TitleAbstractYear(sorted ascending)
autocatalytic processing of the 20s proteasome.the ntn (n-terminal nucleophile) hydrolases are enzymes with an unusual four-layer alpha + beta fold. the amino-terminal residue (cysteine, serine or threonine) of the mature protein is the catalytic nucleophile, and its side chain is activated for nucleophilic attack by transfer of its proton to the free n terminus, although other active-site residues may also be involved. the four currently known ntn hydrolases (glutamine prpp amidotransferase, penicillin acylase, the 20s proteasome and aspart ...19968684489
the effect of cysteine-43 mutation on thermostability and kinetic properties of citrate synthase from thermoplasma this study, we have substituted serine-43 by cysteine in the recombinant citrate synthase from a moderately thermophilic archaeon thermoplasma acidophilum, for site-specific attachment of labels and have investigated the effects of this mutation on the biochemical properties and thermal stability of the enzyme. both wild-type and the mutant enzymes were purified to homogenity using affinity chromatography on matrex gel red a. the mutant thermoplasma citrate synthase is very similar to wild-ty ...19968694816
dolichyl-phosphomannose synthase from the archae thermoplasma acidophilum.archae (formerly archaebacteria) comprise an entire kingdom of organisms placed halfway between prokaryotes and eucaryotes in evolution. this class of organisms lacks murein cell wall and is devoid of organelles, yet archae synthesize and export n-linked and o-linked glycoproteins utilizing only the plasma membrane. study of glycosylation systems in archae is extremely interesting because the plasma membrane must perform many functions normally carried out by the endoplasmic reticulum and golgi ...19969023542
identification of beta-l-gulose as the sugar moiety of the main polar lipid thermoplasma acidophilum.the main polar lipid (mpl) of thermoplasma acidophilum has been purified and its structure determined. nmr, mass spectrometry, and capillary gas chromatography-mass spectrometry experiments have shown that the previously unidentified sugar moiety of mpl is the rare sugar l-gulose. mpl is thus a tetraether lipid with cyclopentane rings and head groups of phosphoglycerol, as previously reported, and beta-l-gulopyranose. further, mpl is also the dominant lipid found in lipid extracts from another s ...19979084501
structure of 20s proteasome from yeast at 2.4 a resolution.the crystal structure of the 20s proteasome from the yeast saccharomyces cerevisiae shows that its 28 protein subunits are arranged as an (alpha1...alpha7, beta1...beta7)2 complex in four stacked rings and occupy unique locations. the interior of the particle, which harbours the active sites, is only accessible by some very narrow side entrances. the beta-type subunits are synthesized as proproteins before being proteolytically processed for assembly into the particle. the proforms of three of t ...19979087403
the human alpha-type proteasomal subunit hsc8 forms a double ringlike structure, but does not assemble into proteasome-like particles with the beta-type subunits hsdelta or hsbpros26.the eukaryotic proteasome is a barrel-shaped protease complex made up of four seven-membered rings of which the outer and inner rings may contain up to seven different alpha- and beta-type subunits, respectively. the assembly of the eukaryotic proteasome is not well understood. we cloned the cdna for hsc8, which is one of the seven known human alpha-type subunits, and produced the protein in escherichia coli. recombinant hsc8 protein forms a complex of about 540 kda consisting of double ringlike ...19979092552
the proteasome.the proteasome is a macromolecular assembly that is designed to confine proteolytic activity to an inner cavity. access to the central proteolytic nanocompartment is restricted to unfolded proteins, which necessitates a functional coupling of the 20s proteasome to a substrate-recognition and unfolding machinery. significant progress has been made during the past two years in elucidating the structural principles and the enzymatic mechanism of the 20s proteasome.19979094332
the thermosome: alternating alpha and beta-subunits within the chaperonin of the archaeon thermoplasma acidophilum.the thermosome of the archaeon thermoplasma acidophilum is composed of two subunits, alpha and beta, which are arranged in two stacked, eight-membered rings. electron cryo-microscopy in conjunction with image analysis revealed a 4-fold symmetry in the heterooligomeric alpha + beta thermosome isolated from thermoplasma, but not in the homooligomeric alpha-only thermosome expressed in escherichia coli. this indicates that alpha and beta-subunits alternate within the rings of the thermoplasma therm ...19979096213
thermo sequenase dna polymerase and t. acidophilum pyrophosphatase: new thermostable enzymes for dna sequencing.a combination of thermostable enzymes has been developed that produces higher quality cycle sequences. thermo sequenase dna polymerase is a thermostable enzyme engineered to catalyze the incorporation of ddntps with an efficiency several thousandfold better than other thermostable dna polymerases. since the enzyme also catalyzes pyrophosphorolysis at dideoxy termini, a thermostable inorganic pyrophosphatase is needed to remove the pyrophosphate produced during sequencing reactions. thermoplasma ...19979105629
cloning, sequencing and expression of vat, a cdc48/p97 atpase homologue from the archaeon thermoplasma acidophilum.a member of the aaa family of mg2(+)-atpases from the archaeon thermoplasma acidophilum has been cloned and expressed in escherichia coli. the protein, vcp-like atpase of thermoplasma acidophilum (vat), is a homologue of sav from sulfolobus acidocaldarius and cdch of halobacterium salinarium, and belongs to the cdc48/vcp/p97 subfamily. the deduced product of the vat gene is 745 residues long (mr 83,000), which has an optimal mg2(+)-atpase activity at 70 degrees c. electron microscopy shows the p ...19979119075
the proteasome: a macromolecular assembly designed to confine proteolysis to a nanocompartment.significant progress has been made over the past few years in elucidating the structural principles and the enzymatic mechanism of the 20s proteasome. as a result, the proteasome has become the prototype of a new family of enzymes, the ntn hydrolases, as well as a paradigm for macromolecular assemblies that confine their proteolytic activity to an inner nanocompartment. since access to this nanocompartment is restricted to unfolded substrate polypeptides, the 20s proteasome must be functionally ...19979165062
new insights into the mechanisms and importance of the proteasome in intracellular protein degradation.recent studies of the 20s proteasome from thermoplasma acidophilum have uncovered some fundamental new properties of its catalytic mechanism. unlike conventional proteases, 20s and 26s proteasomes degrade protein substrates in a highly processive fashion. they cleave a protein substrate to small peptides before attacking another substrate molecule. this processive behavior is an inherent feature of the 20s particle not requiring cofactors or atp hydrolysis. recently, we have described a proteaso ...19979165063
screening for molecules interacting with proteasomes in thermoplasma acidophilum.thermoplasma acidophilum cell extracts were fractionated by gel filtration. proteasomes were eluted as two major peaks. the first one (molecular mass(r) about 2 mda) contained proteasomes associated with dna/protein complexes. proteasomes eluted in the other peak were partially resolved into three subpeaks and based on their preferential hydrolysis of casein, z-ggl-mca, and suc-llvy-mca, were designated c, l and y, respectively. further purification of proteasomes from peak y resulted in a homog ...19979165078
the stereospecificity of hydrogen transfer to nad(p)+ catalyzed by lactol dehydrogenases.the stereochemistry of hydrogen transfer to nad(p)+ has been determined for five lactol dehydrogenases. it was found that d-glucose dehydrogenases from bacillus megaterium and cryptococcus uniguttulatus and l-rhamnose dehydrogenase from aureobasidium pullulans are pro-s (b) specific, while d-glucose dehydrogenase from thermoplasma acidophilum and d-xylose dehydrogenase from procine liver are pro-r (a) specific. the latter two enzymes are the first examples of a-specific dehydrogenases oxidizing ...19979168914
crystal structure of heat shock locus v (hslv) from escherichia coli.heat shock locus v (hslv; also called clpq) is the proteolytic core of the atp-dependent protease hslvu in escherichia coli. it has sequence similarity with the beta-type subunits of the eukaryotic and archaebacterial proteasomes. unlike these particles, which display 72-point symmetry, it is a dimer of hexamers with 62-point symmetry. the crystal structure of hslv at 3.8-a resolution, determined by isomorphous replacement and symmetry averaging, shows that in spite of the different symmetry of ...19979177170
covalent modification of the active site threonine of proteasomal beta subunits and the escherichia coli homolog hslv by a new class of inhibitors.the proteasome is a multicatalytic protease complex that plays a key role in diverse cellular functions. the peptide vinyl sulfone, carboxybenzyl-leucyl-leucyl-leucine vinyl sulfone (z-l3vs) covalently inhibits the trypsin-like, chymotrypsin-like and, unlike lactacystin, also the peptidylglutamyl peptidase activity in isolated proteasomes, and blocks their function in living cells. although described as a class of mechanism-based inhibitors for cysteine proteases, the peptide vinyl sulfone z-l3v ...19979192616
import of human and thermoplasma 20s proteasomes into nuclei of hela cells requires functional nls sequences.proteasomes are present both in the nucleus and cytoplasm of eukaryotic cells. their localization is regulated and changes during the cell cycle. nuclear localization signal (nls) type sequences were identified in proteasomes from various organisms. in addition, acidic complementary sequences were identified (cnls) which could interact with the positively charged nls, masking or unmasking them and thereby modulating nuclear import. in this paper we show that fluorescently labeled human erythrocy ...19979208223
molecular microbial diversity of an anaerobic digestor as determined by small-subunit rdna sequence analysis.the bacterial community structure of a fluidized-bed reactor fed by vinasses (wine distillation waste) was analyzed. after pcr amplification, four small-subunit (ssu) rdna clone libraries of bacteria, archaea, procarya, and eucarya populations were established. the community structure was determined by operational taxonomic unit (otu) phylogenetic analyses of 579 partial rdna sequences (about 500 bp long). a total of 146 otus were found, comprising 133, 6, and 7 from the bacteria, archaea, and e ...19979212428
protein degradation by the proteasome and dissection of its in vivo importance with synthetic inhibitors. 19979228284
regulation of proteasome structure and function.proteasomes are cylindrical particles made up of a stack of four heptameric rings. in animal cells the outer rings are made up of 7 different types of alpha subunits and the inner rings are composed of 7 out of 10 possible different beta subunits. regulatory complexes can bind to the ends of the cylinder. we have investigated aspects of the assembly, activity and subunit composition of core proteasome particles and 26s proteasomes, the localization of proteasome subpopulations, and the possible ...19979228289
structure and structure formation of the 20s proteasome.eukaryotic 20s proteasomes are complex oligomeric proteins. the maturation process of the 14 different alpha- and beta-subunits has to occur in a highly coordinate manner. in addition beta-subunits are synthesized as proproteins and correct processing has to be guaranteed during complex maturation. the structure formation can be subdivided in different phases. the knowledge of the individual phases is summarized in this publication. as a first step the newly synthesized monomers have to adopt th ...19979228290
the crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 a resolution,.the crystal structure of the closed form of citrate synthase, with citrate and coa bound, from the hyperthermophilic archaeon pyrococcus furiosus has been determined to 1.9 a. this has allowed direct structural comparisons between the same enzyme from organisms growing optimally at 37 degrees c (pig), 55 degrees c (thermoplasma acidophilum) and now 100 degrees c (pyrococcus furiosus). the three enzymes are homodimers and share a similar overall fold, with the dimer interface comprising primarily ...19979254593
synthesis, kinetic characterization and x-ray analysis of peptide aldehydes as inhibitors of the 20s proteasomes from thermoplasma acidophilum and saccharomyces cerevisiae.a comparative kinetic characterization of the peptide aldehydes ac-leu-leu-x-h [x = trp, tyr and tyr(tbu)] and z-gly-pro-gly-gly-leu-leu-nle-h as inhibitors of the chymotryptic activity of 20s proteasomes from the archaebacterium t. acidophilum and yeast s. cerevisiae revealed significantly differentiated inhibitory potencies that can be rationalized on the basis of x-ray crystallographic data.19979377486
b12-dependent ribonucleotide reductases from deeply rooted eubacteria are structurally related to the aerobic enzyme from escherichia coli.the ribonucleotide reductases from three ancient eubacteria, the hyperthermophilic thermotoga maritima (tm), the radioresistant deinococcus radiodurans (dr), and the thermophilic photosynthetic chloroflexus aurantiacus, were found to be coenzyme-b12 (class ii) enzymes, similar to the earlier described reductases from the archaebacteria thermoplasma acidophila and pyrococcus furiosus. reduction of cdp by the purified tm and dr enzymes requires adenosylcobalamin and dtt. datp is a positive alloste ...19979391052
biogenesis of eukaryotic 20s proteasomes: the complex maturation pathway of a complex enzyme.eukaryotic 20s proteasomes harbor a remarkably complex architecture and unique proteolytic properties. its catalytic mechanism places this enzyme in a new kind of protease family. the recently solved crystal structure of the yeast 20s complex, along with elucidation of the maturation pathway of human proteasomes, has allowed insight into structure/function relationships. although not all of the unusual enzymatic properties such as broad substrate specificity, predominant generation of peptides w ...19979409542
perspectives of molecular and cellular electron tomography.after a general introduction to three-dimensional electron microscopy and particularly to electron tomography (et), the perspectives of applying et to native (frozen-hydrated) cellular structures are discussed. in et, a set of 2-d images of an object is recorded at different viewing directions and is then used for calculating a 3-d image. et at a resolution of 2-5 nm would allow the 3-d organization of structural cellular components to be studied and would provide important information about spa ...19979441933
tricorn protease exists as an icosahedral supermolecule in vivo.tricorn protease is the core enzyme of a recently discovered modular proteolytic system. we present evidence that tricorn protease exists in vivo in the form of a higher-order assembly, namely as an icosahedral capsid. its size exceeds that of many virus particles and represents by far the largest known homooligomeric enzyme complex. each capsid is built from 20 copies of the tricorn hexameric toroid and thus has a molecular weight of 14.6 mda. three-dimensional reconstructions of ice-embedded c ...19979659903
the b12-dependent ribonucleotide reductase from the archaebacterium thermoplasma acidophila: an evolutionary solution to the ribonucleotide reductase conundrum.a coenzyme b12-dependent ribonucleotide reductase was purified from the archaebacterium thermoplasma acidophila and partially sequenced. using probes derived from the sequence, the corresponding gene was cloned, completely sequenced, and expressed in escherichia coli. the deduced amino acid sequence shows that the catalytic domain of the b12-dependent enzyme from t. acidophila, some 400 amino acids, is related by common ancestry to the diferric tyrosine radical iron(iii)-dependent ribonucleotide ...19978990160
processive degradation of proteins and other catalytic properties of the proteasome from thermoplasma acidophilum.although the structure of the 20 s proteasome from thermoplasma acidophilum has been elucidated, its enzymatic properties have not been explored in depth. thermoplasma proteasomes, which contain one type of active site, exhibit not only "chymotrypsin-like" activity (as reported), but also some "post-glutamyl" and "trypsin-like" activities. like eukaryotic proteasomes, its activity can be stimulated by sds, mg2+, and also guanidine hcl, but not urea. the enzyme was strongly inhibited by novel pep ...19978999862
subunit topology of the rhodococcus proteasome.the 20s proteasome, isolated from the nocardioform actinomycete rhodococcus erythropolis strain ni86/21, is built from two alpha-type and two beta-type subunits. in order to probe the subunit topology, we have set up an expression system which allows coexpression of the genes encoding the alpha- and beta-subunits in all possible combinations. the four respective constructs obtained yielded fully assembled and proteolytically active proteasomes. biochemical, kinetic and electron microscopy analys ...19979000518
novel zinc-containing ferredoxin family in thermoacidophilic archaea.the dicluster-type ferredoxins from the thermoacidophilic archaea such as thermoplasma acidophilum and sulfolobus sp. are known to contain an unusually long extension of unknown function in the n-terminal region. recent x-ray structural analysis of the sulfolobus ferredoxin has revealed the presence of a novel zinc center, which is coordinated by three histidine ligand residues in the n-terminal region and one aspartate in the ferredoxin core domain. we report here the quantitative metal analyse ...19979013590
organic solutes in hyperthermophilic archaea.we examined the accumulation of organic solutes under optimum growth conditions in 12 species of thermophilic and hyperthermophilic archaea belonging to the crenarchaeota and euryarchaeota. pyrobaculum aerophilum, thermoproteus tenax, thermoplasma acidophilum, and members of the order sulfolobales accumulated trehalose. pyrococcus furiosus accumulated di-myo-inositol-1,1(prm1)(3,3(prm1))-phosphate and (beta)-mannosylglycerate, methanothermus fervidus accumulated cyclic-2,3-bisphosphoglycerate an ...199716535556
conformational constraints for protein self-cleavage in the proteasome.the proteasome is the central enzyme of protein degradation in the cytosol and the nucleus. it is involved in the removal of abnormal, misfolded or incorrectly assembled proteins, in the processing or degradation of transcriptional regulators in stress response, in degradation of cyclins in cell-cycle control, in the destruction of transcription factors or metabolic enzymes in cell differentiation and metabolic response, and in mhc class i mediated cellular immune response. by the analysis of th ...19989642094
cloning and overexpression in escherichia coli of the gene encoding citrate synthase from the hyperthermophilic archaeon sulfolobus solfataricus.the citrate synthase (cs) gene from the hyperthermophilic archaeon sulfolobus solfataricus has been cloned and sequenced. the gene encodes a polypeptide of 378 amino acids with a calculated polypeptide molecular mass of 42679. high-level expression was achieved in escherichia coli and the recombinant citrate synthase was purified to homogeneity using a heat step and dye-ligand affinity chromatography. this procedure yielded approximately 26 mg of pure cs per liter of culture, with a specific act ...19989672679
amino acid substitutions in the subunit interface enhancing thermostability of thermoplasma acidophilum citrate synthase.we have used citrate synthase from thermoplasma (tp.) acidophilum as a thermostable model system to investigate the role of hydrophobic interactions in dimer interface for maintaining high temperature stability. three mutant enzymes were constructed by single amino acid substitutions in the interface helices: ala97-->ser, ala104-->thr, and gly209-->ala. all of the mutations enhanced the thermostability of tp. citrate synthase, while improving its catalytic properties (km, vmax, and specific acti ...19989712738
the effect of hydrophobic interactions in the dimer interface of thermoplasma acidophilum citrate synthase on thermostability. 19989723739
decelerated degradation of short peptides by the 20s proteasome.based on a twelve residue master peptide comprising all five specific cleavage sites defined for the proteasome, a set of variant peptides was generated in order to probe specificity and to elucidate the mechanism which determines product size. it is shown that the rate of degradation by the 20s proteasome from thermoplasma acidophilum depends critically on the length of the peptide substrate. peptides of 14 residues and longer are degraded much faster than shorter peptides although the sites of ...19989742954
group ii chaperonin in a thermophilic methanogen, methanococcus thermolithotrophicus. chaperone activity and filament-forming ability.a gene encoding 544 amino acids for a subunit of group ii chaperonin (thermosome) was cloned from a thermophilic methanogen, methanococcus thermolithotrophicus. the deduced amino acid sequence showed 66.5, 56.1, and 20.1% similarities to those of methanopyrus kandleri and thermoplasma acidophilum and group i chaperonin of escherichia coli, respectively. we call this chaperonin mtts (m. thermolithotrophicus thermosome). the mtts gene was expressed in e. coli. the purified recombinant mtts seemed ...19989774467
group ii chaperonin in an open conformation examined by electron tomography. 19989783741
novel euryarchaeotal lineages detected on rice roots and in the anoxic bulk soil of flooded rice microcosmsbecause excised, washed roots of rice (oryza sativa) immediately produce ch4 when they are incubated under anoxic conditions (p. frenzel and u. bosse, fems microbiol. ecol. 21:25-36, 1996), we employed a culture-independent molecular approach to identify the methanogenic microbial community present on roots of rice plants. archaeal small-subunit rrna-encoding genes were amplified directly from total root dna by pcr and then cloned. thirty-two archaeal rice root (arr) gene clones were randomly se ...19989835592
the role of tricorn protease and its aminopeptidase-interacting factors in cellular protein degradation.tricorn protease was previously described as the core enzyme of a modular proteolytic system displaying multicatalytic activity. here we elucidate the mode of cooperation between tricorn and its interacting factors, and we identify two additional factors, f2 and f3, closely related aminopeptidases of 89 kda. in conjunction with these three factors, tricorn degrades oligopeptides in a sequential manner, yielding free amino acids. we have been able to reconstitute a proteolytic pathway comprising ...19989845366
range of sizes of peptide products generated during degradation of different proteins by archaeal proteasomes.the 20 s proteasome processively degrades cell proteins to peptides. information on the sizes and nature of these products is essential for understanding the proteasome's degradative mechanism, the subsequent steps in protein turnover, and major histocompatibility complex class i antigen presentation. using proteasomes from thermoplasma acidophilum and four unfolded polypeptides as substrates (insulin-like growth factor, lactalbumin, casein, and alkaline phosphatase, whose lengths range from 71 ...19989442034
characterization of homo-oligomeric complexes of alpha and beta chaperonin subunits from the acidothermophilic archaeon, sulfolobus sp. strain 7.the chaperonin from the acidothermophilic archaeon, sulfolobus sp. strain 7, is composed of two kinds of subunits designated as scp alpha and scp beta. in this study, we characterized the recombinant scp alpha and scp beta, which were separately expressed in escherichia coli. both of them were able to assemble to homo-oligomeric double-ring complexes, similar to subunits of group ii chaperonins from thermoplasma acidophilum and thermococcus strain ks-1. both complexes have no or at most trace at ...19989464270
lateral diffusion of the total polar lipids from thermoplasma acidophilum in multilamellar liposomes.31p nmr lineshapes of multilamellar liposomes composed mostly of a bilayer-spanning tetraether lipid are consistent with rapid axially symmetric motion about the bilayer normal. the residual chemical shift anisotropy of 36 ppm is comparable to that seen for diacylphosphatidylglycerol systems and suggests comparable headgroup motion. the lateral diffusion rates for thermoplasma acidophilum total polar lipids in mutilamellar liposomes was measured by two dimensional exchange nmr as a function of t ...19989518643
proteasome function is dispensable under normal but not under heat shock conditions in thermoplasma acidophilum.hitherto the biology of proteolysis in prokaryotes, particularly in archaea, is only poorly understood. we have used the tri-peptide vinyl sulfone inhibitor carboxybenzyl-leucyl-leucyl-leucine vinyl sulfone (z-l3vs) to study the in vivo function of proteasomes in thermoplasma acidophilum. z-l3vs is a potent inhibitor of the thermoplasma proteasome and is capable of modifying 75 to 80% of the proteasomal beta-subunits in cell cultures. inhibition of proteasomes has only marginal effects under nor ...19989541012
a proteolytic system that compensates for loss of proteasome function.proteolysis is essential for the execution of many cellular functions. these include removal of incorrectly folded or damaged proteins, the activation of transcription factors, the ordered degradation of proteins involved in cell cycle control, and the generation of peptides destined for presentation by class i molecules of the major histocompatibility complex. a multisubunit protease complex, the proteasome, accomplishes these tasks. here we show that in mammalian cells inactivation of the prot ...19989560160
citrate synthase and 2-methylcitrate synthase: structural, functional and evolutionary relationships.following the complete sequencing of the escherichia coli genome, it has been shown that the proposed second citrate synthase of this organism, recently described by the authors, is in fact a 2-methylcitrate synthase that possesses citrate synthase activity as a minor component. whereas the hexameric citrate synthase is constitutively produced, the 2-methylcitrate synthase is induced during growth on propionate, and the catabolism of propionate to succinate and pyruvate via 2-methylcitrate is pr ...19989579066
discontinuous occurrence of the hsp70 (dnak) gene among archaea and sequence features of hsp70 suggest a novel outlook on phylogenies inferred from this protein.occurrence of the hsp70 (dnak) gene was investigated in various members of the domain archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria aquifex pyrophilus and thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16s rrna sequences. the gene was not detected in 8 of 10 archaea examined but was found in a. pyrophilus and t. maritima, from which it was cloned and sequenced. comparative analyses of the hsp70 amino aci ...19999882656
allosteric control of three b12-dependent (class ii) ribonucleotide reductases. implications for the evolution of ribonucleotide reduction.three separate classes of ribonucleotide reductases are known, each with a distinct protein structure. one common feature of all enzymes is that a single protein generates each of the four deoxyribonucleotides. class i and iii enzymes contain an allosteric substrate specificity site capable of binding effectors (atp or various deoxyribonucleoside triphosphates) that direct enzyme specificity. some (but not all) enzymes contain a second allosteric site that binds only atp or datp. binding of datp ...199910066778
high-resolution afm-imaging and mechanistic analysis of the 20 s macromolecular protease complex, the 20 s proteasome is responsible for the degradation of cellular proteins and the generation of peptide epitopes for antigen presentation. here, structural and functional aspects of the 20 s proteasome from thermoplasma acidophilum have been investigated by atomic force microscopy (afm) and surface plasmon resonance (spr). due to engineered histidine tags introduced at defined positions, the proteasome complex was pre-oriented at ultra-flat chelator lipid me ...199910329196
structure of vat, a cdc48/p97 atpase homologue from the archaeon thermoplasma acidophilum as studied by electron tomography.valosine-containing protein-like atpase from thermoplasma acidophilum is a member of the superfamily of atpases associated with a diversity of cellular activities and is closely related to cdc48 from yeast and p97 from higher eukaryotes and more distantly to n-ethylmaleimide-sensitive fusion protein. we have used electron tomography to obtain low-resolution (2-2.5 nm) three-dimensional maps of both the whole 500 kda complex and the n-terminally truncated valosine-containing protein-like atpase f ...199910356978
3d reconstruction of the atp-bound form of cct reveals the asymmetric folding conformation of a type ii chaperonin.the type ii chaperonin cct (chaperonin containing tcp-1) of eukaryotic cytosol is a heteromeric 16-mer particle composed of eight different subunits. three-dimensional reconstructions of apo-cct and atp-cct have been obtained at 28 a resolution by cryo-electron microscopy. binding of atp generates an asymmetric particle; one ring has a slightly different conformation from the apo-cct ring, while the other has undergone substantial movements in the apical domains. upon atp binding the apical doma ...199910404219
structural conservation of the isolated zinc site in archaeal zinc-containing ferredoxins as revealed by x-ray absorption spectroscopic analysis and its evolutionary implications.the zfx gene encoding a zinc-containing ferredoxin from thermoplasma acidophilum strain ho-62 was cloned and sequenced. it is located upstream of two genes encoding an archaeal homolog of nascent polypeptide-associated complex alpha subunit and a trna nucleotidyltransferase. this gene organization is not conserved in several euryarchaeoteal genomes. the multiple sequence alignments of the zfx gene product suggest significant sequence similarity of the ferredoxin core fold to that of a low potent ...199910438486
isolation and characterization of novel neutral glycolipids from thermoplasma acidophilum.several novel neutral glycolipids (gl-1a, gl-1b, gl-2a, gl-2b and gl-2c) were isolated from thermoplasma acidophilum by high-performance liquid chromatography using phenylboronic acid-silica and preparative thin-layer chromatography. the tentative structures of these lipids were characterized by the combination of gas-liquid chromatography, the methylation procedure, and (1)h-nmr and fab-mass spectrometries. the lipophilic portion of the neutral glycolipids was composed of a simple molecular spe ...199910446424
giant proteases: beyond the proteasome.proteasomes and related proteases are thought to be the principal machinery responsible for intracellular protein degradation. a new class of giant proteases has been discovered that can augment the catabolic functions of proteasomes and, under some conditions, may even substitute for proteasomes altogether.199910469553
an archaebacterial atpase, homologous to atpases in the eukaryotic 26 s proteasome, activates protein breakdown by 20 s eukaryotes, the 20 s proteasome is the proteolytic core of the 26 s proteasome, which degrades ubiquitinated proteins in an atp-dependent process. archaebacteria lack ubiquitin and 26 s proteasomes but do contain 20 s proteasomes. many archaebacteria, such as methanococcus jannaschii, also contain a gene (s4) that is highly homologous to the six atpases in the 19 s (pa700) component of the eukaryotic 26 s proteasome. to test if this putative atpase may regulate proteasome function, we express ...199910473546
archaeal genomics.four euryarchaeal genomes have been completely sequenced and are publicly available: methanococcus jannaschii, methanobacterium thermoautotrophicum, pyrococcus horikoshii and archaeoglobus fulgidus. four more genome sequences, two crenarchaeal and two pyrococci, will soon be released. in addition, seven more archaeal genome sequencing projects are under way, including two halophiles, two thermoplasma, and a methanogen. these projects cover all branches of the archaeal domain and will lead to new ...199910508726
beta-propeller repeats and a pdz domain in the tricorn protease: predicted self-compartmentalisation and c-terminal polypeptide-binding strategies of substrate selection.prokaryotic proteases demonstrate a variety of substrate-selection strategies that prevent uncontrolled protein degradation. proteasomes and clpxp-like proteases form oligomeric structures that exclude large substrates from central solvated chambers containing their active sites. monomeric prolyl oligopeptidases have been shown to contain beta-propeller structures that similarly reduce access to their catalytic residues. by contrast, tsp-like enzymes contain pdz domains that are thought to speci ...199910518749
the solution structure of vat-n reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element.the vat protein of the archaebacterium thermoplasma acidophilum, like all other members of the cdc48/p97 family of aaa atpases, has two atpase domains and a 185-residue amino-terminal substrate-recognition domain, vat-n. vat shows activity in protein folding and unfolding and thus shares the common function of these atpases in disassembly and/or degradation of protein complexes.199910531028
the import pathway of human and thermoplasma 20s proteasomes into hela cell nuclei is different from that of classical nls-bearing proteins.wild-type proteasomes of human erythrocytes and the archaeon thermoplasma acidophilum compete with each other for transport into nuclei of digitonin-permeabilized hela cells in the presence of an energy-regenerating system and rabbit reticulocyte lysate. 'nls'-mutated thermoplasma proteasomes were also able to compete with human proteasomes in the same assay, although with lower efficiency. furthermore, in contrast to the other archaeal and bacterial cell lysates tested, the thermoplasma cytosol ...199910595581
capsids of tricorn protease studied by electron cryomicroscopy.tricorn protease from the archaeon thermoplasma acidophilum acts "downstream" of the proteasome; in conjunction with its aminopeptidase cofactors it converts peptides generated by the proteasome into free amino acids. the basic functional unit of tricorn is a homohexamer of the 121-kda subunit, 20 of which can assemble further to form an icosahedral capsid with a molecular mass of 14.6 mda. we have used electron cryomicroscopy to determine the structure of the tricorn capsids to a resolution of ...199910600560
in vitro assessment of archaeosome stability for developing oral delivery systems.the in vitro stability of archaeosomes made from the total polar lipids of methanosarcina mazei, methanobacterium espanolae or thermoplasma acidophilum, was evaluated under conditions encountered in the human gastrointestinal tract. at acidic ph, multilamellar vesicles (mlv) prepared from t. acidophilum lipids were the most stable, releasing approximately 80, 20, 10 and 5% of encapsulated 14c-sucrose at ph 1.5, 2.0, 2.5 and 6.2, respectively, after 90 min at 37 degrees c. archaeosomes from m. ma ...200010601683
archaeosome vaccine adjuvants induce strong humoral, cell-mediated, and memory responses: comparison to conventional liposomes and alum.ether glycerolipids extracted from various archaeobacteria were formulated into liposomes (archaeosomes) possessing strong adjuvant properties. mice of varying genetic backgrounds, immunized by different parenteral routes with bovine serum albumin (bsa) entrapped in archaeosomes ( approximately 200-nm vesicles), demonstrated markedly enhanced serum anti-bsa antibody titers. these titers were often comparable to those achieved with freund's adjuvant and considerably more than those with alum or c ...200010603368
cysteine biosynthesis pathway in the archaeon methanosarcina barkeri encoded by acquired bacterial genes?the pathway of cysteine biosynthesis in archaea is still unexplored. complementation of a cysteine auxotrophic escherichia coli strain nk3 led to the isolation of the methanosarcina barkeri cysk gene [encoding o-acetylserine (thiol)-lyase-a], which displays great similarity to bacterial cysk genes. adjacent to cysk is an open reading frame orthologous to bacterial cyse (serine transacetylase) genes. these two genes could account for cysteine biosynthesis in this archaeon. analysis of recent geno ...200010613873
identification of and spatio-temporal differences between microbial assemblages from two neighboring sulfurous lakes: comparison by microscopy and denaturing gradient gel electrophoresis.the microbial assemblages of lake cisó and lake vilar (banyoles, northeast spain) were analyzed in space and time by microscopy and by performing pcr-denaturing gradient gel electrophoresis (dgge) and sequence analysis of 16s rrna gene fragments. samples obtained from different water depths and at two different times of the year (in the winter during holomixis and in the early spring during a phytoplankton bloom) were analyzed. although the lakes have the same climatic conditions and the same wa ...200010653710
kinetics and mechanism of the citrate synthase from the thermophilic archaeon thermoplasma acidophilum.the kinetics and mechanism of the citrate synthase from a moderate thermophile, thermoplasma acidophilum (tpcs), are compared with those of the citrate synthase from a mesophile, pig heart (pcs). all discrete steps in the mechanistic sequence of pcs can be identified in tpcs. the catalytic strategies identified in pcs, destabilization of the oxaloacetate substrate carbonyl and stabilization of the reactive species, acetyl-coa enolate, are present in tpcs. conformational changes, which allow the ...200010694395
monomolecular organization of the main tetraether lipid from thermoplasma acidophilum at the water-air interface.the monomolecular organization of the main tetraether phospholipid from the archaeon thermoplasma acidophilum was studied by means of a langmuir film balance integrated into a fluorescence microscope. after transfer to solid surfaces at different pressures the films were further investigated by ellipsometry, small angle x-ray scattering and atomic force microscopy. in order to complete former results about the main tetraether phospholipid of t. acidophilum [strobl, c., six, l., heckmann, k., hen ...200010727112
protein purification by ultrafiltration using a beta-galactosidase fusion tag.the use of beta-galactosidase (465 kda) as a fusion tag for ultrafiltration-based protein purification has been investigated. the target protein studied was thermophilic glucose dehydrogenase (157 kda, gdh) from thermoplasma acidophilum. an expression vector was constructed comprising the lacz gene fused to a factor xa cleavage sequence that was attached to the 5' end of the gdh gene. this gene fusion was expressed in escherichia coli jm109 to yield a soluble protein that exhibited activities fo ...200010753458
conformational rearrangements of an archaeal chaperonin upon atpase cycling.chaperonins are double-ring protein assemblies with a central cavity that provides a sequestered environment for in vivo protein folding. their reaction cycle is thought to consist of a nucleotide-regulated alternation between an open substrate-acceptor state and a closed folding-active state. the cavity of atp-charged group i chaperonins, typified by escherichia coli groel [1], is sealed off by a co-chaperonin, whereas group ii chaperonins--the archaeal thermosome and eukaryotic tric/cct [2]--p ...200010753750
glucosylcaldarchaetidylglycerol, a minor phosphoglycolipid from thermoplasma acidophilum.a novel phosphoglycolipid (gpl-k) was isolated from thermoplasma acidophilum (atcc 27658). the chemical components of gpl-k were analyzed by gas liquid chromatography and gc-ms. the sugar moiety of gpl-k and its anomeric region were analyzed by nmr assignment. the core lipid of gpl-k was caldarchaeol, and its main hydrocarbon chains were acyclic and monocyclic c(40) biphytanyl. the polar head groups were alpha-glucose and glycerophosphate. the negative fab-ms spectrum of gpl-k confirmed that the ...200010760458
drg represents a family of two closely related gtp-binding a previous publication we identified a novel human gtp-binding protein that was related to drg, a developmentally regulated gtp-binding protein from the central nervous system of mouse. here we demonstrate that both the human and the mouse genome possess two closely related drg genes, termed drg1 and drg2. the two genes share 62% sequence identity at the nucleotide and 58% identity at the protein level. the corresponding proteins appear to constitute a separate family within the superfamily o ...200010760581
why does threonine, and not serine, function as the active site nucleophile in proteasomes?proteasomes belong to the n-terminal nucleophile group of amidases and function through a novel proteolytic mechanism, in which the hydroxyl group of the n-terminal threonines is the catalytic nucleophile. however, it is unclear why threonine has been conserved in all proteasomal active sites, because its replacement by a serine in proteasomes from the archaeon thermoplasma acidophilum (t1s mutant) does not alter the rates of hydrolysis of suc-llvy-amc (seemüller, e., lupas, a., stock, d., lowe, ...200010809725
ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the ferroplasmaceae fam. nov., comprising a distinct lineage of the isolate of an acidophilic archaeon, strain yt, was obtained from a bioleaching pilot plant. the organism oxidizes ferrous iron as the sole energy source and fixes inorganic carbon as the sole carbon source. the optimal ph for growth is 1.7, although growth is observed in the range ph 1.3 to 2.2. the cells are pleomorphic and without a cell wall. 16s rrna gene sequence analysis showed this strain to cluster phylogenetically within the order 'thermoplasmales' sensu woese, although with only 89. ...200010843038
conservation of substructures in proteins: interfaces of secondary structural elements in proteasomal is observed that during divergent evolution of two proteins with a common phylogenetic origin, the structural similarity of their backbones is often preserved even when the sequence similarity between them decreases to a virtually undetectable level. here we analyzed, whether the conservation of structure along evolution involves also the local atomic structures in the interfaces between secondary structural elements. we have used as study case one protein family, the proteasomal subunits, fo ...200010843865
the chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists.we present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. a chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. the archaebacterium, a thermoacidophil resembling extant thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to spirochaeta or hollandina that oxidized sulfide to sulfur. selection pressure for speed swimming and oxygen avoi ...200010860956
atpase cycle of an archaeal chaperonin.recent structural data imply differences in allosteric behavior of the group i chaperonins, typified by groel from escherichia coli, and the group ii chaperonins, which comprise archaeal thermosome and eukaryotic tric/cct. therefore, this study addresses the mechanism of interaction of adenine nucleotides with recombinant alpha-only and native alphabeta-thermosomes from thermoplasma acidophilum, which also enables us to analyze the role of the heterooligomeric composition of the natural thermoso ...200010864508
atpase cycle controls the conformation of an archaeal chaperonin as visualized by cryo-electron microscopy.chaperonins are double-ring protein folding machines fueled by atp binding and hydrolysis. conformational rearrangements upon atpase cycling of the group i chaperonins, typified by the escherichia coli groel/groes system, have been thoroughly investigated by cryo-electron microscopy and x-ray crystallography. for archaeal group ii chaperonins, however, these methods have so far failed to provide a correlation between the structural and the functional states. here, we show that the conformation o ...200010908735
distribution and diversity of archaea corresponding to the limnological cycle of a hypersaline stratified lake (solar lake, sinai, egypt).the vertical and seasonal distribution and diversity of archaeal sequences was investigated in a hypersaline, stratified, monomictic lake, solar lake, sinai, egypt, during the limnological development of stratification and mixing. archaeal sequences were studied via phylogenetic analysis of 16s rdna sequences as well as denaturing gradient gel electrophoresis analysis. the 165 clones studied were grouped into four phylogenetically different clusters. most of the clones isolated from both the aer ...200010919780
crystal structure of the beta-apical domain of the thermosome reveals structural plasticity in the protrusion region.the crystal structure of the beta-apical domain of the thermosome, an archaeal group ii chaperonin from thermoplasma acidophilum, has been determined at 2.8 a resolution. the structure shows an invariant globular core from which a 25 a long protrusion emanates, composed of an elongated alpha-helix (h10) and a long extended stretch consisting of residues glub245-thrb253. a comparison with previous apical domain structures reveals a large segmental displacement of the protruding part of helix h10 ...200010926489
the effect of valine substitution for glycine in the dimer interface of citrate synthase from thermoplasma acidophilum on stability and determine the role of hydrophobic interactions in the dimer interface of citrate synthase (cs) from thermoplasma (tp) acidophilum in thermostabilization, we have used site-directed mutagenesis to replace gly 196 by val on the helix l of the subunit interface. recombinant wild-type and gly 196 mutant tpcs enzymes were largely identical in terms of substrate specificities (k(m) for oxaloacetate and acetyl coa). however, the mutation not only reduced catalytic activity (about 10-fold) (i.e., v(m ...200010964687
cloning and characterization of ftsz and pyrf from the archaeon thermoplasma characterize cytoskeletal components of archaea, the ftsz gene from thermoplasma acidophilum was cloned and sequenced. in t. acidophilum ftsz, which is involved in cell division, was found to be in an operon with the pyrf gene, which encodes orotidine-5'-monophosphate decarboxylase (odc), an essential enzyme in pyrimidine biosynthesis. both ftsz and pyrf from t. acidophilum were expressed in escherichia coli and formed functional proteins. ftsz expression in wild-type e. coli resulted in the ...200010973825
use your neighbour's genes. 200011028987
the genome sequence of the thermoacidophilic scavenger thermoplasma acidophilum.thermoplasma acidophilum is a thermoacidophilic archaeon that thrives at 59 degrees c and ph 2, which was isolated from self-heating coal refuse piles and solfatara fields. species of the genus thermoplasma do not possess a rigid cell wall, but are only delimited by a plasma membrane. many macromolecular assemblies from thermoplasma, primarily proteases and chaperones, have been pivotal in elucidating the structure and function of their more complex eukaryotic homologues. our interest in protein ...200011029001
giant vesicles from 72-membered macrocyclic archaeal phospholipid analogues: initiation of vesicle formation by molecular recognition between membrane componentsstereochemically pure archeal acyclic bola-amphiphilic diphosphates 4 and 5, with the basic structure of the phospholipids found in sulfolobus, have been synthesized for the first time. the self-assembly properties have been compared with those of the nearly identical 72-membered macrocyclic tetraether phosphates 3a and 3b, analogues of the major phospholipid components of sulfolobus, thermoplasma, and methanogenic archea, which were also synthesized. phase contrast and fluorescence microscopies ...200011039526
pan, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone.the proteasome-activating nucleotidase (pan) from methanococcus jannaschii is a complex of relative molecular mass 650,000 that is homologous to the atpases in the eukaryotic 26s proteasome. when mixed with 20s archaeal proteasomes and atp, pan stimulates protein degradation. here we show that pan reduces aggregation of denatured proteins and enhances their refolding. these processes do not require atp hydrolysis, although atp binding enhances the ability of pan to prevent aggregation. pan also ...200011056539
thermostability and thermoactivity of citrate synthases from the thermophilic and hyperthermophilic archaea, thermoplasma acidophilum and pyrococcus furiosus.citrate synthases from thermoplasma acidophilum (optimal growth at 55 degrees c) and pyrococcus furiosus (100 degrees c) are homo-dimeric enzymes that show a high degree of structural homology with each other, and thermostabilities commensurate with the environmental temperatures in which their host cells are found. a comparison of their atomic structures with citrate synthases from mesophilic and psychrophilic organisms has indicated the potential importance of inter-subunit contacts for thermo ...200011099387
characterization of caldarchaetidylglycerol analogs, dialkyl-type and trialkyl-type, from thermoplasma acidophilum.the structures of three kinds of phospholipids (pl-x, pl-y, and pl-t) isolated from thermoplasma acidophilum have been characterized. the core lipid of pl-y was caldarchaeol, and that of pl-x was archaeol. the composition of the hydrocarbon chains of the pl-t core lipid was c20 phytane and c40 isoprenoid in a molar ratio of 2 to 1. the major molecular species of the c40 isoprenoid was acyclic without the cyclopentane ring. these three kinds of intact phospholipids commonly had glycerophosphate r ...200011104022
horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches.members of the deinococcaceae (e.g., thermus, meiothermus, deinococcus) contain a/v-atpases typically found in archaea or eukaryotes which were probably acquired by horizontal gene transfer. two methods were used to quantify the extent to which archaeal or eukaryotic genes have been acquired by this lineage. screening of a meiothermus ruber library with probes made against thermoplasma acidophilum dna yielded a number of clones which hybridized more strongly than background. one of these contain ...200011116332
archaeal adaptation to higher temperatures revealed by genomic sequence of thermoplasma volcanium.the complete genomic sequence of the archaeon thermoplasma volcanium, possessing optimum growth temperature (ogt) of 60 degrees c, is reported. by systematically comparing this genomic sequence with the other known genomic sequences of archaea, all possessing higher ogt, a number of strong correlations have been identified between characteristics of genomic organization and the ogt. with increasing ogt, in the genomic dna, frequency of clustering purines and pyrimidines into separate dinucleotid ...200011121031
rotary and unidirectional metal shadowing of vat: localization of the substrate-binding have important roles in manifold cellular processes. vat (valosine-containing protein-like atpase of thermoplasma acidophilum), a hexameric archaeal member of this family, has the tripartite domain structure n-d1-d2 that is characteristic of many members of this family. n, the n-terminal domain of 20.5 kda, has been implicated in substrate binding. we have applied rotary and unidirectional shadowing to vat and an n-terminally deleted mutant, vat(delta n), in order to map the location ...200011162738
structure of the aaa atpase p97.p97, an abundant hexameric atpase of the aaa family, is involved in homotypic membrane fusion. it is thought to disassemble snare complexes formed during the process of membrane fusion. here, we report two structures: a crystal structure of the n-terminal and d1 atpase domains of murine p97 at 2.9 a resolution, and a cryoelectron microscopy structure of full-length rat p97 at 18 a resolution. together, these structures show that the d1 and d2 hexamers pack in a tail-to-tail arrangement, and that ...200011163219
extreme genomes.the complete genome sequence of thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.200011178269
occurrence of d-amino acids and a pyridoxal 5'-phosphate-dependent aspartate racemase in the acidothermophilic archaeon, thermoplasma d-amino acid content in some archaea was investigated and d-forms of several amino acids were found in them. in the acidothermophilic archaeon, thermoplasma acidophilum, the proportion of d-aspartate (d-asp) to total asp was as high as 39.7%. crude extracts of thermoplasma acidophilum had asp-specific racemase activity that was pyridoxal 5'-phosphate (plp)-dependent. the relative insensitivity to a sh-modifying reagent distinguished this activity from those of the plp-independent asp racema ...200111181048
variation in molecular species of polar lipids from thermoplasma acidophilum depends on growth temperature.five types of molecular species of c40 isoprenoid chains, having different numbers of cyclopentane rings, were detected in the ether core lipid of thermoplasma acidophilum. the average cyclization number of the hydrocarbon chains in the lipids increased with increasing growth temperatures.200111214723
mechanosensitive channels in prokaryotes.compared to voltage-dependent or ligand-gated ion channels that have extensively been studied over the last twenty years, there is little knowledge available on structure and function of mechanosensitive (ms) channels that constitute the third major group of ion channels classified according to their gating mechanism. the main purpose of this review is to summarize an area of the ms channel research where major progress has occurred. cloning of mscl and mscs, the ms channels of large and small c ...200111275684
probing stability-activity relationships in the thermophilic proteasome from thermoplasma acidophilum by random mutagenesis.structural perturbations (l65h, v12l/m27t, f35v) generated by random mutation of the beta-subunit were used to probe the relationship between stability and activity in the thermophilic proteasome from thermoplasma acidophilum. the optimum temperature for activity of each mutant (approximately 95 degrees c) remained unchanged; however, each mutant was significantly less stable than the wild type. stability, therefore, is not the factor limiting high-temperature activity. interestingly, mutation l ...200111302500
tricorn protease in bacteria: characterization of the enzyme from streptomyces coelicolor.tricorn protease is believed to act downstream of the proteasome, or of other atp-dependent proteases, cleaving the oligopeptides (mostly 6 to 12 residues) released by them into small peptides (2 to 4 residues), before an array of aminopeptidases finally converts them into free amino acids. hitherto, the occurrence of tricorn protease seemed to be limited to some archaea, but genes encoding tricorn homologs have now been found in several bacterial genomes. among them is streptomyces coelicolor a ...200111347893
identification of the gene that, when mutated, causes the human obesity syndrome bbs4.bardet-biedl syndrome (bbs, mim 209900) is a heterogeneous autosomal recessive disorder characterized by obesity, pigmentary retinopathy, polydactyly, renal malformations, mental retardation, and hypogenitalism. the disorder is also associated with diabetes mellitus, hypertension, and congenital heart disease. six distinct bbs loci map to 11q13 (bbs1), 16q21 (bbs2), 3p13-p12 (bbs3), 15q22.3-q23 (bbs4), 2q31 (bbs5), and 20p12 (bbs6). although bbs is rare in the general population (<1/100,000), th ...200111381270
phylogenetic analysis of archaeal 16s rrna libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens.molecular diversity of rumen archaea was analyzed by pcr amplification and sequencing of two 16s rrna clone libraries prepared from the bovine rumen fluid using two different archaea-specific primer sets. the first library of 19 clones which was generated with primers d30 and d33, produced essentially two groups of sequences, one affiliated with methanomicrobium mobile (21% of clones) and the other -- with the uncultured archaeal sequences from anaerobic digester, which are distantly associated ...200111410351
bacterial origin for the isoprenoid biosynthesis enzyme hmg-coa reductase of the archaeal orders thermoplasmatales and archaeoglobales.the enzyme 3-hydroxy-3-methylglutaryl coenzyme a reductase (hmg-coa reductase or hmgr) fulfills an essential role in archaea, as it is required for the synthesis of isoprenoid ethers, the main component of archaeal cell membranes. there are two clearly homologous but structurally different classes of the enzyme, one found mainly in eukaryotes and archaea (class 1), and the other found in bacteria (class 2). this feature facilitated the identification of several cases of interdomain lateral gene ...200111420376
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