbes and evolutionary relationships with other amylolytic enzymes remain unclear. here, we report the biochemical properties of a thermostable archaeal maase from thermoplasma volcanium gss1 (tpma) for the first time. the primary structure and catalytic properties of tpma were similar to those of maases, ...200717468058
molecular diversity of methanogens in feedlot cattle from ontario and prince edward island, canada.the molecular diversity of rumen methanogens in feedlot cattle and the composition of the methanogen populations in these animals from two geographic locations were investigated using 16s rrna gene libraries prepared from pooled pcr products from 10 animals in ontario (127 clones) and 10 animals from prince edward island (114 clones). a total of 241 clones were examined, with methanobrevibacter ruminantium accounting for more than one-third (85 clones) of the clones identified. from these 241 cl ...200717483285
crystal structure of bovine lipoyltransferase in complex with lipoyl-amp.lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system. it is covalently attached to a specific lysine residue of the subunit of the complexes. the bovine lipoyltransferase (blt) catalyzes the lipoic acid attachment reaction using lipoyl-amp as a substrate, forming a lipoylated protein and amp. to gain insights into the reaction mechanism at the atomic level, we have determined the crystal structure of blt at 2.10 a resolution. unexpect ...200717570395
the 2-oxoacid dehydrogenase multienzyme complex of haloferax volcanii.those aerobic archaea whose genomes have been sequenced possess four adjacent genes that, by sequence comparisons with bacteria and eukarya, appear to encode the 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 thermoplasma acidophilum, evidence has been presented that the heterologously expressed recombinant enzyme possesses activity with the branched chain 2-oxoacids and, to a lesser ...200817571210
characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from archaea.phosphoglycerate mutases (pgm) catalyze the reversible conversion of 3-phosphoglycerate and 2-phosphoglycerate as part of glycolysis and gluconeogenesis. two structural and mechanistically unrelated types of pgms are known, a cofactor (2,3-bisphosphoglycerate)-dependent (dpgm) and a cofactor-independent enzyme (ipgm). here, we report the characterization of the first archaeal cofactor-dependent pgm from thermoplasma acidophilum, which is encoded by orf ta1347. this orf was cloned and expressed i ...200717576516
molecular architecture and divalent cation activation of tvok, a prokaryotic potassium channel.rck (regulator of conductance of potassium) domains form a family of ligand-binding domains found in many prokaryotic k+ channels and transport proteins. although many rck domains contain an apparent nucleotide binding motif, some are known instead to bind ca2+, which can then facilitate channel opening. here we report on the molecular architecture and ligand activation properties of an rck-containing potassium channel cloned from the prokaryote thermoplasma volcanium. this channel, called tvok, ...200717588939
solution structure of the hypothetical novel-fold protein ta0956 from thermoplasma acidophilum. 200717634985
solution structure of the hypothetical protein ta0095 from thermoplasma acidophilum: a novel superfamily with a two-layer sandwich architecture.ta0095 is a 96-residue hypothetical protein from thermoplasma acidophilum that exhibits no sequence similarity to any protein of known structure. also, ta0095 is a member of the cog4004 orthologous group of unknown function found in archaea bacteria. we determined its three-dimensional structure by nmr methods. the structure displays an alpha/beta two-layer sandwich architecture formed by three alpha-helices and five beta-strands following the order beta1-alpha1-beta2-beta3-beta4-beta5-alpha2-al ...200717766377
structural and mutational analysis of trna intron-splicing endonuclease from thermoplasma acidophilum dsm 1728: catalytic mechanism of trna intron-splicing archaea, rna endonucleases that act specifically on rna with bulge-helix-bulge motifs play the main role in the recognition and excision of introns, while the eukaryal enzymes use a measuring mechanism to determine the positions of the universally positioned splice sites relative to the conserved domain of pre-trna. two crystallographic structures of trna intron-splicing endonuclease from thermoplasma acidophilum dsm 1728 (enda(ta)) have been solved to 2.5-a and 2.7-a resolution by molecular ...200717827289
structural and functional insights into dom34, a key component of no-go mrna decay.the yeast protein dom34 is a key component of no-go decay, by which mrnas with translational stalls are endonucleolytically cleaved and subsequently degraded. however, the identity of the endoribonuclease is unknown. homologs of dom34, called pelota, are broadly conserved in eukaryotes and archaea. to gain insights into the structure and function of dom34/pelota, we have determined the structure of pelota from thermoplasma acidophilum (ta pelota) and investigated the ribonuclease activity of dom ...200717889667
the 2-oxoacid dehydrogenase multi-enzyme complex of the archaeon thermoplasma acidophilum - recombinant expression, assembly and characterization.the aerobic archaea possess four closely spaced, adjacent genes that encode proteins showing significant sequence identities with the bacterial and eukaryal components comprising the 2-oxoacid dehydrogenase multi-enzyme complexes. however, catalytic activities of such complexes have never been detected in the archaea, although 2-oxoacid ferredoxin oxidoreductases that catalyze the equivalent metabolic reactions are present. in the current paper, we clone and express the four genes from the therm ...200717894823
microbial populations in acid mineral bioleaching systems of tong shankou copper mine, understand the composition and structure of microbial communities in different acid mineral bioleaching systems, and to present a more complete picture of microbially mediated acid mine drainage production.200717897227
mucosal and systemic immune responses by intranasal immunization using archaeal lipid-adjuvanted vaccines.the utility of archaeal polar lipids as an adjuvant/delivery system for elicitation of antigen-specific mucosal immune responses in intranasally administered vaccines was investigated. although unilamellar archaeosomes (liposomes made from archaeal polar lipids) with encapsulated ovalbumin (ova/archaeosomes) induced anti-ova igg antibody responses in sera, they failed to induce anti-ova iga antibody responses at mucosal sites. however, the addition of cacl2 to convert ova/archaeosomes into an ar ...200717959279
thermogymnomonas acidicola gen. nov., sp. nov., a novel thermoacidophilic, cell wall-less archaeon in the order thermoplasmatales, isolated from a solfataric soil in hakone, japan.a novel thermoacidophilic, cell wall-less archaeon, strain ic-189t, was isolated from a solfataric field in ohwaku-dani, hakone, japan. the cells were irregular cocci, sometimes lobed, club-shaped or catenated, and were highly variable in size, ranging from 0.8 to 8.0 microm in diameter. the strain grew at temperatures in the range 38-68 degrees c (optimally at 60 degrees c) and at ph 1.8-4.0 (optimally at around ph 3.0). strain ic-189t was obligately aerobic and heterotrophic, requiring yeast e ...200717978217
biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a zn ribbon-like domain.we have identified a novel family of proteins, in which the n-terminal cystathionine beta-synthase (cbs) domain is fused to the c-terminal zn ribbon domain. four proteins were overexpressed in escherichia coli and purified: ta0289 from thermoplasma acidophilum, tv1335 from thermoplasma volcanium, pf1953 from pyrococcus furiosus, and ph0267 from pyrococcus horikoshii. the purified proteins had a red/purple color in solution and an absorption spectrum typical of rubredoxins (rds). metal analysis o ...200818021800
the stator complex of the a1a0-atp synthase--structural characterization of the e and h subunits.archaeal atp synthase (a-atpase) is the functional homolog to the atp synthase found in bacteria, mitochondria and chloroplasts, but the enzyme is structurally more related to the proton-pumping vacuolar atpase found in the endomembrane system of eukaryotes. we have cloned, overexpressed and characterized the stator-forming subunits e and h of the a-atpase from the thermoacidophilic archaeon, thermoplasma acidophilum. size exclusion chromatography, cd, matrix-assisted laser desorption ionization ...200818036615
a thermoactive glucoamylase with biotechnological relevance from the thermoacidophilic euryarchaeon thermoplasma acidophilum.a gene encoding an intracellular glucoamylase was identified in the genome of the extreme thermoacidophilic archaeon thermoplasma acidophilum. the gene taga, consisting of 1,911 bp, was cloned and successfully expressed in escherichia coli. the recombinant protein was purified 22-fold to homogeneity using heat treatment, anion-exchange chromatography, and gel filtration. detailed analysis shows that the glucoamylase, with a molecular weight of 66 kda per subunit, is a homodimer in its active sta ...200818080814
functional characterization of the recombinant group ii chaperonin alpha from thermoplasma acidophilum.the functional characteristics of group ii chaperonins, especially those from archaea, have not been elucidated extensively. here, we performed a detailed functional characterization of recombinant chaperonin alpha subunits (16-mer) (ta-cpn alpha) from the thermophilic archaea thermoplasma acidophilum as a model protein of archaeal group ii chaperonins. recombinant ta-cpn alpha formed an oligomeric ring structure similar to that of native protein, and displayed an atp hydrolysis activity (optima ...200818174187
an oligonucleotide prokaryotic acidophile microarray: its validation and its use to monitor seasonal variations in extreme acidic environments with total environmental oligonucleotide microarray that monitors prokaryotic diversity in extremely acidic environments has been developed. the oligonucleotide probes target most known acidophilic microorganisms, including members of the nitrospira phylum, acidithiobacillus genus, acidobacteria, sulfur reducing bacteria, actinobacteria and archaea of the ferroplasma and thermoplasma genera. the probes were tested for their specificity against the corresponding type strain by microarray hybridization using pcr-amplif ...200818248453
structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein.repeat proteins are widespread in nature, with many of them functioning as binding molecules in protein-protein recognition. their simple structural architecture is used in biotechnology for generating proteins with high affinities to target proteins. recent folding studies of ankyrin repeat (ar) proteins revealed a new mechanism of protein folding. the formation of an intermediate state is rate limiting in the folding reaction, suggesting a scaffold function of this transient state for intrinsi ...200818305166
crystallization and preliminary x-ray diffraction analysis of 5,10- methylenetetrahydrofolate dehydrogenase/cyclohydrolase from thermoplasma acidophilum dsm 1728.the methylenetetrahydrofolate dehydrogenase/ cyclohydrolase (mthfdc) from the thermoacidophilic archaeon thermoplasma acidophilum is a 30.6 kda molecular-mass enzyme that sequentially catalyzes the conversion of formyltetrahydrofolate to methylenetetrahydrofolate, with a preference for nadp as a cofactor, rather than nad. in order to elucidate the functional and structural features of mthfdc from archaeons at a molecular level, it was overexpressed in escherichia coli and crystallized in the pre ...200818309272
indicators from archaeal secretomes.just as in the eukarya and the bacteria, members of the archaea need to export proteins beyond the cell membrane. this would be required to fulfill a variety of essential functions such as nutrient acquisition and biotransformations, maintenance of extracellular structures and more. apart from the eukarya and the bacteria however, members of the archaea share a number of unique characteristics. does this uniqueness extend to the protein secretion system? it was the objective of this study to ans ...201018407482
mechanism of gate opening in the 20s proteasome by the proteasomal atpases.substrates enter the cylindrical 20s proteasome through a gated channel that is regulated by the atpases in the 19s regulatory particle in eukaryotes or the homologous pan atpase complex in archaea. these atpases contain a conserved c-terminal hydrophobic-tyrosine-x (hbyx) motif that triggers gate opening upon atp binding. using cryo-electron microscopy, we identified the sites in the archaeal 20s where pan's c-terminal residues bind and determined the structures of the gate in its closed and op ...200818471981
amino acid biases in the n- and c-termini of proteins are evolutionarily conserved and are conserved between functionally related proteins.analysis of the arabidopsis thaliana, saccharomyces cerevisiae, mus musculus, escherichia coli, bacillus subtilis, thermoplasma acidophilum, and sulfolobus tokodaii genomes demonstrate that many amino acid biases occur at the n- and c-termini of proteins, a statistically significant number of these biases are evolutionarily conserved, and these biases occur in amino acids beyond the first and last five amino acids. analyses designed to shed light on the mechanism causing amino acid biases sugges ...200818478318
culturable and molecular phylogenetic diversity of microorganisms in an open-dumped, extremely acidic pb/zn mine tailings.a combination of cultivation-based and molecular-based approaches was used to reveal the culturable and molecular diversity of the microbes inhabiting an open-dumped pb/zn mine tailings that was undergoing intensive acid generation (ph 1.9). culturable bacteria found in the extremely acidic mine tailings were acidithiobacillus ferrooxidans, leptospirillum ferriphilum, sulfobacillus thermotolerans and acidiphilium cryptum, where the number of acidophilic heterotrophs was ten times higher than tha ...200818512002
effects of ph and temperature on the composition of polar lipids in thermoplasma acidophilum ho-62.thermoplasma acidophilum ho-62 was grown at different phs and temperatures, and its polar lipid compositions were determined. although the number of cyclopentane rings in the caldarchaeol moiety increased when t. acidophilum was cultured at high temperature, the number decreased at low phs. glycolipids, phosphoglycolipids, and phospholipids were analyzed by high-performance liquid chromatography with an evaporative light-scattering detector. the amount of caldarchaeol with more than two sugar un ...200818539746
trosy-based nmr evidence for a novel class of 20s proteasome inhibitors.the proteasome plays a central role in maintaining cellular homeostasis, in controlling the cell cycle, in removing misfolded proteins that can be toxic, and in regulating the immune system. it is also an important target for novel anticancer drugs, such as bortezomib, a potent inhibitor that has been used successfully in the treatment of multiple myeloma. here, we show that the antimalaria drug chloroquine inhibits proteasome function in eukaryotic cell extracts and in preparations of purified ...200818540636
compositions and structures of archaeal communities in acid mineral bioleaching systems of dongxiang copper mine and yinshan lead-zinc mine, china.four samples were studied from four separated sites with heap leaching in the yinshan lead-zinc mine and the dongxiang copper mine in jiangxi province, china. the compositions and structures of archaeal communities in four sites were identified by a polymerase chain reaction-based cloning approach. a total of six operational taxonomic units (otus) was obtained from four samples. the highest percentage of overlapped otus was 88.9% between sites dx and d1. phylogenetic analysis revealed that archa ...200818592308
thioredoxin reductase from thermoplasma acidophilum: a new twist on redox regulation.thioredoxin reductases (trxrs) regulate the intracellular redox environment by using nadph to provide reducing equivalents for thioredoxins (trxs). here we present the cloning and biochemical characterization of a putative trxr (ta0984) and a putative trx (ta0866) from thermoplasma acidophilum. our data identify ta0866 as a trx through its capacity to reduce insulin and be reduced by escherichia coli trxr in a nadph-dependent manner. our data also establish ta0984 as a trxr due to its ability to ...200818717593
direct electrochemical analyses of a thermophilic thioredoxin reductase: interplay between conformational change and redox chemistry.thioredoxin reductases (trxrs) are flavin-containing dithioloxidoreductases that couple reduction equivalents from the soluble nad(p)h pool to the soluble protein thioredoxin (trx). previous crystallographic studies of the escherichia coli enzyme ( ectrxr) have shown that low molecular weight trxrs can adopt two distinct conformations: the first (fo) is required for the oxidation of the flavin cofactor and the generation of reduced trx; the second (fr) is adopted for the reduction of the flavin ...200818717594
clioquinol inhibits the proteasome and displays preclinical activity in leukemia and myeloma. 200918754030
thermoplasma acidophilum cdc6 protein stimulates mcm helicase activity by regulating its atpase activity.the minichromosome maintenance (mcm) proteins are thought to function as the replicative helicases in archaea. in most archaeal species studied, the interaction between mcm and the initiator protein, cdc6, inhibits helicase activity. to date, the only exception is the helicase and cdc6 proteins from the archaeon thermoplasma acidophilum. it was previously shown that when the cdc6 protein interacts with mcm it substantially stimulates helicase activity. it is shown here that the mechanism by whic ...200818757887
the stability of the archaeal hu histone-like dna-binding protein from thermoplasma volcanium.the complete genome analysis of the archaeon thermoplasma volcanium has revealed a gene assigned to encode the histone-like dna-binding protein hu. thermoplasma volcanium is a moderate thermophile growing around 60 degrees c and it is adaptable to aerobic and anaerobic environment and therefore it is unique as a candidate for the origin of eukaryotic nuclei in the endosymbiosis hypothesis. the hu protein is the major component of the bacterial nuclei and therefore it is an important protein to b ...200918818867
structure of a haloacid dehalogenase superfamily phosphatase ph1421 from pyrococcus horikoshii ot3: oligomeric state and thermoadaptation mechanism.ph1421 from the hyperthermophilic archaeon pyrococcus horikoshii ot3 is a hypothetical protein belonging to the haloacid dehalogenase (had) superfamily. to gain insight into its biological function and thermostabilization mechanism, the crystal structure of ph1421 has been determined at 1.6 a resolution. the crystallographic asymmetric unit contains a homodimer. the monomeric protomer is composed of two distinct domains, a small cap domain and a large core domain, which agrees well with the typi ...200818931414
crystallization and preliminary x-ray analysis of the thermoplasma acidophilum 20s proteasome in complex with protein substrates.the 20s proteasome is a 700 kda barrel-shaped proteolytic complex that is traversed by an internal channel which widens into three cavities: two antechambers and one central chamber. entrance to the complex is restricted by the narrow opening of the channel, which only allows unfolded substrates to reach the active sites located within the central cavity. the x-ray structures of 20s proteasomes from different organisms with and without inhibitors bound have led to a detailed knowledge of their s ...200818931431
atomic structure of the keops complex: an ancient protein kinase-containing molecular machine.kae1 is a universally conserved atpase and part of the essential gene set in bacteria. in archaea and eukaryotes, kae1 is embedded within the protein kinase-containing keops complex. mutation of keops subunits in yeast leads to striking telomere and transcription defects, but the exact biochemical function of keops is not known. as a first step to elucidating its function, we solved the atomic structure of archaea-derived keops complexes involving kae1, bud32, pcc1, and cgi121 subunits. our stud ...200818951093
biochemical characterization of the minichromosome maintenance protein from the archaeon thermoplasma acidophilum.minichromosome maintenance (mcm) proteins are thought to function as the replicative helicases in archaea. studies have shown that the mcm complex from the thermoacidophilic euryarchaeon thermoplasma acidophilum (tamcm) has some properties not reported in other archaeal mcm helicases. here, the biochemical properties of the tamcm are studied. the protein binds single-stranded dna, has dna-dependent atpase activity and atp-dependent 3' --> 5' helicase activity. the optimal helicase conditions wit ...200919002376
a ppm-family protein phosphatase from the thermoacidophile thermoplasma volcanium hydrolyzes protein-bound phosphotyrosine.the genomes of virtually all free-living archaeons encode one or more deduced protein-serine/threonine/tyrosine kinases belonging to the so-called eukaryotic protein kinase superfamily. however, the distribution of their cognate protein-serine/threonine/phosphatases displays a mosaic pattern. thermoplasma volcanium is unique among the archaea inasmuch as it is the sole archaeon whose complement of deduced phosphoprotein phosphatases includes a member of the ppm-family of protein-serine/threonine ...200919039517
[evolution of prokaryotic cytoskeleton]. 200819044289
heterologous expression and characterization of an alcohol dehydrogenase from the archeon thermoplasma acidophilum.analysis of the thermoplasma acidophilum dsm 1728 genome identified two putative alcohol dehydrogenase (adh) open reading frames showing 50.4% identity against each other. the corresponding genes ta0841 and ta1316 encode proteins of 336 and 328 amino acids with molecular masses of 36.48 and 36.01 kda, respectively. the genes were expressed in escherichia coli and the recombinant enzymes were functionally assessed for activity. throughout the study only ta1316 adh resulted active in the oxidative ...200919058034
c-terminal tail derived from the neighboring subunit is critical for the activity of thermoplasma acidophilum d-aldohexose dehydrogenase.the d-aldohexose dehydrogenase from the thermoacidophilic archaeon thermoplasma acidophilum (aldt) is a homotetrameric enzyme that catalyzes the oxidation of several d-aldohexoses, especially d-mannose. aldt comprises a unique c-terminal tail motif (residues 247-255) that shuts the active-site pocket of the neighboring subunit. the functional role of the c-terminal tail of aldt has been investigated using mutational and crystallographic analyses. a total of four c-terminal deletion mutants (delt ...200919089950
adpase activity of recombinantly expressed thermotolerant atpases may be caused by copurification of adenylate kinase of escherichia coli.except for apyrases, atpases generally target only the gamma-phosphate of a nucleotide. some non-apyrase atpases from thermophilic microorganisms are reported to hydrolyze adp as well as atp, which has been described as a novel property of the atpases from extreme thermophiles. here, we describe an apparent adp hydrolysis by highly purified preparations of the aaa+ atpase ntrc1 from an extremely thermophilic bacterium, aquifex aeolicus. this activity is actually a combination of the activities o ...200919143839
domain architecture of the stator complex of the a1a0-atp synthase from thermoplasma acidophilum.a key structural element in the ion translocating f-, a-, and v-atpases is the peripheral stalk, an assembly of two polypeptides that provides a structural link between the atpase and ion channel domains. previously, we have characterized the peripheral stalk forming subunits e and h of the a-atpase from thermoplasma acidophilum and demonstrated that the two polypeptides interact to form a stable heterodimer with 1:1 stoichiometry (kish-trier, e., briere, l. k., dunn, s. d., and wilkens, s. (200 ...200919234304
characterization of the cdc6 homologues from the euryarchaeon thermoplasma acidophilum.archaeal cell division cycle protein 6 (cdc6) homologues are thought to be involved in the initiation process of dna replication. in the present study, a biochemical characterization of the two cdc6 proteins from the archaeon thermoplasma acidophilum has been performed. both tacdc6-1 and tacdc6-2 behave as monomers in solution and both are abundantly expressed in vivo. further, tacdc6-1 shows strong ability to undergo autophosphorylation compared to tacdc6-2 and the autophosphorylation activity ...200819238189
the origins of phagocytosis and eukaryogenesis.phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion.200919245710
microbial communities in acid mine drainage and their interaction with pyrite surface.microbes such as acidithiobacillus ferrooxidans and leptospirillum ferrooxidans have been investigated a lot, because of their important role in acid mine drainage (amd) generation. in this article, the composition of microbial communities in two amd samples was studied. a culture-independent 16s rdna-based cloning approach, restriction fragment length polymorphism has been used. the interaction between microbes and natural pyrite specimen surface was researched by scanning electrode microscopy ...200919319595
identifying catalytic residues in cpaf, a chlamydia-secreted protease.a secreted chlamydial protease designated cpaf (chlamydial protease/proteasome-like activity factor) degrades host proteins, enabling chlamydia to evade host defenses and replicate. the mechanistic details of cpaf action, however, remain obscure. we used a computational approach to search the protein databank for structures that are compatible with the cpaf amino acid sequence. the results reveal that cpaf possesses a fold similar to that of the catalytic domains of the tricorn protease from the ...200919388144
characterization of an acid-labile, thermostable beta-glycosidase from thermoplasma acidophilum.a recombinant putative beta-galactosidase from thermoplasma acidophilum was purified as a single 57 kda band of 82 u mg(-1). the molecular mass of the native enzyme was 114 kda as a dimer. maximum activity was observed at ph 6.0 and 90 degrees c. the enzyme was unstable below ph 6.0: at ph 6 its half-life at 75 degrees c was 28 days but at ph 4.5 was only 13 h. catalytic efficiencies decreased as p-nitrophenyl(pnp)-beta-d-fucopyranoside (1067) > pnp-beta-d-glucopyranoside (381) > pnp-beta-d-gala ...200919458917
the thermoplasma acidophilum lpla-lplb complex defines a new class of bipartite lipoate-protein ligases.lipoic acid is a covalently bound cofactor found throughout the domains of life that is required for aerobic metabolism of 2-oxoacids and for c(1) metabolism. utilization of exogenous lipoate is catalyzed by a ligation reaction that proceeds via a lipoyl-adenylate intermediate to attach the cofactor to the epsilon-amino group of a conserved lysine residue of protein lipoyl domains. the lipoyl ligases of demonstrated function have a large n-terminal catalytic domain and a small c-terminal accesso ...200919520844
importance of non-conserved distal carboxyl terminal amino acids in two peptidases belonging to the m1 family: thermoplasma acidophilum tricorn interacting factor f2 and escherichia coli peptidase n.enzymes belonging to the m1 family play important cellular roles and the key amino acids (aa) in the catalytic domain are conserved. however, c-terminal domain aa are highly variable and demonstrate distinct differences in organization. to address a functional role for the c-terminal domain, progressive deletions were generated in tricorn interacting factor f2 from thermoplasma acidophilum (f2) and peptidase n from escherichia coli (pepn). catalytic activity was partially reduced in pepn lacking ...200919527767
cloning and overexpression of a thermostable signal peptide peptidase (sppa) from thermoplasma volcanium gss1 in e. this study, a gene coding for thermophilic serine protease of the clpp class from the thermoacidophilic archaeon thermoplasma volcanium (tpv) was cloned and expressed in escherichia coli. the primary sequence and domain analysis of this enzyme showed similarities (50-60% similarity) to signal peptide peptidases (sppa) of bacteria and other archaea. an increase of about tenfold in the activity was achieved by overexpression of tpv sppa in e. coli, as detected by enzyme assays conducted using a ...200919557795
prevalence and molecular diversity of archaea in subgingival pockets of periodontitis patients.the aim of this study was to investigate the prevalence and molecular diversity of archaea in the subgingival crevices of patients with chronic periodontitis.200919572899
a unique lipoylation system in the archaea. lipoylation in thermoplasma acidophilum requires two proteins.members of the 2-oxoacid dehydrogenase multienzyme complex family play a key role in the pathways of central metabolism. post-translational lipoylation of the dihydrolipoyl acyltransferase component of these complexes is essential for their activity, the lipoyllysine moiety performing the transfer of substrates and intermediates between the different active sites within these multienzyme systems. we have previously shown that the thermophilic archaeon, thermoplasma acidophilum, has a four-gene c ...200919594830
size distribution of native cytosolic proteins of thermoplasma acidophilum.we used molecular sieve chromatography in combination with lc-ms/ms to identify protein complexes that can serve as templates in the template matching procedures of visual proteomics approaches. by this method the sample complexity was lowered sufficiently to identify 464 proteins and - on the basis of size distribution and bioinformatics analysis - 189 of them could be assigned as subunits of macromolecular complexes over the size of 300 kda. from these we purified six stable complexes of therm ...200919639595
the partial substrate dethiaacetyl-coenzyme a mimics all critical carbon acid reactions in the condensation half-reaction catalyzed by thermoplasma acidophilum citrate synthase.citrate synthase (cs) performs two half-reactions: the mechanistically intriguing condensation of acetyl-coa with oxaloacetate (oaa) to form citryl-coa and the subsequent, slower hydrolysis of citryl-coa that generally dominates steady-state kinetics. the condensation reaction requires the abstraction of a proton from the methyl carbon of acetyl-coa to generate a reactive enolate intermediate. the carbanion of that intermediate then attacks the oaa carbonyl to furnish citryl-coa, the initial pro ...200919645419
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
interaction of the thermoplasma acidophilum a1a0-atp synthase peripheral stalk with the catalytic domain.the peripheral stalk of the archaeal atp synthase (a1a0)-atp synthase is formed by the heterodimeric eh complex and is part of the stator domain, which counteracts the torque of rotational catalysis. here we used nuclear magnetic resonance spectroscopy to probe the interaction of the c-terminal domain of the eh heterodimer (e(ct1)h(ct)) with the n-terminal 23 residues of the b subunit (b(nt)). the data show a specific interaction of b(nt) peptide with 26 residues of the e(ct1)h(ct) domain, there ...200919720061
a potentially versatile nucleotide hydrolysis activity of group ii chaperonin monomers from thermoplasma acidophilum.compared to the group i chaperonins such as escherichia coli groel, which facilitate protein folding, many aspects of the functional mechanism of archaeal group ii chaperonins are still unclear. here, we show that monomeric forms of archaeal group ii chaperonin alpha and beta from thermoplasma acidophilum may be purified stably and that these monomers display a strong ampase activity in the presence of divalent ions, especially co(2+) ion, in addition to atpase and adpase activities. furthermore ...200919728744
bax1 is a novel endonuclease: implications for archaeal nucleotide excision repair.the helicases xpb and xpd are part of the tfiih complex, which mediates transcription initiation as well as eukaryotic nucleotide excision repair (ner). although there is no tfiih complex present in archaea, most species contain both xpb and xpd and serve as a model for their eukaryotic homologs. recently, a novel binding partner for xpb, bax1 (binds archeal xpb), was identified in archaea. to gain insights into its role in ner, bax1 from thermoplasma acidophilum was characterized. we identified ...200919759013
structural models for interactions between the 20s proteasome and its pan/19s activators.proteasome activity is regulated by sequestration of its proteolytic centers in a barrel-shaped structure that limits substrate access. substrates enter the proteasome by means of activator complexes that bind to the end rings of proteasome alpha subunits and induce opening of an axial entrance/exit pore. the pa26 activator binds in a pocket on the proteasome surface using main chain contacts of its c-terminal residues and uses an internal activation loop to trigger gate opening by repositioning ...201019889631
characterization of thermophilic archaeal isopentenyl phosphate kinases.archaea synthesize isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp), the essential building blocks of isoprenoid compounds, from mevalonate (mva). however, an analysis of the genomes of several members of the archaea failed to identify genes for the enzymes required to convert phosphomevalonate (pm) to ipp in eukaryotes. the recent discovery of an isopentenyl kinase (ipk) in methanocaldococcus jannaschii (mj) suggests a new variation of the mva pathway where pm is decarboxylat ...201019928876
crystal structure and molecular modeling study of n-carbamoylsarcosine amidase ta0454 from thermoplasma acidophilum.a crystal structure of the putative n-carbamoylsarcosine amidase (cshase) ta0454 from thermoplasma acidophilum was solved by single-wavelength anomalous diffraction and refined at a resolution of 2.35a. cshases are involved in the degradation of creatinine. ta0454 shares a similar fold and a highly conserved c-d-k catalytic triad (cys123, asp9, and lys90) with the structures of three cysteine hydrolases (pdb codes 1nba, 1im5, and 2h0r). molecular dynamics (md) simulations of ta0454/n-carbamoylsa ...201019932181
structure and filament dynamics of the psk41 actin-like parm protein: implications for plasmid dna segregation.type ii plasmid partition systems utilize parm ntpases in coordination with a centromere-binding protein called parr to mediate accurate dna segregation, a process critical for plasmid retention. the staphylococcus aureus psk41 plasmid is a medically important plasmid that confers resistance to multiple antibiotics, disinfectants, and antiseptics. in the first step of partition, the psk41 parr binds its dna centromere to form a superhelical partition complex that recruits parm, which then mediat ...201020106979
a reported archaeal mechanosensitive channel is a structural homolog of marr-like transcriptional regulators.several archaeal mechanosensitive (ms) channels have been reported, including one from thermoplasma volcanium designated msctv. here, we report the crystal structure of msctv at 1.6-a resolution. unexpectedly, msctv was found to be a water-soluble protein exhibiting a winged helix-turn-helix (whth) motif, which is the signature of the marr (multiple antibiotic resistance regulator) family of transcriptional regulators. a cell-based osmotic downshock functional assay demonstrated that msctv was u ...201020162616
discovery of a putative acetoin dehydrogenase complex in the hyperthermophilic archaeon sulfolobus many other aerobic archaea, the hyperthermophile sulfolobus solfataricus possesses a gene cluster encoding components of a putative 2-oxoacid dehydrogenase complex. in the current paper, we have cloned and expressed the first two genes of this cluster and demonstrate that the protein products form an alpha(2)beta(2) hetero-tetramer possessing the catalytic activity characteristic of the first component enzyme of an acetoin dehydrogenase multienzyme complex. this represents the first report ...201020171216
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