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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
thermal stability and biochemical properties of isocitrate dehydrogenase from the thermoacidophilic archaeon thermoplasma acidophilum.isocitrate dehydrogenase [idh; ec 1.1.1.42] 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
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
nmr structure of the conserved novel-fold protein ta0743 from thermoplasma acidophilum. 200616374782
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
purification and characterization of an intracellular chymotrypsin-like serine protease from thermoplasma volcanium.an 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
identification and characterization of thermoplasma acidophilum glyceraldehyde dehydrogenase: a new class of nadp+-specific aldehyde dehydrogenase.thermoacidophilic archaea such as thermoplasma acidophilum and sulfolobus solfataricus are known to metabolize d-glucose via the ned (non-phosphorylated entner-doudoroff) pathway. in the present study, we identified and characterized a glyceraldehyde dehydrogenase involved in the downstream portion of the ned pathway. this glyceraldehyde dehydrogenase was purified from t. acidophilum cell extracts by sequential chromatography on deae-sepharose, q-sepharose, phenyl-sepharose and affi-gel blue col ...200616566751
insights into extreme thermoacidophily based on genome analysis of picrophilus torridus and other thermoacidophilic archaea.thermoacidophiles are prokaryotic microorganisms with the stunning capability to survive and multiply at extremely low ph and simultaneously at high temperatures. the mechanisms by which these organisms, exclusively members of the archaea, cope with their harsh surroundings are poorly understood. the genome sequences of several representatives of the thermoacidophilic genera picrophilus, thermoplasma and sulfolobus have recently become available. genome-wide comparison has revealed a number of f ...200616621083
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 http://www.biovirus.org and viral bioinformatics - canada http://www.virology.ca, 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
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, australia.to 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
a voyage to the inner space of cells. 200515608126
crystal structure of a predicted precorrin-8x methylmutase from thermoplasma acidophilum. 200515609338
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 torridus.in 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
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
protein-based biosensors for diabetic patients.in 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
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 assembly.to 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 spectroscopy.in 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 region.group 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
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 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
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
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
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
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