| using molecular dynamics to probe the structural basis for enhanced stability in thermal stable cytochromes p450. | high-temperature molecular dynamics (md) has been used to assess if md can be employed as a useful tool for probing the structural basis for enhanced stability in thermal stable cytochromes p450. cyp119, the most thermal stable p450 known, unfolds more slowly during 500 k md simulations than p450s that melt at lower temperatures, p450cam and p450cin. a comparison of the 500 k md trajectories shows that the cys ligand loop, a critically important structural feature just under the heme, in both p4 ... | 2010 | 20593793 |
| crystallization and preliminary x-ray diffraction studies of hyperthermophilic archaeal rieske-type ferredoxin (arf) from sulfolobus solfataricus p1. | the hyperthermophilic archaeal rieske-type [2fe-2s] ferredoxin (arf) from sulfolobus solfataricus p1 contains a low-potential rieske-type [2fe-2s] cluster that has served as a tractable model for ligand-substitution studies on this protein family. recombinant arf harbouring a pet30a vector-derived n-terminal extension region plus a hexahistidine tag has been heterologously overproduced in escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using 0.05 m sodium ... | 2010 | 20606288 |
| evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins. | the unfolding speed of some hyperthermophilic proteins is dramatically lower than that of their mesostable homologs. ribonuclease hii from the hyperthermophilic archaeon thermococcus kodakaraensis (tk-rnase hii) is stabilized by its remarkably slow unfolding rate, whereas rnase hi from the thermophilic bacterium thermus thermophilus (tt-rnase hi) unfolds rapidly, comparable with to that of rnase hi from escherichia coli (ec-rnase hi). | 2010 | 20615256 |
| life in blue: copper resistance mechanisms of bacteria and archaea used in industrial biomining of minerals. | industrial biomining processes to extract copper, gold and other metals involve the use of extremophiles such as the acidophilic acidithiobacillus ferrooxidans (bacteria), and the thermoacidophilic sulfolobus metallicus (archaea). together with other extremophiles these microorganisms subsist in habitats where they are exposed to copper concentrations higher than 100mm. herein we review the current knowledge on the cu-resistance mechanisms found in these microorganisms. recent information sugges ... | 2010 | 20627124 |
| exploring the catalytic mechanism of the first dimeric bcp: functional, structural and docking analyses of bcp4 from sulfolobus solfataricus. | the detoxification from peroxides in sulfolobus solfataricus is performed by the bacterioferritin comigratory proteins (bcps), bcp1 (sso2071), bcp2 (sso2121), bcp3 (sso2255) and bcp4 (sso2613), antioxidant enzymes belonging to one of the subfamilies of the peroxiredoxins. in this paper we report on the functional, structural and docking analyses of bcp4, characterized by the cxxxxc motif in the active site. bcp4 represents the first dimeric bcp so far investigated. biochemical studies showed tha ... | 2010 | 20637256 |
| microbial metalloproteomes are largely uncharacterized. | metal ion cofactors afford proteins virtually unlimited catalytic potential, enable electron transfer reactions and have a great impact on protein stability. consequently, metalloproteins have key roles in most biological processes, including respiration (iron and copper), photosynthesis (manganese) and drug metabolism (iron). yet, predicting from genome sequence the numbers and types of metal an organism assimilates from its environment or uses in its metalloproteome is currently impossible bec ... | 2010 | 20639861 |
| discontinuity and limited linkage in the homologous recombination system of a hyperthermophilic archaeon. | genetic transformation of sulfolobus acidocaldarius by a multiply marked pyre gene provided a high-resolution assay of homologous recombination in a hyperthermophilic archaeon. analysis of 100 pyr(+) transformants revealed that this recombination system could transfer each of 23 nonselected base pair substitutions to the recipient chromosome along with the selected marker. in 30% of the recombinants, donor markers were transferred as multiple blocks. in at least 40% of the recombinants, donor ma ... | 2010 | 20644140 |
| a novel dienelactone hydrolase from the thermoacidophilic archaeon sulfolobus solfataricus p1: purification, characterization, and expression. | dienelactone hydrolases catalyze the hydrolysis of dienelactone to maleylacetate, which play a key role for the microbial degradation of chloroaromatics via chlorocatechols. here, a thermostable dienelactone hydrolase from thermoacidophilic archaeon sulfolobus solfataricus p1 was the first purified and characterized and then expressed in escherichia coli. | 2010 | 20655986 |
| replication-biased genome organisation in the crenarchaeon sulfolobus. | species of the crenarchaeon sulfolobus harbour three replication origins in their single circular chromosome that are synchronously initiated during replication. | 2010 | 20667100 |
| improving the promiscuous nerve agent hydrolase activity of a thermostable archaeal lactonase. | the thermostable phosphotriesterase-like lactonase from sulfolobus solfataricus (ssopox) hydrolyzes lactones and, at a lower rate, neurotoxic organophosphorus compounds. the persistent demand of detoxification tools in the field of agricultural wastes and restoring of conditions after terrorist acts prompted us to exploit ssopox as a "starter" to evolve its ancillary nerve agents hydrolytic capability. a directed evolution strategy yielded, among several variants, the single mutant w263f with k( ... | 2010 | 20667718 |
| characterization of a new rnase hii and its essential amino acid residues in the archaeon sulfolobus tokodaii reveals a regulatory c-terminus. | the archaea possess rnase h proteins that share features of both prokaryotic and eukaryotic forms. although the sulfolobus rnase hi has been reported to have unique structural and biochemical properties, its rnase hii has not yet been investigated and its biochemical properties remain unknown. in the present study, we have characterized the st0519 rnase hii from s. tokodaii as a new form. the enzyme utilized hybrid rna/dna as a substrate and had an optimal temperature between 37 to 50 degrees c. ... | 2010 | 20673218 |
| repair of dna double-strand breaks following uv damage in three sulfolobus solfataricus strains. | dna damage repair mechanisms have been most thoroughly explored in the eubacterial and eukaryotic branches of life. the methods by which members of the archaeal branch repair dna are significantly less well understood but have been gaining increasing attention. in particular, the approaches employed by hyperthermophilic archaea have been a general source of interest, since these organisms thrive under conditions that likely lead to constant chromosomal damage. in this work we have characterized ... | 2010 | 20675475 |
| new cultural approaches for microaerophilic hyperthermophiles. | this article reports on a new culture system designed for studying the effects of nutritional factors on the growth of hyperthermophilic and chemolithotrophic microorganisms. the system comprises 5-l stainless steel jars, an automatic gas dispenser, propylene microplates, and a robotic platform. the culture system was validated using aquifex aeolicus, a hyperthermophilic, chemolithotrophic, and microaerophilic bacterium, which requires hydrogen, oxygen, co₂, and minerals for growth. we demonstra ... | 2011 | 20676678 |
| crystal structures of two archaeal pelotas reveal inter-domain structural plasticity. | dom34 from saccharomyces cerevisiae is one of the key players in no-go mrna decay, a surveillance pathway by which an abnormal mrna stalled during translation is degraded by an endonucleolytic cleavage. its homologs called pelota are found in other species. we showed previously that s. cerevisiae dom34 (domain 1) has an endoribonuclease activity, which suggests its direct catalytic role in no-go decay. pelota from thermoplasma acidophilum and dom34 from s. cerevisiae have been structurally chara ... | 2010 | 20682285 |
| structurally informed site-directed mutagenesis of a stereochemically promiscuous aldolase to afford stereochemically complementary biocatalysts. | 2-keto-3-deoxygluconate aldolase from the hyperthermophile sulfolobus solfataricus is a highly thermostable type i aldolase that can catalyze carbon-carbon bond formation using nonphosphorylated substrates. however, it exhibits poor diastereocontrol in many of its aldol reactions, including the reaction of its natural substrates, pyruvate and d-glyceraldehyde, which afford a 55:45 mixture of d-2-keto-3-deoxygluconate (d-kdglu) and d-2-keto-3-deoxy-galactonate (d-kdgal). we have employed detailed ... | 2010 | 20684556 |
| the molecular characterization of a novel gh38 α-mannosidase from the crenarchaeon sulfolobus solfataricus revealed its ability in de-mannosylating glycoproteins. | α-mannosidases, important enzymes in the n-glycan processing and degradation in eukaryotes, are frequently found in the genome of bacteria and archaea in which their function is still largely unknown. the α-mannosidase from the hyperthermophilic crenarchaeon sulfolobus solfataricus has been identified and purified from cellular extracts and its gene has been cloned and expressed in escherichia coli. the gene, belonging to retaining gh38 mannosidases of the carbohydrate active enzyme classificati ... | 2010 | 20696204 |
| revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method. | organisms belonging to the crenarchaeota lineage contain three proliferating cell nuclear antigen (pcna) subunits, while those in the euryarchaeota have only one, as for eukarya. to study the mechanism of archaeal sliding clamps, we sought to generate knockouts for each pcna gene in sulfolobus islandicus, a hyperthermophilic crenarchaeon, but failed with two conventional knockout methods. then, a new knockout scheme, known as marker insertion and target gene deletion (mid), was developed, with w ... | 2010 | 20705666 |
| mutational analysis of an archaeal minichromosome maintenance protein exterior hairpin reveals critical residues for helicase activity and dna binding. | the mini-chromosome maintenance protein (mcm) complex is an essential replicative helicase for dna replication in archaea and eukaryotes. while the eukaryotic complex consists of six homologous proteins (mcm2-7), the archaeon sulfolobus solfataricus has only one mcm protein (ssomcm), six subunits of which form a homohexamer. we have recently reported a 4.35a crystal structure of the near full-length ssomcm. the structure reveals a total of four beta-hairpins per subunit, three of which are locat ... | 2010 | 20716382 |
| hyperthermophilic phosphotriesterases/lactonases for the environment and human health. | in the last decades the idea to use enzymes for environmental bioremediation has been more and more proposed and, in the light of this, new solutions have been suggested and detailed studies on some classes of enzymes have been performed. in particular, our attention in the last few years has been focused on the enzymes belonging to the amidohydrolase superfamily. several members of this superfamily are endowed with promiscuous activities. the term 'catalytic promiscuity' describes the capabilit ... | 2010 | 20718294 |
| transcription termination in the plasmid/virus hybrid pssvx from sulfolobus islandicus. | the pssvx from sulfolobus islandicus, strain rey15/4, is a hybrid between a plasmid and a fusellovirus. a systematic study previously performed revealed the presence of nine major transcripts, the expression of which was differentially and temporally regulated over the growth cycle of s. islandicus. in this study, two new transcripts were identified. then, 3' termini of all the rnas were mapped using adaptor rt-pcr and rnase protection assays, and termination/arrest positions were identified for ... | 2010 | 20734095 |
| metabolism of pentose sugars in the hyperthermophilic archaea sulfolobus solfataricus and sulfolobus acidocaldarius. | we have previously shown that the hyperthermophilic archaeon, sulfolobus solfataricus, catabolizes d-glucose and d-galactose to pyruvate and glyceraldehyde via a non-phosphorylative version of the entner-doudoroff pathway. at each step, one enzyme is active with both c6 epimers, leading to a metabolically promiscuous pathway. on further investigation, the catalytic promiscuity of the first enzyme in this pathway, glucose dehydrogenase, has been shown to extend to the c5 sugars, d-xylose and l-ar ... | 2010 | 20736170 |
| extensive lysine methylation in hyperthermophilic crenarchaea: potential implications for protein stability and recombinant enzymes. | in eukarya and bacteria, lysine methylation is relatively rare and is catalysed by sequence-specific lysine methyltransferases that typically have only a single-protein target. using rna polymerase purified from the thermophilic crenarchaeum sulfolobus solfataricus, we identified 21 methyllysines distributed across 9 subunits of the enzyme. the modified lysines were predominantly in alpha-helices and showed no conserved sequence context. a limited survey of the thermoproteus tenax proteome revea ... | 2010 | 20811616 |
| evolution of diverse cell division and vesicle formation systems in archaea. | recently a novel cell division system comprised of homologues of eukaryotic escrt-iii (endosomal sorting complex required for transport iii) proteins was discovered in the hyperthermophilic crenarchaeote sulfolobus acidocaldarius. on the basis of this discovery, we undertook a comparative genomic analysis of the machineries for cell division and vesicle formation in archaea. archaea possess at least three distinct membrane remodelling systems: the ftsz-based bacterial-type system, the escrt-iii- ... | 2010 | 20818414 |
| metal-ion dependence of the active-site conformation of the translesion dna polymerase dpo4 from sulfolobus solfataricus. | crystal structures of a binary mg2+-form dpo4-dna complex with 1,n2-etheno-dg in the template strand as well as of ternary mg2+-form dpo4-dna-dctp/dgtp complexes with 8-oxog in the template strand have been determined. comparison of their conformations and active-site geometries with those of the corresponding ca2+-form complexes revealed that the dna and polymerase undergo subtle changes as a result of the catalytically more active mg2+ occupying both the a and b sites. | 2010 | 20823515 |
| heterologous gene expression in the hyperthermophilic archaeon sulfolobus solfataricus. | one of the few available systems for gene expression in (hyper)thermophilic archaea is the virus-based shuttle vector pmj05 for sulfolobus solfataricus. although it is still not fully developed and there are some difficulties arising from the large size of the vector (>20 kb), it has successfully been used for the production of foreign and own proteins in s. solfataricus. most often, the development of genetic tools for archaea is held back by the lack of an efficient transformation system. in t ... | 2010 | 20830559 |
| "protoisochores" in certain archaeal species are formed by replication-associated mutational pressure. | this report shows that isochore-like structures can be found not only in warm-blooded animals, some reptiles, fishes and yeast, but also in certain archaeal species. in perfectly shaped isochore-like structures (in "protoisochores") from sulfolobus acidocaldarius and thermofilum pendens genomes the difference in 3gc levels between genes from different "protoisochores" is about 30%. in these archaeal species gc-poor "protoisochores" are situated near the origin of replication, while gc-rich "prot ... | 2011 | 20850498 |
| use of cellular crispr (clusters of regularly interspaced short palindromic repeats) spacer-based microarrays for detection of viruses in environmental samples. | it is currently difficult to detect unknown viruses in any given environment. the recent discovery of crispr (clusters of regularly interspaced short palindromic repeats) loci within bacterial and archaeal cellular genomes may provide an alternative approach to detect new viruses. it has been shown that the spacer sequences between the direct repeat units of the crispr loci are often derived from viruses and likely function as guide sequences to protect the cell from viral infection. the spacer ... | 2010 | 20851987 |
| roles of l5-7 loop in the structure and chaperone function of sshsp14.1. | the small heat shock protein sshsp14.1 from the hyper-thermophilic archeaon, sulfolobus solfataricus (s. solfataricus) was able to protect proteins from thermal aggregation and prevent enzymes from heat induced inactivation. according to the 3d (dimensional) structural model of sshsp14.1 developed by us before, the region l5-7 (β5-β7, 68-82 residues) plays an important role for the oligomerization of sshsp14.1 and its chaperone function. here, to validate the findings, an in-depth investigation ... | 2011 | 20858200 |
| iron-sulfur world in aerobic and hyperthermoacidophilic archaea sulfolobus. | the general importance of the fe-s cluster prosthetic groups in biology is primarily attributable to specific features of iron and sulfur chemistry, and the assembly and interplay of the fe-s cluster core with the surrounding protein is the key to in-depth understanding of the underlying mechanisms. in the aerobic and thermoacidophilic archaea, zinc-containing ferredoxin is abundant in the cytoplasm, functioning as a key electron carrier, and many fe-s enzymes are produced to participate in the ... | 2010 | 20885930 |
| protein acetylation in archaea, bacteria, and eukaryotes. | proteins can be acetylated at the alpha-amino group of the n-terminal amino acid (methionine or the penultimate amino acid after methionine removal) or at the epsilon-amino group of internal lysines. in eukaryotes the majority of proteins are n-terminally acetylated, while this is extremely rare in bacteria. a variety of studies about n-terminal acetylation in archaea have been reported recently, and it was revealed that a considerable fraction of proteins is n-terminally acetylated in haloarcha ... | 2010 | 20885971 |
| phenol biodegradation by the thermoacidophilic archaeon sulfolobus solfataricus 98/2 in a fed-batch bioreactor. | toxic at low concentrations, phenol is one of the most common organic pollutants in air and water. in this work, phenol biodegradation was studied in extreme conditions (80°c, ph = 3.2) in a 2.7 l bioreactor with the thermoacidophilic archaeon sulfolobus solfataricus 98/2. the strain was first acclimatized to phenol on a mixture of glucose (2000 mg l(-1)) and phenol (94 mg l(-1)) at a constant dissolved oxygen concentration of 1.5 mg l(-1). after a short lag-phase, only glucose was consumed. phe ... | 2010 | 20886261 |
| crispr associated diversity within a population of sulfolobus islandicus. | predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. a new form of microbial resistance, crisprs (clustered regularly interspaced short palindromic repeats) are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral dna is inserted into the host's chromosome, thereby rendering the host resistant to further infection. few studies hav ... | 2010 | 20927396 |
| [advances in lactamases from microbes--a review]. | gamma-lactamase belongs to the amidase. the (+) gamma-lactamses can be applied in the kinetic resolution of racemic gamma-lactam, which can produce (-) gamma-lactam efficiently. the (-) gamma-lactam enantiomer is an important synthon for the synthesis of carbocyclic nucleosides. up to now seven strains of microbes were reported that produced gamma-lactamses. the crystal structure of (-) lactamase from aureoacterium sp. was resoluted, and the catalytic mechanism based on the structure data analys ... | 2010 | 20931864 |
| the s-layer glycoprotein of the crenarchaeote sulfolobus acidocaldarius is glycosylated at multiple sites with chitobiose-linked n-glycans. | glycosylation of the s-layer of the crenarchaea sulfolobus acidocaldarius has been investigated using glycoproteomic methodologies. the mature protein is predicted to contain 31 n-glycosylation consensus sites with approximately one third being found in the c-terminal domain spanning residues l(1004)-q(1395). since this domain is rich in lys and arg and therefore relatively tractable to glycoproteomic analysis, this study has focused on mapping its n-glycosylation. our analysis identified nine o ... | 2010 | 20936123 |
| a novel class of protease targets of phosphatidylethanolamine-binding proteins (pebp): a study of the acylpeptide hydrolase and the pebp inhibitor from the archaeon sulfolobus solfataricus. | this work describes the identification and characterization of a sulfolobus solfataricus acylpeptide hydrolase, named apeh(ss), recognised as a new protease target of the endogenous pebp inhibitor, sscei. apeh is one of the four members of the prolyl oligopeptidase (pop) family, which removes acylated amino acid residues from the n terminus of oligopeptides. apeh(ss) is a cytosolic homodimeric protein with a molecular mass of 125 kda. it displays a similar exopeptidase and endopeptidase activity ... | 2010 | 20941418 |
| the structure of sso2064, the first representative of pfam family pf01796, reveals a novel two-domain zinc-ribbon ob-fold architecture with a potential acyl-coa-binding role. | sso2064 is the first structural representative of pf01796 (duf35), a large prokaryotic family with a wide phylogenetic distribution. the structure reveals a novel two-domain architecture comprising an n-terminal, rubredoxin-like, zinc ribbon and a c-terminal, oligonucleotide/oligosaccharide-binding (ob) fold domain. additional n-terminal helical segments may be involved in protein-protein interactions. domain architectures, genomic context analysis and functional evidence from certain bacterial ... | 2010 | 20944206 |
| structural basis for proficient incorporation of dttp opposite o6-methylguanine by human dna polymerase iota. | o(6)-methylguanine (o(6)-methylg) is highly mutagenic and is commonly found in dna exposed to methylating agents, even physiological ones (e.g. s-adenosylmethionine). the efficiency of a truncated, catalytic dna polymerase ι core enzyme was determined for nucleoside triphosphate incorporation opposite o(6)-methylg, using steady-state kinetic analyses. the results presented here corroborate previous work from this laboratory using full-length pol ι, which showed that dttp incorporation occurs wit ... | 2010 | 20961860 |
| kinetic basis of sugar selection by a y-family dna polymerase from sulfolobus solfataricus p2. | dna polymerases use either a bulky active site residue or a backbone segment to select against ribonucleotides in order to faithfully replicate cellular genomes. here, we demonstrated that an active site mutation (y12a) within sulfolobus solfataricus dna polymerase iv (dpo4) caused an average increase of 220-fold in matched ribonucleotide incorporation efficiency and an average decrease of 9-fold in correct deoxyribonucleotide incorporation efficiency, leading to an average reduction of 2000-fol ... | 2010 | 20973506 |
| evolutionary rates and gene dispensability associate with replication timing in the archaeon sulfolobus islandicus. | in bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. however, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. to test this hypothesis, six archaeal genomes from the g ... | 2010 | 20978102 |
| engineering the stability and the activity of a glycoside hydrolase. | glycosidases, the enzymes responsible in nature for the catabolism of carbohydrates, are well-studied catalysts widely used in industrial biotransformations and oligosaccharide synthesis, which are also attractive targets for drug development. glycosidases from hyperthermophilic organisms (thriving at temperatures > 85 °c) are also interesting models to understand the molecular basis of protein stability and to produce robust tools for industrial applications. here, we review the results obtaine ... | 2010 | 20980336 |
| cytochrome p450 compound i: capture, characterization, and c-h bond activation kinetics. | cytochrome p450 enzymes are responsible for the phase i metabolism of approximately 75% of known pharmaceuticals. p450s perform this and other important biological functions through the controlled activation of c-h bonds. here, we report the spectroscopic and kinetic characterization of the long-sought principal intermediate involved in this process, p450 compound i (p450-i), which we prepared in approximately 75% yield by reacting ferric cyp119 with m-chloroperbenzoic acid. the mössbauer spectr ... | 2010 | 21071661 |
| compressibilities and volume fluctuations of archaeal tetraether liposomes. | bipolar tetraether lipids (btls) are abundant in crenarchaeota, which thrive in both thermophilic and nonthermophilic environments, with wide-ranging growth temperatures (4-108°c). btl liposomes can serve as membrane models to explore the role of btls in the thermal stability of the plasma membrane of crenarchaeota. in this study, we focus on the liposomes made of the polar lipid fraction e (plfe). plfe is one of the main btls isolated from the thermoacidophilic crenarchaeon sulfolobus acidocald ... | 2010 | 21081080 |
| molecular simulations on the thermal stabilization of dna by hyperthermophilic chromatin protein sac7d, and associated conformational transitions. | sac7d belongs to a family of chromosomal proteins, which are crucial for thermal stabilization of dna at higher growth temperatures. it is capable of binding dna nonspecifically, and is responsible for the increase in the melting temperature of dna in the bound form up to 85 °c. molecular dynamics (md) simulations were performed at different temperatures on two protein-dna complexes of sac7d. various structural and energetic parameters were calculated to examine the dna stability and to investig ... | 2010 | 21086967 |
| ligand-induced formation of a transient tryptophan synthase complex with αββ subunit stoichiometry. | the prototypical tryptophan synthases form a stable heterotetrameric αββα complex in which the constituting trpa and trpb1 subunits activate each other in a bidirectional manner. the hyperthermophilic archaeon sulfolobus solfataricus does not contain a trpb1 protein but instead two members of the phylogenetically distinct family of trpb2 proteins, which are encoded within (strpb2i) and outside (strpb2a) the tryptophan operon. it has previously been shown that strpb2a does not functionally or str ... | 2010 | 21090805 |
| the structure of the crispr-associated protein csa3 provides insight into the regulation of the crispr/cas system. | adaptive immune systems have recently been recognized in prokaryotic organisms where, in response to viral infection, they incorporate short fragments of invader-derived dna into loci called clustered regularly interspaced short palindromic repeats (crisprs). in subsequent infections, the crispr loci are transcribed and processed into guide sequences for the neutralization of the invading rna or dna. the crispr-associated protein machinery (cas) lies at the heart of this process, yet many of the ... | 2010 | 21093452 |
| structural and functional insights into aeropyrum pernix oppa, a member of a novel archaeal oppa subfamily. | in this study we gain insight into the structural and functional characterization of the aeropyrum pernix oligopeptide-binding protein (oppa(ap)) previously identified from the extracellular medium of an aeropyrum pernix cell culture at late stationary phase. oppa(ap) showed an n-terminal q32 in a pyroglutamate form and c-terminal processing at the level of a threonine-rich region probably involved in protein membrane anchoring. moreover, the oppa(ap) protein released into the medium was identif ... | 2010 | 21097609 |
| replication termination and chromosome dimer resolution in the archaeon sulfolobus solfataricus. | archaea of the genus sulfolobus have a single-circular chromosome with three replication origins. all three origins fire in every cell in every cell cycle. thus, three pairs of replication forks converge and terminate in each replication cycle. here, we report 2d gel analyses of the replication fork fusion zones located between origins. these indicate that replication termination involves stochastic fork collision. in bacteria, replication termination is linked to chromosome dimer resolution, a ... | 2010 | 21113132 |
| identification of an rnase j ortholog in sulfolobus solfataricus: implications for 5'-to-3' directional decay and 5'-end protection of mrna in crenarchaeota. | in both bacteria and eukaryotes, degradation is known to start at the 5' and at the 3' extremities of mrnas. until the recent discovery of 5'-to-3' exoribonucleases in hyperthermophilic euryarchaeota, the exosome was assumed to be the key enzyme in mrna degradation in archaea. by means of zymogram assays and bioinformatics, we have identified a 5'-to-3' exoribonuclease activity in the crenarchaeum sulfolobus solfataricus (sso), which is affected by the phosphorylation state of the 5'-end of the ... | 2010 | 21115637 |
| crenarchaeal biofilm formation under extreme conditions. | biofilm formation has been studied in much detail for a variety of bacterial species, as it plays a major role in the pathogenicity of bacteria. however, only limited information is available for the development of archaeal communities that are frequently found in many natural environments. | 2010 | 21124788 |
| single-stranded dna binding activity of xpbi, but not xpbii, from sulfolobus tokodaii causes double-stranded dna melting. | xpb helicase is the largest subunit of transcription factor iih (tfiih), a ten-subunit protein complex essential for transcription initiation and nucleotide excision repair (ner) in eukarya. two xpb homologues (xpbi and xpbii) are present in the genome of most crenarchaeota, one of the two major phyla of archaea; however, the biochemical properties have not been fully characterized and their cellular roles have not been clearly defined. here, we report that xpbi from the hyperthermophilic crenar ... | 2010 | 21132514 |
| proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. | protein synthesis occurs in macromolecular particles called ribosomes. all ribosomes are composed of rna and proteins. while the protein composition of bacterial and eukaryotic ribosomes has been well-characterized, a systematic analysis of archaeal ribosomes has been lacking. here we report the first comprehensive two-dimensional page and mass spectrometry analysis of archaeal ribosomes isolated from the thermophilic pyrobaculum aerophilum and the thermoacidophilic sulfolobus acidocaldarius cre ... | 2010 | 21134383 |
| in vivo assembly of an archaeal virus studied with whole-cell electron cryotomography. | we applied whole-cell electron cryotomography to the archaeon sulfolobus infected by sulfolobus turreted icosahedral virus (stiv), which belongs to the prd1-adeno lineage of dsdna viruses. stiv infection induced the formation of pyramid-like protrusions with sharply defined facets on the cell surface. they had a thicker cross-section than the cytoplasmic membrane and did not contain an exterior surface protein layer (s-layer). intrapyramidal bodies often occupied the volume of the pyramids. matu ... | 2010 | 21134637 |
| pamt11, a novel plasmid isolated from a thermococcus sp. strain closely related to the virus-like integrated element tkv1 of the thermococcus kodakaraensis genome. | a novel extrachromosomal element that we called pamt11 was discovered in a deep-sea vent isolate belonging to the hyperthermophilic euryarchaeal order thermococcales. it consists of a double-stranded dna of 20,534bp which encodes 30 putative open reading frames (orfs) of which six could be assigned to a putative function on the basis of sequence similarity to known genes or to protein domain families. most of the orfs of pamt1 showed homology and synteny with a genomic island of thermococcus kod ... | 2010 | 21144896 |
| the lrp family of transcription regulators in archaea. | archaea possess a eukaryotic-type basal transcription apparatus that is regulated by bacteria-like transcription regulators. a universal and abundant family of transcription regulators are the bacterial/archaeal lrp-like regulators. the lrp family is one of the best studied regulator families in archaea, illustrated by investigations of proteins from the archaeal model organisms: sulfolobus, pyrococcus, methanocaldococcus, and halobacterium. these regulators are extremely versatile in their dna- ... | 2010 | 21151646 |
| dynamic properties of the sulfolobus crispr/cas and crispr/cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. | the adaptive immune crispr/cas and crispr/cmr systems of the crenarchaeal thermoacidophile sulfolobus were challenged by a variety of viral and plasmid genes, and protospacers preceded by different dinucleotide motifs. the genes and protospacers were constructed to carry sequences matching individual spacers of crispr loci, and a range of mismatches were introduced. constructs were cloned into vectors carrying pyre/pyrf genes and transformed into uracil auxotrophic hosts derived from sulfolobus ... | 2010 | 21166892 |
| characterization of a phosphotriesterase-like lactonase from sulfolobus solfataricus and its immobilization for disruption of quorum sensing. | ssopox, a bifunctional enzyme with organophosphate hydrolase and n-acyl homoserine lactonase activities from the hyperthermophilic archaeon sulfolobus solfataricus, was overexpressed and purified from recombinant pseudomonas putida kt2440 with a yield of 9.4 mg of protein per liter of culture. the enzyme has a preference for n-acyl homoserine lactones (ahls) with acyl chain lengths of at least 8 carbon atoms, mainly due to lower k(m) values for these substrates. the highest specificity constant ... | 2010 | 21183649 |
| sulfur oxidation activities of pure and mixed thermophiles and sulfur speciation in bioleaching of chalcopyrite. | the sulfur oxidation activities of four pure thermophilic archaea acidianus brierleyi (jcm 8954), metallosphaera sedula (yn 23), acidianus manzaensis (yn 25) and sulfolobus metallicus (yn 24) and their mixture in bioleaching chalcopyrite were compared. meanwhile, the relevant surface sulfur speciation of chalcopyrite leached with the mixed thermophilic archaea was investigated. the results showed that the mixed culture, with contributing significantly to the raising of leaching rate and accelera ... | 2010 | 21194927 |
| spectroscopic characterization of cytochrome p450 compound i. | the cytochrome p450 protein-bound porphyrin complex with the iron-coordinated active oxygen atom as fe(iv)o is called compound i (cpd i). cpd i is the intermediate species proposed to hydroxylate directly the inert carbon-hydrogen bonds of p450 substrates. in the natural reaction cycle of cytochrome p450 cpd i has not yet been detected, presumably because it is very short-lived. a great variety of experimental approaches has been applied to produce cpd i artificially aiming to characterize its e ... | 2010 | 21195047 |
| dimer structure and conformational variability in the n-terminal region of an archaeal small heat shock protein, sthsp14.0. | small heat shock proteins (shsps), which are categorized into a class of molecular chaperones, bind and stabilize denatured proteins to prevent aggregation. the shsps undergo transition between different oligomeric states to control their hydrophobicity. so far, only the structures of shsps in large oligomeric states have been reported. here we report the structure of sthsp14.0 from sulfolobus tokodaii in the dimeric state, which is formed by means of a mutation at the c-terminal ixi/v motif. th ... | 2010 | 21195185 |
| the carboxyl terminal of the archaeal nuclease nura is involved in the interaction with single-stranded dna-binding protein and dimer formation. | the nuclease nura is present in all known thermophilic archaea and has been implicated to facilitate efficient dna double-strand break end processing in mre11/rad50-mediated homologous recombinational repair. to understand the structural and functional relationship of this enzyme, we constructed five site-directed mutants of nura from sulfolobus tokodaii (stonura), d56a, e114a, d131a, y291a, and h299a, at the conserved motifs, and four terminal deletion mutants, stonuraδn (19-331), stonuraδnδc ( ... | 2011 | 21197557 |
| c68 from the sulfolobus islandicus plasmid-virus pssvx is a novel member of the abrb-like transcription factor family. | the genetic element pssvx from sulfolobus islandicus, strain rey15/4, is a hybrid between a plasmid and a fusellovirus. this plasmid-virus hybrid infects several species of the hyperthermophilic acidophilic crenarchaeon sulfolobus. the open reading frame orfc68 of pssvx encodes a 7.7 kda protein that does not show significant sequence homology with any protein with known three-dimensional structure. emsa (electrophoretic mobility-shift assay) experiments, dna footprinting and cd analyses indicat ... | 2011 | 21208189 |
| dangerous weapons: a cautionary tale of crispr defence. | | 2011 | 21210528 |
| microbial diversity in nonsulfur, sulfur and iron geothermal steam vents. | fumaroles, commonly called steam vents, are ubiquitous features of geothermal habitats. recent studies have discovered microorganisms in condensed fumarole steam, but fumarole deposits have proven refractory to dna isolation. in this study, we report the development of novel dna isolation approaches for fumarole deposit microbial community analysis. deposit samples were collected from steam vents and caves in hawaii volcanoes national park, yellowstone national park and lassen volcanic national ... | 2011 | 21223339 |
| molecular determinants of origin discrimination by orc1 initiators in archaea. | unlike bacteria, many eukaryotes initiate dna replication from genomic sites that lack apparent sequence conservation. these loci are identified and bound by the origin recognition complex (orc), and subsequently activated by a cascade of events that includes recruitment of an additional factor, cdc6. archaeal organisms generally possess one or more orc1/cdc6 homologs, belonging to the initiator clade of atpases associated with various cellular activities (aaa(+)) superfamily; however, these pro ... | 2011 | 21227921 |
| resonance assignments of a putative pilt n-terminus domain protein sso1118 from hyperthermophilic archaeon sulfolobus solfataricus p2. | pilt n-terminus (pin) domains exist broadly in all three kingdoms of life, but the functions are not clear for most of them. archaea species often encode multiple pin domain-containing proteins, and the signaling and stress response roles have been proposed for these proteins. some pin domain proteins possess nuclease activities, which were proposed to be important in toxin-antitoxin stress response, nonsense-mediated mrna decay, or rna interference. sso1118 from hyperthermophilic archaeon sulfo ... | 2011 | 21229398 |
| the bindosome is a structural component of the sulfolobus solfataricus cell envelope. | sugar binding proteins of the thermoacidophile sulfolobus solfataricus function together with abc transporters in the uptake of sugars. they are synthesized as precursors with a class iii signal peptide that are normally found in archaeal flagellins and bacterial type iv pilins. the functional expression of sugar binding proteins at the cell surface is dependent on the bindosome assembly system (bas) that is homologous to bacterial type iv pilin assembly systems. the bas system consists of an as ... | 2011 | 21234771 |
| absence of diauxie during simultaneous utilization of glucose and xylose by sulfolobus acidocaldarius. | sulfolobus acidocaldarius utilizes glucose and xylose as sole carbon sources, but its ability to metabolize these sugars simultaneously is not known. we report the absence of diauxie during growth of s. acidocaldarius on glucose and xylose as co-carbon sources. the presence of glucose did not repress xylose utilization. the organism utilized a mixture of 1 g/liter of each sugar simultaneously with a specific growth rate of 0.079 h(-1) and showed no preference for the order in which it utilized e ... | 2011 | 21239580 |
| molecular and structural basis of escrt-iii recruitment to membranes during archaeal cell division. | members of the crenarchaeal kingdom, such as sulfolobus, divide by binary fission yet lack genes for the otherwise near-ubiquitous tubulin and actin superfamilies of cytoskeletal proteins. recent work has established that sulfolobus homologs of the eukaryotic escrt-iii and vps4 components of the escrt machinery play an important role in sulfolobus cell division. in eukaryotes, several pathways recruit escrt-iii proteins to their sites of action. however, the positioning determinants for archaeal ... | 2011 | 21255729 |
| archaeal rna polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the rpo13 subunit. | we review recent results on the complete structure of the archaeal rnap (rna polymerase) enzyme of sulfolobus shibatae. we compare the three crystal forms in which this rnap packs (space groups p212121, p21212 and p21) and provide a preliminary biophysical characterization of the newly identified 13-subunit rpo13. the availability of different crystal forms for this rnap allows the analysis of the packing degeneracy and the intermolecular interactions that determine this degeneracy. we observe t ... | 2011 | 21265742 |
| crispr-based immune systems of the sulfolobales: complexity and diversity. | crispr (cluster of regularly interspaced palindromic repeats)/cas and crispr/cmr systems of sulfolobus, targeting dna and rna respectively of invading viruses or plasmids are complex and diverse. we address their classification and functional diversity, and the wide sequence diversity of ramp (repeat-associated mysterious protein)-motif containing proteins encoded in cmr modules. factors influencing maintenance of partially impaired crispr-based systems are discussed. the capacity for whole cris ... | 2011 | 21265746 |
| an additional glucose dehydrogenase from sulfolobus solfataricus: fine-tuning of sugar degradation? | within the sulfosys (sulfolobus systems biology) project, the effect of temperature on a metabolic network is investigated at the systems level. sulfolobus solfataricus utilizes an unusual branched ed (entner-doudoroff) pathway for sugar degradation that is promiscuous for glucose and galactose. in the course of metabolic pathway reconstruction, a glucose dehydrogenase isoenzyme (gdh-2, sso3204) was identified. gdh-2 exhibits high similarity to the previously characterized gdh-1 (sso3003, 61% am ... | 2011 | 21265750 |
| archaeal promoter architecture and mechanism of gene activation. | sulfolobus solfataricus and sulfolobus islandicus contain several genes exhibiting d-arabinose-inducible expression and these systems are ideal for studying mechanisms of archaeal gene expression. at sequence level, only two highly conserved cis elements are present on the promoters: a regulatory element named ara box directing arabinose-inducible expression and the basal promoter element tata, serving as the binding site for the tata-binding protein. strikingly, these promoters possess a modula ... | 2011 | 21265754 |
| potential role of cellular escrt proteins in the stiv life cycle. | we are examining the archaeal virus stiv (sulfolobus turreted icosahedral virus) in order to elucidate the details of its replication cycle and its interactions with its cellular host, sulfolobus solfataricus. infection of sulfolobus by stiv initiates an unusual cell lysis pathway. one component of this pathway is the formation of pyramid-like structures on the surface of infected cells. multiple seven-sided pyramid-like structures are formed on infected cells late in the stiv replication cycle. ... | 2011 | 21265756 |
| thermophilic archaeal enzymes and applications in biocatalysis. | thermophilic enzymes have advantages for their use in commercial applications and particularly for the production of chiral compounds to produce optically pure pharmaceuticals. they can be used as biocatalysts in the application of 'green chemistry'. the thermophilic archaea contain enzymes that have already been used in commercial applications such as the l-aminoacylase from thermococcus litoralis for the resolution of amino acids and amino acid analogues. this enzyme differs from bacterial l-a ... | 2011 | 21265764 |
| structural basis for site-specific ribose methylation by box c/d rna protein complexes. | box c/d rna protein complexes (rnps) direct site-specific 2'-o-methylation of rna and ribosome assembly. the guide rna in c/d rnp forms base pairs with complementary substrates and selects the modification site using a molecular ruler. despite many studies of c/d rnp structure, the fundamental questions of how c/d rnas assemble into rnps and how they guide modification remain unresolved. here we report the crystal structure of an entire catalytically active archaeal c/d rnp consisting of a bipar ... | 2011 | 21270896 |
| genome analyses of icelandic strains of sulfolobus islandicus, model organisms for genetic and virus-host interaction studies. | the genomes of two sulfolobus islandicus strains obtained from icelandic solfataras were sequenced and analyzed. strain rey15a is a host for a versatile genetic toolbox. it exhibits a genome of minimal size, is stable genetically, and is easy to grow and manipulate. strain hve10/4 shows a broad host range for exceptional crenarchaeal viruses and conjugative plasmids and was selected for studying their life cycles and host interactions. the genomes of strains rey15a and hve10/4 are 2.5 and 2.7 mb ... | 2011 | 21278296 |
| simple and elegant design of a virion egress structure in archaea. | some viruses of archaea use an unusual egress mechanism that involves the formation of virus-associated pyramids (vaps) on the host cell surface. at the end of the infection cycle, these structures open outward and create apertures through which mature virions escape from the cell. here we describe in detail the structure and composition of vaps formed by the sulfolobus islandicus rod-shaped virus 2 (sirv2) in cells of its hyperthermophilic archaeal host. we show that the vaps are stable and aut ... | 2011 | 21282609 |
| stabilization by fusion to the c-terminus of hyperthermophile sulfolobus tokodaii rnase hi: a possibility of protein stabilization tag. | rnase hi from the hyperthermophile sulfolobus tokodaii (sto-rnase hi) is stabilized by its c-terminal residues. in this work, the stabilization effect of the sto-rnase hi c-terminal residues was investigated in detail by thermodynamic measurements of the stability of variants lacking the disulfide bond (c58/145a), or the six c-terminal residues (?c6) and by structural analysis of ?c6. the results showed that the c-terminal does not affect overall structure and stabilization is caused by local in ... | 2011 | 21283826 |
| subcellular localization of rna degrading proteins and protein complexes in prokaryotes. | the archaeal exosome is a prokaryotic protein complex with rna processing and degrading activities. recently it was shown that the exosome is localized at the periphery of the cell in the thermoacidophilic archaeon sulfolobus solfataricus. this localization is most likely mediated by the archaeal dnag protein and depends on (direct or indirect) hydrophobic interactions with the membrane. a localization of rna degrading proteins and protein complexes was also demonstrated in several bacteria. in ... | 2011 | 21289488 |
| thermal stability and unfolding pathways of sso7d and its mutant f31a: insight from molecular dynamics simulation. | the thermo-stability and unfolding behaviors of a small hyperthermophilic protein sso7d as well as its single-point mutation f31a are studied by molecular dynamics simulation at temperatures of 300 k, 371 k and 500 k. simulations at 300 k show that the f31a mutant displays a much larger flexibility than the wild type, which implies that the mutation obviously decreases the protein's stability. in the simulations at 371 k, although larger fluctuations were observed, both of these two maintain the ... | 2011 | 21294584 |
| horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. | gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. while there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. we analyzed closely related prokaryote strains or species with small genomes (helicobacter, neisseria, stre ... | 2011 | 21298028 |
| structure of the dimeric form of ctp synthase from sulfolobus solfataricus. | ctp synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. active ctp synthase is a tetrameric enzyme composed of a dimer of dimers. the tetramer is favoured in the presence of the substrate nucleotides atp and utp; when saturated with nucleotide, the tetramer completely dominates the oligomeric state of the enzyme. furthermore, phosphorylation has been shown to regulate the oligomeric states of the enzymes from yeast and human. the crystal structure of a dimer ... | 2011 | 21301086 |
| backbone assignment of the little finger domain of a y-family dna polymerase. | sulfolobus solfataricus dna polymerase iv (dpo4), a prototype y-family dna polymerase, contains a unique little finger domain besides a catalytic core. here, we report the chemical shift assignments for the backbone nitrogens, a and ß carbons, and amide protons of the little finger domain of dpo4. this work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of dpo4 during catalysis using solution nmr spectroscopy. | 2011 | 21337030 |
| a novel heterotetrameric structure of the crenarchaeal pcna2-pcna3 complex. | proliferating cell nuclear antigen (pcna) is a key protein that orchestrates the arrangement of dna-processing proteins on dna during dna metabolism. in crenarchaea, pcna forms a heterotrimer (pcna123) consisting of pcna1, pcna2, and pcna3, while in most eukaryotes and many archaea pcnas form a homotrimer. interestingly, unique oligomeric pcnas from sulfolobus tokodaii were reported in which pcna2 and pcna3 form a heterotrimer without pcna1. in this paper, we describe the crystal structure of th ... | 2011 | 21352919 |
| active-site residues move independently from the rest of the protein in a 200 ns molecular dynamics simulation of cytochrome p450 cyp119. | the conformational dynamics of cytochrome p450 enzymes are critical to their catalytic activity. in this study, the correlated motion between residues in a 200 ns molecular dynamics trajectory of the thermophilic cyp119 was analyzed to parse out conformational relationships. residues that are structurally related, for example residues within a helix, generally have highly correlated motion. in addition, clusters of non-adjacent residues that show correlated motion ("hot spots") are seen in vario ... | 2011 | 21356195 |
| monooxygenation by a thermophilic cytochrome p450 via direct electron donation from nadh. | the catalysis of cytochrome p450s requires two-electron donation for the activation of an oxygen molecule. here, we report the enzymatic catalysis of cytochrome p450, cyp119a2 (p450st), from a thermoacidophilic crenarchaeon, sulfolobus tokodaii strain 7, with nad(p)h as an electron donor and no redox partners and the crystallographic analysis of p450st at high resolution. p450st can catalyse styrene epoxidation with either nadh or nadph as an electron donor. the p450st reaction with nadh exhibit ... | 2011 | 21359359 |
| the interplay of dna binding, atp hydrolysis and helicase activities of the archaeal mcm helicase. | the mcm (minichromosome maintenance) proteins of archaea are widely believed to be the replicative dna helicase of these organisms. most archaea possess a single mcm orthologue that forms homo-multimeric assemblies with a single hexamer believed to be the active form. in the present study we characterize the roles of highly conserved residues in the atpase domain of the mcm of the hyperthermophilic archaeon sulfolobus solfataricus. our results identify a potential conduit for communicating dna-b ... | 2011 | 21361871 |
| a novel intermediate in the reaction of seleno cyp119 with m-chloroperbenzoic acid. | cytochrome p450-mediated monooxygenation generally proceeds via a reactive ferryl intermediate coupled to a ligand radical [fe(iv)ôòéo]+ôçó termed compound i (cpd i). the proximal cysteine thiolate ligand is a critical determinant of the spectral and catalytic properties of p450 enzymes. to explore the effect of an increased level of donation of electrons by the proximal ligand in the p450 catalytic cycle, we recently reported successful incorporation of secys into the active site of cyp119, a t ... | 2011 | 21381758 |
| characterization of the specific interaction between archaeal fha domain-containing protein and the promoter of a flagellar-like gene-cluster and its regulation by phosphorylation. | the mechanism and target genes of regulation by forkhead (fha) domain-containing transcription factors have not yet been documented in archaea. in this study, using a bacterial one-hybrid technique, we successfully screened and identified for the first time a target gene regulated by st0829, an fha domain-containing potential transcriptional factor in the hyperthermophilic archaeon sulfolobus tokodaii. we show that st0829 could specifically bind to the promoter region of st2519p, the archaeal fl ... | 2011 | 21382340 |
| in vivo activity of crispr-mediated virus defence in a hyperthermophilic archaeon. | clustered regularly interspaced short palindromic repeats (crispr)/cas systems are found widespread in bacterial and archaeal genomes and exhibit considerable diversity. however, closer insights into the action of most of the crispr modules have remained elusive in particular in archaea as a result of the lack of suitable in vivo test systems. here we demonstrate crispr/cas-based immune defence in the hyperthermophilic archaeon sulfolobus solfataricus. recombinant variants of the ssv1 virus cont ... | 2011 | 21385233 |
| 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 |
| in vivo virus structures: simultaneous classification, resolution enhancement, and noise reduction in whole-cell electron tomography. | sulfolobus turreted icosahedral virus (stiv) experiences an extra-cellular environment of near boiling acid (80-¦c, ph 3) and particles purified under these conditions were previously analyzed by cryo electron microscopy and image reconstruction. here we describe cryo-tomograms of solfolobus cells infected with stiv and the maximum likelihood algorithm employed to compute reconstructions of virions within the cell. virions in four different tomograms were independently reconstructed with an aver ... | 2011 | 21396453 |
| erratum to: heterologous gene expression in the hyperthermophilic archaeon sulfolobus solfataricus. | | 2010 | 21409849 |
| the y-family dna polymerase dpo4 uses a template slippage mechanism to create single-base deletions. | the y-family polymerases help cells tolerate dna damage by performing translesion synthesis, yet they also can be highly error prone. one distinctive feature of the dinb class of y-family polymerases is that they make single-base deletion errors at high frequencies in repetitive sequences, especially those that contain two or more identical pyrimidines with a 5' flanking guanosine. intriguingly, different deletion mechanisms have been proposed, even for two archaeal dinb polymerases that share 5 ... | 2011 | 21421759 |
| 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 |
| stabilization of a metabolic enzyme by library selection in thermus thermophilus. | the anthranilate phosphoribosyl transferase from the hyperthermophilic archaeon sulfolobus solfataricus (sanprt, encoded by strpd), which catalyzes the third step in tryptophan biosynthesis, is a thermostable homodimer with low enzymatic activity at room temperature. we have combined two mutations leading to the monomerization and two mutations leading to the activation of sanprt. the resulting "activated monomer" sanprt-i36e-m47d+d83g-f149s, which is much more labile than wild-type sanprt, was ... | 2011 | 21455924 |
| conserved residues in membrane-bound acid pyrophosphatase from sulfolobus tokodaii, a thermoacidophilic archaeon. | a membrane-intrinsic acid pyrophosphatase (st2226) from sulfolobus tokodaii, a thermoacidophilic archaeon, is possibly involved in glycoprotein biosynthesis and belongs to the phosphatidic acid phosphatase class 2 superfamily, including both membrane-intrinsic and soluble enzymes with divergent functions ranging from dephosphorylation of undecaprenylpyrophosphate and phospho-monoesters such as glucose-6-phosphate to vanadium-containing chloroperoxidation. st2226 is an archaeal ortholog of these ... | 2011 | 21461791 |
| stability of heterochiral hybrid membrane made of bacterial sn-g3p lipids and archaeal sn-g1p lipids. | the structure of membrane lipids in archaea is different from those of bacteria and eucarya in many ways including the chirality of the glycerol backbone. until now, heterochiral membranes were believed to be unstable; thus, no cellular organism could have existed before the separation of the groups of life. in this study, we tested the formation of heterochiral hybrid membrane made of bacterial sn-glycerol-3-phosphate-type polar lipid and archaeal sn-glycerol-1-phosphate-type polar lipid using ... | 2011 | 21473653 |
| an hflx-type gtpase from sulfolobus solfataricus binds to the 50s ribosomal subunit in all nucleotide-bound states. | hflx gtpases are found in all three domains of life, the bacteria, archaea, and eukarya. hflx from escherichia coli has been shown to bind to the 50s ribosomal subunit in a nucleotide-dependent manner, and this interaction strongly stimulates its gtpase activity. we recently determined the structure of an hflx ortholog from the archaeon sulfolobus solfataricus (ssohflx). it revealed the presence of a novel hflx domain that might function in rna binding and is linked to a canonical g domain. this ... | 2011 | 21478358 |
| development of a genetic system for the archaeal virus sulfolobus turreted icosahedral virus (stiv). | our understanding of archaeal viruses has been limited by the lack of genetic systems for examining viral function. we describe the construction of an infectious clone for the archaeal virus sulfolobus turreted icosahedral virus (stiv). stiv was isolated from a high temperature (82°c) acidic (ph 2.2) hot spring in yellowstone national park and replicates in the archaeal model organism sulfolobus solfataricus (rice et al., 2004). while stiv is one of most studied archaeal viruses, little is known ... | 2011 | 21496857 |