| structure and mutation analysis of archaeal geranylgeranyl reductase. | the crystal structure of geranylgeranyl reductase (ggr) from sulfolobus acidocaldarius was determined in order to elucidate the molecular mechanism of the catalytic reaction. the enzyme is a flavoprotein and is involved in saturation of the double bonds on the isoprenoid moiety of archaeal membranes. the structure determined in this study belongs to the p-hydroxybenzoate hydroxylase family in the glutathione reductase superfamily. ggr functions as a monomer and is divided into the fad-binding, c ... | 2011 | 21515284 |
| sulfolobus turreted icosahedral virus c92 protein responsible for formation of pyramid-like cellular lysis structures. | host cells infected by sulfolobus turreted icosahedral virus (stiv) have been shown to produce unusual pyramid-like structures on their cell surface. these structures represent a viral-induced lysis mechanism that is present in archaea and appears to be distinct from the holin/endolysin system described for dna bacteriophages. this study investigated the stiv gene products required for pyramid formation in its host sulfolobus solfataricus. over-expression of stiv orf c92 in s. solfataricus alone ... | 2011 | 21525343 |
| architectures of archaeal gins complexes, essential dna replication initiation factors. | abstract: background: in the early stage of eukaryotic dna replication, the template dna is unwound by the mcm helicase, which is activated by forming a complex with the cdc45 and gins proteins. the eukaryotic gins forms a heterotetramer, comprising four types of subunits. on the other hand, the archaeal gins appears to be either a tetramer formed by two types of subunits in a 2:2 ratio (alpha2beta2) or a homotetramer of a single subunit (alpha4). due to the low sequence similarity between the a ... | 2011 | 21527023 |
| the activity of an ancient atypical protein kinase is stimulated by adp-ribose in vitro. | the pid261/bud32 protein kinases are universal amongst the members of the eucarya and archaea. despite the fact that phylogenetic analyses indicate that the pid261/bud32 protein kinases descend directly from the primordial ancestor of the "eukaryotic" protein kinase superfamily, our knowledge of their physiological role is relatively fragmentary and largely limited to two eucaryal representatives: pid261/bud32 from yeast and the p53-related protein kinase from humans. a deduced archaeal homolog, ... | 2011 | 21527241 |
| crystallization and preliminary x-ray diffraction analysis of the hyperthermophilic sulfolobus islandicus lactonase. | phosphotriesterase-like lactonases (plls) constitute an interesting family of enzymes that are of paramount interest in biotechnology with respect to their catalytic functions. as natural lactonases, they may act against pathogens such as-ápseudomonas aeruginosa by shutting down their quorum-sensing system (quorum quenching) and thus decreasing pathogen virulence. owing to-átheir promiscuous phosphotriesterase activity, which can inactivate toxic organophosphorus compounds such as pesticides and ... | 2011 | 21393842 |
| free energy simulations of a gtpase: gtp and gdp binding to archaeal initiation factor 2. | archaeal initiation factor 2 (aif2) is a protein involved in the initiation of protein biosynthesis. in its gtp-bound, "on" conformation, aif2 binds an initiator trna and carries it to the ribosome. in its gdp-bound, "off" conformation, it dissociates from trna. to understand the specific binding of gtp and gdp and its dependence on the on or off conformational state of aif2, molecular dynamics free energy simulations (mdfe) are a tool of choice. however, the validity of the computed free energi ... | 2011 | 21534562 |
| crystal structure of sulfolobus tokodaii sua5 complexed with l-threonine and amppnp. | the hypermodified nucleoside n(6) -threonylcarbamoyladenosine resides at position 37 of trna molecules bearing u at position 36 and maintains translational fidelity in the three kingdoms of life. the n(6) -threonylcarbamoyl moiety is composed of l-threonine and bicarbonate, and its synthesis was genetically shown to require yrdc/sua5. yrdc/sua5 binds to trna and atp. in this study, we analyzed the l-threonine-binding mode of sua5 from the archaeon sulfolobus tokodaii. isothermal titration calori ... | 2011 | 21538543 |
| strand annealing and terminal transferase activities of a b-family dna polymerase. | dna replication polymerases have the inherent ability to faithfully and rapidly copy a dna template according to precise watson-crick base pairing. the primary b-family dna replication polymerase (dpo1) in the hyperthermophilic archaeon, sulfolobus solfataricus, is shown here to possess a remarkable dna stabilizing ability for maintaining weak base pairing interactions to facilitate primer extension. this thermal stabilization by dpo1 allowed for template-directed synthesis at temperatures more ... | 2011 | 21545141 |
| the dna-recognition fold of sso7c4 suggests a new member of spovt-abrb superfamily from archaea. | organisms growing at elevated temperatures face the challenge of maintaining the integrity of their genetic materials. archaea possess unique chromatin proteins for gene organization and information processing. we present the solution structure of sso7c4 from sulfolobus solfataricus, which has a homodimeric dna-binding fold forming a swapped β-loop-β 'tai-chi' topology. the fold is reminiscent of the n-terminal dna-binding domain of abrb and maze. in addition, several amide resonances in the het ... | 2011 | 21546550 |
| steric exclusion and wrapping of the excluded dna strand occurs along discrete external binding paths during mcm helicase unwinding. | the minichromosome maintenance (mcm) helicase complex is essential for the initiation and elongation of dna replication in both the eukaryotic and archaeal domains. the archaeal homohexameric mcm helicase from sulfolobus solfataricus serves as a model for understanding mechanisms of dna unwinding. in this report, the displaced 5'-tail is shown to provide stability to the mcm complex on dna and contribute to unwinding. mutations in a positively charged patch on the exterior surface of the mcm hex ... | 2011 | 21576224 |
| growth phase-dependent gene regulation in vivo in sulfolobus solfataricus. | ribosomal genes are strongly regulated dependent on growth phase in all organisms, but this regulation is poorly understood in archaea. moreover, very little is known about growth phase-dependent gene regulation in archaea. ssv1-based lacs reporter gene constructs containing the sulfolobus 16s/23s rrna gene core promoter, the tf55α core promoter, or the native lacs promoter were tested in sulfolobus solfataricus cells lacking the lacs gene. the 42-bp 16s/23s rrna gene and 39-bp tf55α core promot ... | 2011 | 21595744 |
| archaeal flagellar atpase motor shows atp-dependent hexameric assembly and activity stimulation by specific lipid binding. | microbial motility frequently depends on flagella or type iv pili. using recently developed archaeal genetic tools, archaeal flagella and its assembly machinery have been identified. archaeal flagella are functionally similar to bacterial flagella and their assembly systems are homologous to type iv pili assembly systems of gram negative bacteria. therefore, elucidating their biochemistry may result in insights in both archaea and bacteria. flai, a critical cytoplasmic component of the archaeal ... | 2011 | 21506936 |
| genomic analysis of acidianus hospitalis w1 a host for studying crenarchaeal virus and plasmid life cycles. | the acidianus hospitalis w1 genome consists of a minimally sized chromosome of about 2.13 mb and a conjugative plasmid pah1 and it is a host for the model filamentous lipothrixvirus afv1. the chromosome carries three putative replication origins in conserved genomic regions and two large regions where non-essential genes are clustered. within these variable regions, a few orphan orfb and other elements of the is200/607/605 family are concentrated with a novel class of mite-like repeat elements. ... | 2011 | 21607549 |
| site-specific labeling of proteins by using biotin protein ligase conjugated with fluorophores. | biotin protein ligase (bpl) mediates the covalent attachment of biotin to a specific lysine residue of biotin carboxyl carrier protein (bccp). this biotinylation in sulfolobus tokodaii is unique in that bpl forms a tight complex with the product, biotinylated bccp, and this property was exploited for fluorescent labeling of a membrane protein. thus, the truncated form of bccp (bccpδ100, 69 residues) was fused to either the n or c terminus of the bradykinin b2 receptor (b2r). the resulting fusion ... | 2011 | 21608095 |
| archaeosomes with encapsulated antigens for oral vaccine delivery. | traditional phosphodiester lipid vesicles (liposomes) are not stable and could be easily degraded in the gastrointestinal (gi) tract. we prepared a novel lipid based oral delivery system: archaeosomes, made of the polar lipid fraction e (plfe) extracted from sulfolobus acidocaldarius, and tested their immunogenic potentials as oral vaccine delivery vehicles. our study showed that the archaeosomes had significant superior stability in simulated gastric and intestinal fluids, and would help fluore ... | 2011 | 21609747 |
| vapc6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote sulfolobus solfataricus. | the phylum crenarchaeota includes hyperthermophilic micro-organisms subjected to dynamic thermal conditions. previous transcriptomic studies of sulfolobus solfataricus identified vapbc6 as a heat-shock (hs)-inducible member of the vap toxin-antitoxin gene family. in this study, the inactivation of the vapbc6 operon by targeted gene disruption produced two recessive phenotypes related to fitness, hs sensitivity and a heat-dependent reduction in the rate of growth. in-frame vapbc6 deletion mutants ... | 2011 | 21622901 |
| the gins complex from the thermophilic archaeon, thermoplasma acidophilum may function as a homotetramer in dna replication. | the eukaryotic gins heterotetramer, consisting of sld5, psf1, psf2, and psf3, participates in "cmg complex" formation with mini-chromosome maintenance (mcm) and cdc45 as a key component of a replicative helicase. there are only two homologs of the gins proteins in archaea, and these proteins, gins51 and gins23, form a heterotetrameric gins with a 2:2 molar ratio. the pyrococcus furiosus gins stimulates the atpase and helicase activities of its cognate mcm, whereas the sulfolobus solfataricus gin ... | 2011 | 21656171 |
| sthsp14.0, a small heat shock protein of sulfolobus tokodaii strain 7, protects denatured proteins from aggregation in the partially dissociated conformation. | the small heat shock protein (shsp), categorized into a class of molecular chaperones, binds and stabilizes denatured proteins for the purpose of preventing aggregation. the shsps undergo transition between different oligomeric states to control their nature. we have been studying the function of shsp of sulfolobus tokodaii, sthsp14.0. sthsp14.0 exists as 24meric oligomer, and exhibits oligomer dissociation and molecular chaperone activity over 80 ┬░c. we constructed and characterized sthsp14.0 ... | 2011 | 21659385 |
| oral peptide delivery by tetraether lipid liposomes. | the aim of this study is to improve of oral peptide delivery by a novel type of liposomes containing tetraether lipids (tels) derived from archaea bacteria. liposomes were used for the oral delivery of the somatostatin analogue octreotide. tels were extracted from sulfolobus acidocaldarius and subsequently purified to single compounds. liposomes were prepared by the film method followed by extrusion. vesicles in size between 130 and 207 nm were obtained as confirmed by photon correlation spectro ... | 2011 | 21664955 |
| exceptional virion release mechanism: one more surprise from archaeal viruses. | virion release from the host cell is the final and essential step for completion of the viral life cycle and spread of virions in the environment. although for eukaryotic and bacterial viruses the egress mechanisms are reasonably well understood, this subject has not been studied in detail for archaeal viruses until recently. here we summarize available data on the extraordinary egress mechanism exploited by the sulfolobus islandicus rod-shaped virus sirv2 and the sulfolobus turreted icosahedral ... | 2011 | 21531608 |
| engineering thermoacidophilic archaea using linear dna recombination. | thermoacidophilic archaea comprise one of the major classes of extremophiles. most belong to the family sulfolobales within the phylum crenarchaeota. they are of applied interest as sources of hyperstable enzymes, for biomining of base and precious metals, and for evolutionary studies because of their use of eukaryotic-like subcellular mechanisms. genetic methods are available for several species particularly sulfolobus solfataricus. this organism has a considerable number of methods available f ... | 2011 | 21815108 |
| bypass of aflatoxin b(1) adducts by the sulfolobus solfataricus dna polymerase iv. | aflatoxin b(1) (afb(1)) is oxidized to an epoxide in vivo, which forms an n7-dg dna adduct (afb(1)-n7-dg). the afb(1)-n7-dg can rearrange to a formamidopyrimidine (afb(1)-fapy) derivative. both afb(1)-n7-dg and the ß-anomer of the afb(1)-fapy adduct yield g?t transversions in escherichia coli, but the latter is more mutagenic. we show that the sulfolobus solfataricus p2 dna polymerase iv (dpo4) bypasses afb(1)-n7-dg in an error-free manner but conducts error-prone replication past the afb(1)-fap ... | 2011 | 21790157 |
| sulfolobus mutants, generated via pcr products, which lack putative enzymes of uv photoproduct repair. | in order to determine the biological relevance of two s. acidocaldarius proteins to the repair of uv photoproducts, the corresponding genes (saci_1227 and saci_1096) were disrupted, and the phenotypes of the resulting mutants were examined by various genetic assays. the disruption used integration by homologous recombination of a functional but heterologous pyre gene, promoted by short sequences attached to both ends via pcr. the phenotypic analyses of the disruptants confirmed that orf saci_122 ... | 2011 | 21785574 |
| roles of the four dna polymerases of the crenarchaeon sulfolobus solfataricus and accessory proteins in dna replication. | the hyperthermophilic crenarchaeon sulfolobus solfataricus p2 encodes three b-family dna polymerase genes-b1 (dpo1), b2 (dpo2), and b3 (dpo3)-and one y-family dna polymerase gene, dpo4, which are related to eukaryotic counterparts. both mrnas and proteins of all four dna polymerases were constitutively expressed in all growth phases. dpo2 and dpo3 possessed very low dna polymerase and 3' to 5' exonuclease activities in vitro. steady-state kinetic efficiencies (kcat/km) for correct nucleotide ins ... | 2011 | 21784862 |
| the initiation factor tfe and the elongation factor spt4/5 compete for the rnap clamp during transcription initiation and elongation. | tfiie and the archaeal homolog tfe enhance dna strand separation of eukaryotic rnapii and the archaeal rnap during transcription initiation by an unknown mechanism. we have developed a fluorescently labeled recombinant m. jannaschii rnap system to probe the archaeal transcription initiation complex, consisting of promoter dna, tbp, tfb, tfe, and rnap. we have localized the position of the tfe winged helix (wh) and zinc ribbon (zr) domains on the rnap using single-molecule fret. the interaction s ... | 2011 | 21777815 |
| topr2, the second reverse gyrase of sulfolobus solfataricus, exhibits unusual properties. | whereas reverse gyrase is considered as a strong marker of thermophily, the function of this peculiar type ia topoisomerase still remains to be elucidated. the archaeon sulfolobus solfataricus encodes two reverse gyrases, topr1 and topr2. this duplication seems to be important because most of crenarcheota exhibit two copies of reverse gyrase. however, to date, while topr1 has been well characterized, no characterization of topr2 has been reported. in this study, we describe for the first time th ... | 2011 | 21435345 |
| macromolecular fingerprinting of sulfolobus species in biofilm: a transcriptomic and proteomic approach combined with spectroscopic analysis. | microorganisms in nature often live in surface-associated sessile communities, encased in a self-produced matrix, referred to as biofilms. biofilms have been well studied in bacteria but in a limited way for archaea. we have recently characterized biofilm formation in three closely related hyperthermophilic crenarchaeotes: sulfolobus acidocaldarius, s. solfataricus, and s. tokodaii. these strains form different communities ranging from simple carpet structures in s. solfataricus to high density ... | 2011 | 21761944 |
| copr of sulfolobus solfataricus represents a novel class of archaeal-specific copper-responsive activators of transcription. | in trace amounts, copper is essential for the function of key enzymes in prokaryotes and eukaryotes. organisms have developed sophisticated mechanisms to control the cytosolic level of the metal, manage its toxicity and survive in copper-rich environments. here we show that the sulfolobus copr represent a novel class of copper-responsive regulators, unique to the archaeal domain. furthermore, by disruption of the open reading frame sso2652 (copr) of the s. solfataricus genome, we demonstrated th ... | 2011 | 21757491 |
| characterization of sulfolobus islandicus rod-shaped virus 2 gp19, a single-strand specific endonuclease. | the hyperthermophilic sulfolobus islandicus rod-shaped virus 2 (sirv2) encodes a 25-kda protein (sirv2gp19) annotated as a hypothetical protein with sequence homology to the recb nuclease superfamily. even though sirv2gp19 homologs are conserved throughout the rudivirus family and presumably play a role in the viral life cycle, sirv2gp19 has not been functionally characterized. to define the minimal requirements for activity, sirv2gp19 was purified and tested under varying conditions. sirv2gp19 ... | 2011 | 21667093 |
| parallel evolution of transcriptome architecture during genome reorganization. | assembly of genes into operons is generally viewed as an important process during the continual adaptation of microbes to changing environmental challenges. however, the genome reorganization events that drive this process are also the roots of instability for existing operons. we have determined that there exists a statistically significant trend that correlates proportion of genes encoded in operons in archaea to their phylogenetic lineage. we have further characterized how microbes deal with ... | 2011 | 21750103 |
| the thermoacidophilic archaeon sulfolobus acidocaldarius contains an unsually short, highly reduced dolichyl phosphate. | polyprenoids, polymers containing varied numbers of isoprene subunits, serve numerous roles in biology. in eukarya, dolichyl phosphate, a phosphorylated polyprenol bearing a saturated a-end isoprene subunit, serves as the glycan carrier during n-glycosylation, namely that post-translational modification whereby glycans are covalently linked to select asparagine residues of a target protein. as in eukarya, n-glycosylation in archaea also relies on phosphorylated dolichol. in this report, lc-esi/m ... | 2011 | 21745590 |
| bio-oxidation of h(2)s by sulfolobus metallicus. | sulfolobus metallicus is a hyperthermophilic and chemolithoautotrophic archaeon that uses elemental sulfur as an energy source. its ability to oxidize h(2)s was measured either in the presence or absence of elemental sulphur, showing its ability for using both as an energy source. a biotrickling filter was set up and a biofilm of s. metallicus was established over the support. the maximum removal capacity of the biotrickling filter reached at 55°c was 40 g s/m(3)h for input loads higher than 70 ... | 2011 | 21744275 |
| design and synthesis of atp-based nucleotide analogues and profiling of nucleotide-binding proteins. | two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. we focused on the profiling of adenine nucleotide-binding proteins. two properties were considered in the design of the probes: the bait needs to bind adenine nucleotide-binding proteins with high affinity and carry a second functional group suitable and easily accessible for coupling to a chromatography resin. for this purpose, we synthesized ... | 2011 | 21692528 |
| the sulfolobicin genes of sulfolobus acidocaldariusencode novel antimicrobial proteins. | crenarchaea, such as sulfolobus acidocaldariusand sulfolobus tokodaii, produce antimicrobial proteins called sulfolobicins. these antimicrobial proteins inhibit the growth of closely related species. here we report the identification of the sulfolobicin-encoding genes in s. acidocaldarius. the active sulfolobicin comprises two proteins that are equipped with a classical signal sequence. these proteins are secreted by the cells and found to be membrane vesicle associated. gene inactivation studie ... | 2011 | 21725003 |
| deletion of the topoisomerase iii gene in the hyperthermophilic archaeon sulfolobus islandicus results in slow growth and defects in cell cycle control. | topoisomerase iii (topo iii), a type ia topoisomerase, is widespread in hyperthermophilic archaea. in order to interrogate the in-ávivo role of archaeal topo iii, we constructed and characterized a topo iii gene deletion mutant of sulfolobus islandicus. the mutant was viable but grew more slowly than the wild-type strain, especially in a nutrient-poor medium. flow cytometry analysis revealed changes of the mutant in growth cycle characteristics including an increase in proportion of cells contai ... | 2011 | 21703549 |
| stability of monomolecular films of archaebacterial tetraether lipids on silicon wafers: a comparison of physisorbed and chemisorbed monolayers. | the monomolecular organisation of symmetric, chemically modified tetraether lipids caldarchaeol-po(4) was studied using langmuir film balance, ellipsometry, and atomic force microscopy (afm). solid silicon wafer substrates were modified to hydrophobic, hydrophilic, and amino-silanised surfaces; and langmuir-blodgett (lb)-films were transferred onto each. lb-caldarchaeol-po(4) films were subjected to further rinsing with organic solvent and additional physical treatments, to compare their resista ... | 2011 | 21689910 |
| 1,n2-etheno-2'-deoxyguanosine adopts the syn conformation about the glycosyl bond when mismatched with deoxyadenosine. | the oligodeoxynucleotide 5'-cgcatxgaatcc-3'-à5'-ggattcaatgcg-3' containing 1,n(2)-etheno-2'-deoxyguanosine (1,n(2)-+ádg) opposite deoxyadenosine (named the 1,n(2)-+ádg-àda duplex) models the mismatched adenine product associated with error-prone bypass of 1,n(2)-+ádg by the sulfolobus solfataricus p2 dna polymerase iv (dpo4) and by escherichia coli polymerases pol i exo(-) and pol ii exo(-). at ph 5.2, the t(m) of this duplex was increased by 3 -¦c as compared to the duplex in which the 1,n(2)-+ ... | 2011 | 21675798 |
| Identification and Physicochemical Characterization of BldR2 from Sulfolobus solfataricus, a Novel Archaeal Member of the MarR Transcription Factor Family. | The multiple antibiotic resistance regulators (MarR) constitute a family of ligand-responsive transcriptional regulators abundantly distributed throughout the bacterial and archaeal domains. Here we describe the identification and characterization of BldR2, as a new member of this family, in the archaeon Sulfolobus solfataricus and report physiological, biochemical, and biophysical investigation of its stability and DNA binding ability. Transcriptional analysis revealed the upregulation of BldR2 ... | 2011 | 21714562 |
| fossil record of an archaeal hk97-like provirus. | one of the outstanding questions in biology today is the origin of viruses. we have discovered a protein in the hyperthermophile sulfolobus solfataricus while following proteome regulation during viral infection that led to the discovery of a fossil provirus. characterization of the wild type and recombinant protein revealed that it assembled into virus-like particles with a diameter of ~32nm. sequence and structural analyses showed that the likely proviral capsid protein, sso2749, is homologous ... | 2011 | 21764098 |
| interaction between the antibiotic tetracycline and the elongation factor 1α from the archaeon sulfolobus solfataricus. | the interaction between tetracycline and the archaeal elongation factor 1α from sulfolobus solfataricus (ssef-1α) was investigated. the effects produced by this eubacterial antibiotic indicated that this interaction involved the g-domain of the ssef-1α, although also the m-domain was required. in fact, in the presence of the antibiotic an increase in the fluorescence quantum yield of the aromatic region was observed for ssef-1α and its truncated form lacking the c-terminal domain, but not for th ... | 2011 | 21599854 |
| the eubacterial protein synthesis inhibitor pulvomycin interacts with archaeal elongation factor 1α from sulfolobus solfataricus. | the effect of pulvomycin on the biochemical and fluorescence spectroscopic properties of the archaeal elongation factor 1α from sulfolobus solfataricus (ssef-1α), the functional analog of eubacterial ef-tu, was investigated. the antibiotic was able to reduce in vitro the rate of protein synthesis however, the concentration of pulvomycin leading to 50% inhibition (173 μm) was two order of magnitude higher but one order lower than that required in eubacteria and eukarya, respectively. the effect o ... | 2011 | 21924318 |
| Identification of an entire set of tRNA molecules and characterization of cleavage sites of the intron-containing tRNA precursors in acidothermophilic crenarchaeon Sulfolobus tokodaii strain7. | The acidothermophilic crenarchaeon, Sulfolobus tokodaii strain7, was isolated from a hot spring in Beppu, Kyushu, Japan. Whole genomic data of this microorganism indicated that among 46 putative tRNA genes identified, 24 were interrupted tRNA genes containing an intron. A sequence comparison between the cDNA sequences for unspliced and spliced tRNAs indicated that all predicted tRNAs were expressed and all intron portions were spliced in this microorganism. However, the actual cleavage site in t ... | 2011 | 21872648 |
| exceptional thermal stability and organic solvent tolerance of an esterase expressed from a thermophilic host. | a protein expression system recently developed for the thermophilic crenarchaeon sulfolobus islandicus was employed to produce recombinant protein for esta, a thermophilic esterase encoded in the same organism. large amounts of protein were readily obtained by an affinity protein purification, giving sisesta. upon escherichia coli expression, only the thioredoxin-tagged esta recombinant protein was soluble. the fusion protein was then purified, and removing the protein tag yielded ecsisesta. bot ... | 2011 | 21847512 |
| archaeal translation initiation factor aif2 can substitute for eukaryotic eif2 in ribosomal scanning during mammalian 48s complex formation. | heterotrimeric translation initiation factor (if) a/eif2 (archaeal/eukaryotic if 2) is present in both eukarya and archaea. despite strong structural similarity between a/eif2 orthologs from the two domains of life, their functional relationship is obscure. here, we show that aif2 from sulfolobus solfataricus can substitute for its mammalian counterpart in the reconstitution of eukaryotic 48s initiation complexes from purified components. aif2 is able to correctly place the initiator met-trna(i) ... | 2011 | 21884705 |
| characterization of a β-glucosidase from sulfolobus solfataricus for isoflavone glycosides. | the specific activity of a recombinant β-glucosidase from sulfolobus solfataricus for isoflavones was: daidzin > glycitin > genistin > malonyl genistin > malonyl daidzin > malonyl glycitin. the hydrolytic activity of this enzyme for daidzin was highest at ph 5.5 and 90°c with a half-life of 18 h, a k (m) of 0.5 mm, and a k (cat) of 2532 s(-1). the enzyme converted 1 mm daidzin to 1 mm daidzein after 1 h with a molar yield of 100% and a productivity of 1 mm h(-1). among β-glucosidases, that from ... | 2012 | 21898127 |
| sulfoquinovose synthase - an important enzyme in the n-glycosylation pathway of sulfolobus acidocaldarius. | recently, the surface (s)-layer glycoprotein of the thermoacidophilic crenarchaeote sulfolobus acidocaldarius was found to be n-glycosylated with a heterogeneous family of glycans, with the largest having a composition glc(1)man(2)glcnac(2) plus 6-sulfoquinovose. however, genetic analyses of genes involved in the n-glycosylation process in crenarchaeota were missing so far. in this study we identify a gene cluster involved in the biosynthesis of sulfoquinovose and important for the assembly of t ... | 2011 | 22059775 |
| complementation of sulfolobus solfataricus pbl2025 with an α-mannosidase: effects on surface attachment and biofilm formation. | compared to sulfolobus solfataricus p2, the s. solfataricus mutant pbl2025 misses 50 genes (sso3004-3050), including genes coding for a multitude of enzymes possibly involved in sugar degradation or metabolism. we complemented pbl2025 with two of the missing proteins, the α-mannosidase (sso3006, ssα-man) and the β-galactosidase lacs (sso3019), and performed comparative fluorescence microscopy and confocal laser scanning microscopy to analyze the recombinant strains. we demonstrated that the ssα- ... | 2012 | 22094829 |
| Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences. | The thermoacidophiles Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 are considered key model organisms representing a major phylum of the Crenarchaeota. Because maintaining current, accurate genome information is indispensable for modern biology, we have updated gene function annotation using the arCOGs database, plus other available functional, structural and phylogenetic information. The goal of this initiative is continuous improvement of genome annotation with the support of the Sulf ... | 2011 | 21912952 |
| an expansion of age constraints for microbial clades that lack a conventional fossil record using phylogenomic dating. | most microbial taxa lack a conventional microfossil or biomarker record, and so we currently have little information regarding how old most microbial clades and their associated traits are. building on the previously published oxygen age constraint, two new age constraints are proposed based on the ability of microbial clades to metabolize chitin and aromatic compounds derived from lignin. using the archaeal domain of life as a test case, phylogenetic analyses, along with published metabolic and ... | 2011 | 22105429 |
| dissection of the functional domains of an archaeal holliday junction helicase. | helicases and nucleases form complexes that play very important roles in dna repair pathways some of which interact with each other at holliday junctions. in this study, we present in vitro and in vivo analysis of hjm and its interaction with hjc in sulfolobus. in vitro studies employed hjm from the hyperthermophilic archaeon sulfolobus tokodaii (stohjm) and its truncated derivatives, and characterization of the stohjm proteins revealed that the n-terminal module (residues 1-431) alone was capab ... | 2011 | 22062475 |
| kinetics of ferrous iron oxidation by batch and continuous cultures of thermoacidophilic archaea at extremely low ph of 1.1-1.3. | the extreme acid conditions required for scorodite (feaso(4)·2h(2)o) biomineralization (ph below 1.3) are suboptimal for growth of most thermoacidophilic archaea. with the objective to develop a continuous process suitable for biomineral production, this research focuses on growth kinetics of thermoacidophilic archaea at low ph conditions. ferrous iron oxidation rates were determined in batch-cultures at ph 1.3 and a temperature of 75°c for acidianus sulfidivorans, metallosphaera prunea and a mi ... | 2011 | 21751006 |
| Structure of indole-3-glycerol phosphate synthase from Thermus thermophilus HB8: implications for thermal stability. | The three-dimensional structure of indole-3-glycerol phosphate synthase (IGPS) from the thermophilic bacterium Thermus thermophilus HB8 (TtIGPS) has been determined at 1.8 Å resolution. The structure adopts a typical (ß/a)(8)-barrel fold with an additional N-terminal extension of 46 residues. A detailed comparison of the crystal structure of TtIGPS with available structures of IGPS from the archaeon Sulfolobus solfataricus (SsIGPS) and the bacteria Thermotoga maritima (TmIGPS) and Escherichia co ... | 2011 | 22120743 |
| hydration studies on the archaeal protein sso7d using nmr measurements and md simulations. | how proteins approach surrounding molecules is fundamental to our understanding of the specific interactions that occur at the surface of proteins. the enhanced surface accessibility of small molecules such as organic solvents and paramagnetic probes to protein binding sites has been observed; however, the molecular basis of this finding has not been fully established. recently, it has been suggested that hydration dynamics play a predominant role in controlling the distribution of hot spots on ... | 2011 | 22017970 |
| influence of cell surface structures on crenarchaeal biofilm formation using a thermostable green fluorescent protein. | the thermoacidophilic crenarchaeote sulfolobus acidocaldarius displays three distinct type iv pili-like structures on its surface: (i) the flagellum, (ii) the uv-induced pili and (iii) the adhesive pili. in bacteria, surface appendages play an important role in the spatial organization of cells from initial surface attachment to the development of mature community structures. to investigate the influence of the diverse set of type iv pili-like structures in s. acidocaldarius, single, double and ... | 2011 | 22059595 |
| template-dependent polymerization across discontinuous templates by the heterodimeric primase from the hyperthermophilic archaeon sulfolobus solfataricus. | the eukaryotic-like primase from the hyperthermophilic archaeon sulfolobus solfataricus (ssoprisl) exhibits a range of activities including template-dependent de novo primer synthesis, primer extension and template-independent terminal nucleotidyl transfer using either rntps or dntps. remarkably, the enzyme is able to synthesize products far longer than templates in vitro. here we show that the long products resulted from template-dependent polymerization across discontinuous templates (padt) by ... | 2011 | 22189102 |
| biochemical characterization of a structure-specific resolving enzyme from sulfolobus islandicus rod-shaped virus 2. | sulfolobus islandicus rod shaped virus 2 (sirv2) infects the archaeon sulfolobus islandicus at extreme temperature (70°c-80°c) and acidity (ph 3). sirv2 encodes a holliday junction resolving enzyme (sirv2 hjr) that has been proposed as a key enzyme in sirv2 genome replication. the molecular mechanism for sirv2 hjr four-way junction cleavage bias, minimal requirements for four-way junction cleavage, and substrate specificity were determined. sirv2 hjr cleaves four-way dna junctions with a prefere ... | 2011 | 21858199 |
| repair of dna double-strand breaks induced by ionizing radiation damage correlates with upregulation of homologous recombination genes in sulfolobus solfataricus. | the mechanisms used by members of the archaeal branch of life to repair dna damage are not well understood. dna damage responses have been of particular interest in hyperthermophilic archaea, since these microbes live under environmental conditions that constantly elevate the potential for dna damage. the work described here focuses on the response of four sulfolobus solfataricus strains to ionizing radiation (ir) damage. cellular survival of three wild-type strains and a defined deletion mutant ... | 2011 | 22033479 |
| first crenarchaeal chitinase found in sulfolobus tokodaii. | this is the first description of a functional chitinase gene within the crenarchaeotes. here we report of the heterologues expression of the orf bab65950 from sulfolobus tokodaii in e. coli. the resulting protein degraded chitin and was hence classified as chitinase (ec 3.2.4.14). the protein characterization revealed a specific activity of 75mu/mg using colloidal chitin as substrate. the optimal activity of the enzyme was measured at ph 2.5 and 70°c, respectively. a dimeric enzyme configuration ... | 2011 | 22154063 |
| thermotolerance and molecular chaperone function of the small heat shock protein hsp20 from hyperthermophilic archaeon, sulfolobus solfataricus p2. | small heat shock proteins are ubiquitous in all three domains (archaea, bacteria and eukarya) and possess molecular chaperone activity by binding to unfolded polypeptides and preventing aggregation of proteins in vitro. the functions of a small heat shock protein (s.so-hsp20) from the hyperthermophilic archaeon, sulfolobus solfataricus p2 have not been described. in the present study, we used real-time polymerase chain reaction analysis to measure mrna expression of s.so-hsp20 in s. solfataricus ... | 2012 | 21853411 |
| UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. | Archaea, like bacteria and eukaryotes, contain proteins involved in various mechanisms of DNA repair, highlighting the importance of these processes for all forms of life. Species of the order Sulfolobales of hyperthermophilic crenarchaeota are equipped with a strongly UV-inducible type IV pilus system that promotes cellular aggregation. Here we demonstrate by fluorescence in situ hybridization that cellular aggregates are formed based on a species-specific recognition process and that UV-induce ... | 2011 | 21999488 |
| crystallographic and spectroscopic characterizations of sulfolobus solfataricus trxa1 provide insights into the determinants of thioredoxin fold stability. | structural characterizations of thioredoxins (trxs) are important for their involvement in severe pathologies and for their stable scaffold. here we report a combined structural and spectroscopic characterization of a trx isolated from the hyperthermophilic archaeon sulfolobus solfataricus (sstrxa1). thermal denaturation unveils that sstrxa1 is endowed with a remarkable stability in the explored temperature range 50-105°c. the structure of the oxidized form of sstrxa1 determined at 1.9å resoluti ... | 2011 | 22085748 |
| Study on binding modes between cellobiose and ß-glucosidases from glycoside hydrolase family 1. | The hydrolysis of cellobiose by ß-glucodisases is an important step of cellulose biodegradation. However, the interactive mechanism between cellobiose and ß-glucosidases is still unclear until now. Thus, in this study, we explored the binding modes between cellobiose and three ß-glucosidases from glycoside hydrolase family 1 by means of molecular docking. The three ß-glucosidases were named as TmGH1 (from bacterium Thermotoga), SsGH1 (from archaea Sulfolobus solfataricus) and TrGH1 (from fungus ... | 2011 | 22209489 |
| functional promiscuity of the cog0720 family. | the biosynthesis of gtp derived metabolites such as tetrahydrofolate (thf), biopterin (bh(4)), and the modified trna nucleosides queuosine (q) and archaeosine (g(+)) relies on several enzymes of the tunnel-fold superfamily. a subset of these proteins includes the 6-pyruvoyltetrahydropterin (ptps-ii), ptps-iii, and ptps-i homologues, all members of the cog0720 family that have been previously shown to transform 7,8-dihydroneopterin triphosphate (h(2)ntp) into different products. ptps-ii catalyzes ... | 2011 | 21999246 |
| changes in the composition of an acid mine drainage microbial community upon successive transfers in medium containing low-grade copper sulfide. | a consortium of microorganisms from acid mine drainage samples was cultured in modified 9 k medium containing low-grade copper sulfide. the culture was maintained for sixty days and then transferred to fresh medium. this process was repeated three more times and a final consortium exhibiting a copper extraction rate of 89.3% was obtained. rflp and microarrays analysis of 16s rrna sequences retrieved from the consortia showed that acidithiobacilluscaldus, leptospirillumferriphilum, sulfobacillus ... | 2011 | 21862325 |
| Purification of the poly-ADP-ribose polymerase-like thermozyme from the archaeon Sulfolobus solfataricus. | Several different protocols have been developed to purify the ADP-ribosylating enzyme from Sulfolobus solfataricus. A number of techniques have been applied in regard to the crude homogenate preparation and protein extraction. Either mechanical cell lysis with DNAase digestion or freeze-thawing with sonication allowed to obtain fairly similar amounts of the thermozyme in the homogenate. While similar recovery of thermozyme was obtained by employing both purification protocols, the proteins were ... | 2011 | 21870277 |
| Development of a Simvastatin Selection Marker for a Hyperthermophilic Acidophile, Sulfolobus islandicus. | We report here a novel selectable marker for the hyperthermophilic crenarchaeon Sulfolobus islandicus. The marker cassette is composed of the sac7d promoter and the hmg gene coding for the 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (P(sac7d)-hmg), which confers simvastatin resistance to this crenarchaeon. The basic plasmid vector pSSR was constructed by substituting the pyrEF gene of the expression vector pSeSD for P(sac7d)-hmg with which the Sulfolobus expression plasmids pSSRlac ... | 2012 | 22081574 |
| Structure and phase behavior of archaeal lipid monolayers. | We report X-ray reflectivity (XRR) and grazing incidence X-ray diffraction (GIXD) measurements of archaeal bipolar tetraether lipid monolayers at the air-water interface. Specifically, Langmuir films made of the polar lipid fraction E (PLFE) isolated from the thermoacidophilic archaeon Sulfolobus acidocaldarius grown at three different temperatures, i.e., 68, 76, and 81 °C, were examined. The dependence of the structure and packing properties of PLFE monolayers on surface pressure were analyze ... | 2011 | 21910469 |
| thermal unfolding of nucleoside hydrolases from the hyperthermophilic archaeon sulfolobus solfataricus: role of disulfide bonds. | nucleoside hydrolases are metalloproteins that hydrolyze the n-glycosidic bond of β-ribonucleosides, forming the free purine/pyrimidine base and ribose. we report the stability of the two hyperthermophilic enzymes sulfolobus solfataricus pyrimidine-specific nucleoside hydrolase (sscu-nh) and sulfolobus solfataricus purine-specific inosine-adenosine-guanosine nucleoside hydrolase (ssiag-nh) against the denaturing action of temperature and guanidine hydrochloride by means of circular dichroism and ... | 2011 | 22185502 |
| structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase. | enzymes catalyse specific reactions and are essential for maintaining life. although some are referred to as being bifunctional, they consist of either two distinct catalytic domains or a single domain that displays promiscuous substrate specificity. thus, one enzyme active site is generally responsible for one biochemical reaction. in contrast to this conventional concept, archaeal fructose-1,6-bisphosphate (fbp) aldolase/phosphatase (fbpa/p) consists of a single catalytic domain, but catalyses ... | 2011 | 21983966 |
| transcriptome-wide discovery of circular rnas in archaea. | circular rna forms had been described in all domains of life. such rnas were shown to have diverse biological functions, including roles in the life cycle of viral and viroid genomes, and in maturation of permuted trna genes. despite their potentially important biological roles, discovery of circular rnas has so far been mostly serendipitous. we have developed circrna-seq, a combined experimental/computational approach that enriches for circular rnas and allows profiling their prevalence in a wh ... | 2011 | 22140119 |
| aaa atpase p529 of acidianus two-tailed virus atv and host receptor recognition. | the two structural domains of p529, a predicted aaa atpase of acidianus two-tailed virus (atv), were expressed and purified. the n-terminal domain was demonstrated by loss-of-function mutations to carry atpase activity with a temperature optimum of 60°c. this domain also showed dna binding activity that was stronger for the whole protein and was weakened in the presence of atp. the c-terminal domain exhibits mg(2+)-dependent endonuclease activity that was eliminated by site-directed mutagenesis ... | 2011 | 21982819 |
| Activity and regulation of an archaeal DNA-alkyltransferase: a conserved protein involved in repair of DNA alkylation damage. | Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA-alkyltransferases. These are proteins conserved in Eucarya, Bacteria and Archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA-alkyltransferases is inactive and in eukaryotes is rapidly directed to degradation. ... | 2011 | 22167184 |
| tRNAs marked with CCACCA are targeted for degradation. | The CCA-adding enzyme [ATP(CTP):tRNA nucleotidyltransferase] adds CCA to the 3' ends of transfer RNAs (tRNAs), a critical step in tRNA biogenesis that generates the amino acid attachment site. We found that the CCA-adding enzyme plays a key role in tRNA quality control by selectively marking structurally unstable tRNAs and tRNA-like small RNAs for degradation. Instead of adding CCA to the 3' ends of these transcripts, CCA-adding enzymes from all three kingdoms of life add CCACCA. In addition, hy ... | 2011 | 22076379 |
| the swimming behavior of selected archaea. | the swimming behavior of bacteria has been studied extensively, at least for some species like escherichia coli. in contrast alomost no data have been published for archaea in this respect. in a systematic study we asked how the archaeal model organisms halobacterium salinarum, methanococcus voltae, methanococcus maripaludis, methanocaldococcus jannaschii, methanocaldococcus villosus, pyrococcus furiosus and sulfolobus acidocaldarius swim and which swimming behavior they exhibit. the two euryarc ... | 2012 | 22247169 |
| modulation of crispr locus transcription by the repeat-binding protein cbp1 in sulfolobus. | crispr loci are essential components of the adaptive immune system of archaea and bacteria. they consist of long arrays of repeats separated by dna spacers encoding guide rnas (crrna), which target foreign genetic elements. cbp1 (crispr dna repeat binding protein) binds specifically to the multiple direct repeats of crispr loci of members of the acidothermophilic, crenarchaeal order sulfolobales. cbp1 gene deletion from sulfolobus islandicus rey15a produced a strong reduction in pre-crrna yields ... | 2011 | 22139923 |
| Molecular analysis of the crenarchaeal flagellum. | The ability to move towards favourable conditions provides fundamental advantages to organisms. Interestingly, flagella as motility structures evolved independently in the bacterial and the archaeal kingdom. Whereas bacterial flagella have been intensively studied, our knowledge regarding the archaeal counterpart is mostly restricted to Euryarchaeota rather than crenarchaeal flagella. We therefore investigated the flagellar assembly system of the crenarchaeal model organism Sulfolobus acidocalda ... | 2012 | 22081969 |
| swapping genes to survive - a new role for archaeal type iv pili. | type iv pili are filamentous structures that are found on the surface of many bacterial and archaeal cells, they are involved in cell motility and surface adhesion. in the crenarchaeon sulfolobus solfataricus, type iv pili formation is strongly induced by uv irradiation and leads to cellular aggregation. the study by ajon et al. (2011) published in this issue of molecular microbiology shows that uv-induced cellular aggregation greatly stimulates the exchange of chromosomal markers among irradiat ... | 2011 | 21992544 |
| development of a thermostable β-glucuronidase-based reporter system for monitoring gene expression in hyperthermophiles. | mesophilic glucuronidases are the most widely used reporters of gene expression in plants, but unsuitable as reporters in (hyper-)thermophiles due their insufficient thermal stability. here we present the native 66.8 kda thermostable β-glucuronidase of sulfolobus solfataricus. the enzyme activity is characterized in a wide temperature range ideal for, but not limited to, in vivo genetic study of hyperthermophiles. as a proof of concept, we demonstrate its use as a reporter of gene expression in ... | 2012 | 22234844 |