Archaeal Proteins: Proteins found in any species of archaeon.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Ribosome Subunits, Small, Archaeal: The small subunit of archaeal RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 28 different RIBOSOMAL PROTEINS.Methanobacteriaceae: A family of anaerobic, coccoid to rod-shaped METHANOBACTERIALES. Cell membranes are composed mainly of polyisoprenoid hydrocarbons ether-linked to glycerol. Its organisms are found in anaerobic habitats throughout nature.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Genes, Archaeal: The functional genetic units of ARCHAEA.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Archaeal Viruses: Viruses whose hosts are in the domain ARCHAEA.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.Sulfolobus: A genus of aerobic, chemolithotrophic, coccoid ARCHAEA whose organisms are thermoacidophilic. Its cells are highly irregular in shape, often lobed, but occasionally spherical. It has worldwide distribution with organisms isolated from hot acidic soils and water. Sulfur is used as an energy source.Methanococcales: An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. They are pseudosarcina, coccoid or sheathed rod-shaped and catabolize methyl groups. The cell wall is composed of protein. The order includes one family, METHANOCOCCACEAE. (From Bergey's Manual of Systemic Bacteriology, 1989)Crenarchaeota: A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.Chromosomes, Archaeal: Structures within the nucleus of archaeal cells consisting of or containing DNA, which carry genetic information essential to the cell.Methanococcus: A genus of anaerobic coccoid METHANOCOCCACEAE whose organisms are motile by means of polar tufts of flagella. These methanogens are found in salt marshes, marine and estuarine sediments, and the intestinal tract of animals.Sulfolobus solfataricus: A species of thermoacidophilic ARCHAEA in the family Sulfolobaceae, found in volcanic areas where the temperature is about 80 degrees C and SULFUR is present.Haloferax volcanii: A species of halophilic archaea found in the Dead Sea.Pyrococcus furiosus: A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.Ribosome Subunits, Large, Archaeal: The large subunit of the archaeal 70s ribosome. It is composed of the 23S RIBOSOMAL RNA, the 5S RIBOSOMAL RNA, and about 40 different RIBOSOMAL PROTEINS.Pyrococcus abyssi: A species of gram-negative hyperthermophilic ARCHAEA found in deep ocean hydrothermal vents. It is an obligate anaerobe and obligate chemoorganotroph.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Archaeoglobus fulgidus: A species of extremely thermophilic, sulfur-reducing archaea. It grows at a maximum temperature of 95 degrees C. in marine or deep-sea geothermal areas.Methanosarcina: A genus of anaerobic, irregular spheroid-shaped METHANOSARCINALES whose organisms are nonmotile. Endospores are not formed. These archaea derive energy via formation of methane from acetate, methanol, mono-, di-, and trimethylamine, and possibly, carbon monoxide. Organisms are isolated from freshwater and marine environments.Sulfolobus acidocaldarius: A species of aerobic, chemolithotrophic ARCHAEA consisting of coccoid cells that utilize sulfur as an energy source. The optimum temperature for growth is 70-75 degrees C. They are isolated from acidic fields.Pyrococcus horikoshii: Anaerobic hyperthermophilic species of ARCHAEA, isolated from hydrothermal fluid samples. It is obligately heterotrophic with coccoid cells that require TRYPTOPHAN for growth.Ribonuclease P: An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.RNA, Catalytic: RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.Proliferating Cell Nuclear Antigen: Nuclear antigen with a role in DNA synthesis, DNA repair, and cell cycle progression. PCNA is required for the coordinated synthesis of both leading and lagging strands at the replication fork during DNA replication. PCNA expression correlates with the proliferation activity of several malignant and non-malignant cell types.Nucleotidases: A class of enzymes that catalyze the conversion of a nucleotide and water to a nucleoside and orthophosphate. EC 3.1.3.-.Haloferax mediterranei: A species of halophilic archaea found in the Mediterranean Sea. It produces bacteriocins active against a range of other halobacteria.5'-Nucleotidase: A glycoprotein enzyme present in various organs and in many cells. The enzyme catalyzes the hydrolysis of a 5'-ribonucleotide to a ribonucleoside and orthophosphate in the presence of water. It is cation-dependent and exists in a membrane-bound and soluble form. EC 3.1.3.5.Uracil-DNA Glycosidase: An enzyme that catalyzes the HYDROLYSIS of the N-glycosidic bond between sugar phosphate backbone and URACIL residue during DNA synthesis.UracilDNA Glycosylases: A family of DNA repair enzymes that recognize damaged nucleotide bases and remove them by hydrolyzing the N-glycosidic bond that attaches them to the sugar backbone of the DNA molecule. The process called BASE EXCISION REPAIR can be completed by a DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE which excises the remaining RIBOSE sugar from the DNA.N-Glycosyl Hydrolases: A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.Salinity: Degree of saltiness, which is largely the OSMOLAR CONCENTRATION of SODIUM CHLORIDE plus any other SALTS present. It is an ecological factor of considerable importance, influencing the types of organisms that live in an ENVIRONMENT.Nuclear Magnetic Resonance, Biomolecular: NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.Nitrogen Isotopes: Stable nitrogen atoms that have the same atomic number as the element nitrogen, but differ in atomic weight. N-15 is a stable nitrogen isotope.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Carbon Isotopes: Stable carbon atoms that have the same atomic number as the element carbon, but differ in atomic weight. C-13 is a stable carbon isotope.Deoxyribonucleoproteins: Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.Pyrococcus: A genus of strictly anaerobic ultrathermophilic archaea, in the family THERMOCOCCACEAE, occurring in heated seawaters. They exhibit heterotrophic growth at an optimum temperature of 100 degrees C.Computer Security: Protective measures against unauthorized access to or interference with computer operating systems, telecommunications, or data structures, especially the modification, deletion, destruction, or release of data in computers. It includes methods of forestalling interference by computer viruses or so-called computer hackers aiming to compromise stored data.Confidentiality: The privacy of information and its protection against unauthorized disclosure.Privacy: The state of being free from intrusion or disturbance in one's private life or affairs. (Random House Unabridged Dictionary, 2d ed, 1993)RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Patents as Topic: Exclusive legal rights or privileges applied to inventions, plants, etc.Methanosarcinaceae: A family of anaerobic METHANOSARCINALES whose cells are mesophilic or thermophilic and appear as irregular spheroid bodies or sheathed rods. These methanogens are found in any anaerobic environment including aquatic sediments, anaerobic sewage digesters and gastrointestinal tracts. There are four genera: METHANOSARCINA, Methanolobus, Methanothrix, and Methanococcoides.Inventions: A novel composition, device, or process, independently conceived de novo or derived from a pre-existing model.Xeroderma Pigmentosum Group D Protein: A DNA helicase that is a component of TRANSCRIPTION FACTOR TFIIH. It plays an essential role in NUCLEOTIDE EXCISION REPAIR, and mutations in this protein are associated with XERODERMA PIGMENTOSUM.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Biotechnology: Body of knowledge related to the use of organisms, cells or cell-derived constituents for the purpose of developing products which are technically, scientifically and clinically useful. Alteration of biologic function at the molecular level (i.e., GENETIC ENGINEERING) is a central focus; laboratory methods used include TRANSFECTION and CLONING technologies, sequence and structure analysis algorithms, computer databases, and gene and protein structure function analysis and prediction.Methanomicrobiaceae: A family of anaerobic METHANOMICROBIALES whose cells are coccoid to straight or slightly curved rods. There are six genera.

An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (1/2280)

Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite the prokaryotic cell and genome organization, basal transcriptional elements of members of the domain Archaea (i.e., TATA box-like sequences, RNA polymerase, and transcription factors TBP, TFIIB, and TFIIS) are of the eukaryotic type. However, open reading frames potentially coding for bacterium-type transcription regulation factors have been recognized in different archaeal strains. This finding raises the question of how bacterial and eukaryotic elements interact in regulating gene expression in Archaea. We have identified a gene coding for a bacterium-type transcription factor in the hyperthermophilic archaeon Sulfolobus solfataricus. The protein, named Lrs14, contains a potential helix-turn-helix motif and is related to the Lrp-AsnC family of regulators of gene expression in the class Bacteria. We show that Lrs14, expressed in Escherichia coli, is a highly thermostable DNA-binding protein. Bandshift and DNase I footprint analyses show that Lrs14 specifically binds to multiple sequences in its own promoter and that the region of binding overlaps the TATA box, suggesting that, like the E. coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus.  (+info)

Mutants in ABC10beta, a conserved subunit shared by all three yeast RNA polymerases, specifically affect RNA polymerase I assembly. (2/2280)

ABC10beta, a small polypeptide common to the three yeast RNA polymerases, has close homology to the N subunit of the archaeal enzyme and is remotely related to the smallest subunit of vaccinial RNA polymerase. The eucaryotic, archaeal, and viral polypeptides share an invariant motif CX2C. CC that is strictly essential for yeast growth, as shown by site-directed mutagenesis, whereas the rest of the ABC10beta sequence is fairly tolerant to amino acid replacements. ABC10beta has Zn2+ binding properties in vitro, and the CX2C. CC motif may therefore define an atypical metal-chelating site. Hybrid subunits that derive most of their amino acids from the archaeal subunit are functional in yeast, indicating that the archaeal and eucaryotic polypeptides have a largely equivalent role in the organization of their respective transcription complexes. However, all eucaryotic forms of ABC10beta harbor a HVDLIEK motif that, when mutated or replaced by its archaeal counterpart, leads to a polymerase I-specific lethal defect in vivo. This is accompanied by a specific lack in the largest subunit of RNA polymerase I (A190) in cell-free extracts, showing that the mutant enzyme is not properly assembled in vivo.  (+info)

Isolation and characterization of a second subunit of molecular chaperonin from Pyrococcus kodakaraensis KOD1: analysis of an ATPase-deficient mutant enzyme. (3/2280)

The cpkA gene encoding a second (alpha) subunit of archaeal chaperonin from Pyrococcus kodakaraensis KOD1 was cloned, sequenced, and expressed in Escherichia coli. Recombinant CpkA was studied for chaperonin functions in comparison with CpkB (beta subunit). The effect on decreasing the insoluble form of proteins was examined by coexpressing CpkA or CpkB with CobQ (cobyric acid synthase from P. kodakaraensis) in E. coli. The results indicate that both CpkA and CpkB effectively decrease the amount of the insoluble form of CobQ. Both CpkA and CpkB possessed the same ATPase activity as other bacterial and eukaryal chaperonins. The ATPase-deficient mutant proteins CpkA-D95K and CpkB-D95K were constructed by changing conserved Asp95 to Lys. Effect of the mutation on the ATPase activity and CobQ solubilization was examined. Neither mutant exhibited ATPase activity in vitro. Nevertheless, they decreased the amount of the insoluble form of CobQ by coexpression as did wild-type CpkA and CpkB. These results implied that both CpkA and CpkB could assist protein folding for nascent protein in E. coli without requiring energy from ATP hydrolysis.  (+info)

Universal conservation in translation initiation revealed by human and archaeal homologs of bacterial translation initiation factor IF2. (4/2280)

Binding of initiator methionyl-tRNA to ribosomes is catalyzed in prokaryotes by initiation factor (IF) IF2 and in eukaryotes by eIF2. The discovery of both IF2 and eIF2 homologs in yeast and archaea suggested that these microbes possess an evolutionarily intermediate protein synthesis apparatus. We describe the identification of a human IF2 homolog, and we demonstrate by using in vivo and in vitro assays that human IF2 functions as a translation factor. In addition, we show that archaea IF2 can substitute for its yeast homolog both in vivo and in vitro. We propose a universally conserved function for IF2 in facilitating the proper binding of initiator methionyl-tRNA to the ribosomal P site.  (+info)

A fission yeast gene for mitochondrial sulfide oxidation. (5/2280)

A cadmium-hypersensitive mutant of the fission yeast Schizosaccharomyces pombe was found to accumulate abnormally high levels of sulfide. The gene required for normal regulation of sulfide levels, hmt2(+), was cloned by complementation of the cadmium-hypersensitive phenotype of the mutant. Cell fractionation and immunocytochemistry indicated that HMT2 protein is localized to mitochondria. Sequence analysis revealed homology between HMT2 and sulfide dehydrogenases from photosynthetic bacteria. HMT2 protein, produced in and purified from Escherichia coli, was soluble, bound FAD, and catalyzed the reduction of quinone (coenzyme Q2) by sulfide. HMT2 activity was also detected in isolated fission yeast mitochondria. We propose that HMT2 functions as a sulfide:quinone oxidoreductase. Homologous enzymes may be widespread in higher organisms, as sulfide-oxidizing activities have been described previously in animal mitochondria, and genes of unknown function, but with similarity to hmt2(+), are present in the genomes of flies, worms, rats, mice, and humans.  (+info)

Tubulin-like protofilaments in Ca2+-induced FtsZ sheets. (6/2280)

The 40 kDa protein FtsZ is a major septum-forming component of bacterial cell division. Early during cytokinesis at midcell, FtsZ forms a cytokinetic ring that constricts as septation progresses. FtsZ has a high propensity to polymerize in vitro into various structures, including sheets and filaments, in a GTP-dependent manner. Together with limited sequence homology, the occurrence of the tubulin signature motif in FtsZ and a similar three-dimensional structure, this leads to the conclusion that FtsZ is the bacterial tubulin homologue. We have polymerized FtsZ1 from Methanococcus jannaschii in the presence of millimolar concentrations of Ca2+ ions to produce two-dimensional crystals of plane group P2221. Most of the protein precipitates and forms filaments approximately 23.0 nm in diameter. A three-dimensional reconstruction of tilted micrographs of FtsZ sheets in negative stain between 0 and 60 degrees shows protofilaments of FtsZ running along the sheet axis. Pairs of parallel FtsZ protofilaments associate in an antiparallel fashion to form a two-dimensional sheet. The antiparallel arrangement is believed to generate flat sheets instead of the curved filaments seen in other FtsZ polymers. Together with the subunit spacing along the protofilament axis, a fitting of the FtsZ crystal structure into the reconstruction suggests a protofilamant structure very similar to that of tubulin protofilaments.  (+info)

The effect of carboxyl group modification on the chromophore regeneration of archaeopsin-1 and bacterioopsin. (7/2280)

Carboxyl group modification with DCCD and NCD-4 was employed to investigate the chemical environment of the side chains of archaeopsin-1 (aO-1) and bacterioopsin (bO). Some differences were observed between aO-1 and bO. Although DCCD or NCD-4 did not modify aO-1 in bleached membrane, they modified bO in bleached membrane and in mixed DMPC/CHAPS/SDS micelles at neutral pH, thereby affecting the opsin shift and the photocycle of the regenerated chromophore. On the contrary, after solubilization with SDS, aO-1 and bO were modified by DCCD and NCD-4, which decreased the chromophore regeneration. In particular, the reaction of aO-1 in SDS with NCD-4 proceeded in a 1:1 ratio at neutral pH. The fluorescence and CD spectra indicated that the modified site was located in the hydrophobic, asymmetrical region. Lysyl-endopeptidase digestion of NCD-4 modified aO-1 produced a fluorescent fragment and amino acid sequence analysis showed that Asp85 or Asp96 in helix C is a probable candidate for the modified residue at present. Kinetic CD measurements revealed that the introduction of N-acylurea at an Asp residue in helix C did not affect the formation of the transient intermediate but inhibited the side chain packing during refolding.  (+info)

Structure of VAT, a CDC48/p97 ATPase homologue from the archaeon Thermoplasma acidophilum as studied by electron tomography. (8/2280)

Valosine-containing protein-like ATPase from Thermoplasma acidophilum is a member of the superfamily of ATPases associated with a diversity of cellular activities and is closely related to CDC48 from yeast and p97 from higher eukaryotes and more distantly to N-ethylmaleimide-sensitive fusion protein. We have used electron tomography to obtain low-resolution (2-2.5 nm) three-dimensional maps of both the whole 500 kDa complex and the N-terminally truncated valosine-containing protein-like ATPase from T. acidophilum complex lacking the putative substrate binding domain.  (+info)

Archaea are best known in their capacities as extremophiles, i.e. micro-organisms able to thrive in some of the most drastic environments on Earth. The protein-based surface layer that envelopes many archaeal strains must thus correctly assemble and maintain its structural integrity in the face of the physical challenges associated with, for instance, life in high salinity, at elevated temperatures or in acidic surroundings. Study of archaeal surface-layer (glyco)proteins has thus offered insight into the strategies employed by these proteins to survive direct contact with extreme environments, yet has also served to elucidate other aspects of archaeal protein biosynthesis, including glycosylation, lipid modification and protein export. In this mini-review, recent advances in the study of archaeal surface-layer (glyco)proteins are discussed.
We analyzed length differences of eukaryotic, bacterial and archaeal proteins in relation to function, conservation and environmental factors. Comparing Eukaryotes and Prokaryotes, we found that the greater length of eukaryotic proteins is pervasive over all functional categories and involves the va …
Thermococcus kodakarensis is a species of thermophilic archaea. The type strain T. kodakarensis KOD1 is one of the best studied members of the genus. T. kodakarensis was isolated from a solfatara near the shore of Kodakara Island, Kagoshima, Japan. The isolate was originally named Pyrococcus kodakarensis KOD1, but reclassified as a species of Thermococcus, based on 16S rRNA sequence. Early research with T. kodakarensis was directed mostly at its thermostable enzymes, but its relative ease of handling and genetic manipulation facilitated by natural competence has made it an attractive system for the study of several biological processes. T. kodakarensis cells are irregular cocci 1-2 μm in diameter, often occurring in pairs, and are highly motile by means of lophotrichous archaella. The cell wall consists of a layer of di-ether and tetra-ether lipids, and an outer glycoprotein coat. T. kodakarensis is an obligate anaerobe, and a heterotroph, growing rapidly on a variety of organic substrates in ...
Kirkland, P. A. and Maupin-Furlow, J. A. (2009), Stabilization of an archaeal DNA-sliding clamp protein, PCNA, by proteasome-activating nucleotidase gene knockout in Haloferax volcanii. FEMS Microbiology Letters, 294: 32-36. doi: 10.1111/j.1574-6968.2009.01547.x ...
TY - JOUR. T1 - Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. AU - Silva, Ana P G. AU - Chechik, Maria. AU - Byrne, Robert T.. AU - Waterman, David G.. AU - Ng, Chyan Leong. AU - Dodson, Eleanor J.. AU - Koonin, Eugene V.. AU - Antson, Alfred A.. AU - Smits, Callum. PY - 2011/5/11. Y1 - 2011/5/11. N2 - MTH1203, a β-CASP metallo-β-lactamase family nuclease from the archaeon Methanothermobacter thermautotrophicus, was identified as a putative nuclease that might contribute to RNA processing. The crystal structure of MTH1203 reveals that, in addition to the metallo-β-lactamase nuclease and the β-CASP domains, it contains two contiguous KH domains that are unique to MTH1203 and its orthologs. RNA-binding experiments indicate that MTH1203 preferentially binds U-rich sequences with a dissociation constant in the micromolar range. In vitro nuclease activity assays demonstrated that MTH1203 is a zinc-dependent nuclease. MTH1203 is also shown to be a dimer ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
RN [1] RM PMID:12562787 RT CDP-2,3-Di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase) in the methanogenic archaeon Methanothermobacter thermautotrophicus. RA Morii H, Koga Y RL J Bacteriol. 2003 Feb;185(4):1181-9 ...
The majority of cells in nature probably exist in a stationary-phase-like state, due to nutrient limitation in most environments. Studies on bacteria and yeast reveal morphological and physiological changes throughout the stationary phase, which lead to an increased ability to survive prolonged nutrient limitation. However, there is little information on archaeal stationary phase responses. We investigated protein- and lipid-level changes in Thermococcus kodakarensis with extended time in the stationary phase. Adaptations to time in stationary phase included increased proportion of membrane lipids with a tetraether backbone, synthesis of proteins that ensure translational fidelity, specific regulation of ABC transporters (upregulation of some, downregulation of others), and upregulation of proteins involved in coenzyme production. Given that the biological mechanism of tetraether synthesis is unknown, we also considered whether any of the protein-level changes in T. kodakarensis might shed light ...
Endosymbiotic Actinidic Archaeal Digoxin Inhibited Sodium Potassium ATPase Mediated ATP Synthesis and Archaeal Ectoatpases Produce Neuro-Immuno- Metabolic-Endocrine/Cell Cycle Regulation
View Notes - chapter+19 from BIOL 2051 at LSU. Chapter 19 Archaeal Diversity Archaeal Traits and Diversity Widest temperature range 2C121C Widest range of environments pH 0, high pressure,
Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the existence of a vast diversity of uncultivated archaea for which metabolic information is lacking. We sequenced DNA from complex sediment- and groundwater-associated microbial communities sampled prior to and during an acetate biostimulation field experiment to investigate the diversity and physiology of uncultivated subsurface archaea. We sampled 15 genomes that improve resolution of a new phylum within the TACK superphylum and 119 DPANN genomes that highlight a major subdivision within the archaeal domain that separates DPANN from TACK/Euryarchaeota lineages. Within the DPANN superphylum, which lacks any isolated representatives, we defined two new phyla using sequences from 100 newly sampled genomes. The first new phylum, for which we propose the name Woesearchaeota, was defined using 54 new sequences. We reconstructed a complete (finished) genome for an ...
Relative abundance of archaeal OTUs defined using the 16S rRNA gene hyper-variable region V3V4. The bar chart shows the diversity of Archaea at the lowest relia
1J22: X-Ray and Biochemical Anatomy of an Archaeal XPF/Rad1/Mus81 Family Nuclease. Similarity between Its Endonuclease Domain and Restriction Enzymes
By employing next generation DNA sequencing of genomes isolated from single cells, great strides are being made in the monumental task of systematically bringing to light and filling in uncharted branches in the bacterial and archaeal tree of life.
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Eukaryotic initiation factor 2 (eIF2) is a heterotrimeric protein composed of alpha, beta, and gamma subunits, of which the alpha subunit (eIF2 alpha) plays a crucial role in regulation of protein synthesis through phosphorylation at Ser51. All three subunit genes are conserved in Archaea. To examine the properties of archaeal initiation factor 2 alpha (aIF2 alpha), three genes encoding alpha, beta, and gamma subunits of aIF2 from the hyperthermophilic archaeon Pyrococcus horikoshii OT3 were expressed in Escherichia coli cells, and the resulting proteins, aIF2 alpha, aIF2 beta, and aIF2 gamma, were characterized with reference to the properties of eIF2. aIF2 alpha preferentially interacts with aIF2 gamma, but does not interact with aIF2 beta, which is consistent with data obtained with eIF2, of which eIF2 gamma serves as a core subunit, interacting with eIF2 alpha and eIF2 beta. It was found that aIF2 alpha was, albeit to a lower degree, phosphorylated by double-stranded RNA-dependent protein kinase
The cytoplasmic hydrogenase (SHI) of the hyperthermophilic archaeon Pyrococcus furiosus is an NADP(H)-dependent heterotetrameric enzyme that contains a nickel-iron catalytic site, flavin, and six iron-sulfur clusters. It has potential utility in a range of bioenergy systems in vitro, but a major obstacle in its use is generating sufficient amounts. We have engineered P. furiosus to overproduce SHI utilizing a recently developed genetic system. In the overexpression (OE-SHI) strain, transcription of the four-gene SHI operon was under the control of a strong constitutive promoter, and a Strep-tag II was added to the N terminus of one subunit. OE-SHI and wild-type P. furiosus strains had similar rates of growth and H 2 production on maltose. Strain OE-SHI had a 20-fold higher transcription of the polycistronic hydrogenase mRNA encoding SHI, and the specific activity of the cytoplasmic hydrogenase was ∼10-fold higher when compared with the wild-type strain, although the expression levels of genes
cansSAR 3D Structure of 1S3Q_D | CRYSTAL STRUCTURES OF A NOVEL OPEN PORE FERRITIN FROM THE HYPERTHERMOPHILIC ARCHAEON ARCHAEOGLOBUS FULGIDUS | 1S3Q
cansSAR 3D Structure of 1S3Q_B | CRYSTAL STRUCTURES OF A NOVEL OPEN PORE FERRITIN FROM THE HYPERTHERMOPHILIC ARCHAEON ARCHAEOGLOBUS FULGIDUS | 1S3Q
Adenylylsulphate (adenosine-5′-phosphosulphate, APS) reductase from the extremely thermophilic sulphate-reducing archaeon Archaeoglobus fulgidus is an iron-sulphur flavoprotein containing one non-covalently bound flavin group, eight non-haem iron and six labile sulphide atoms per molecule. Re-evaluation of the enzyme structure revealed the presence of two different subunits with molecular masses of 80 and 18.5 kDa. The subunits are arranged in an α2β subunit structure. We have cloned and sequenced a 2.7 kb segment of DNA containing the genes for the α and β subunits, which we designate aprA and aprB, respectively. The two genes are separated by 17 bp and localized in the order aprBA. While a putative promoter could not be identified in the vicinity of aprBA a probable termination signal was found just downstream of the translation stop codon of aprA. The codon usage for aprBA shows strong preferences for G and C in the third codon position. aprA encodes a 73.3 kDa polypeptide, which shows
Hydrolytic deamination of DNA cytosine residues results in U/G mispairs, pre-mutagenic lesions threatening long-term genetic stability. Hence, DNA uracil repair is ubiquitous throughout all extant life forms and base excision repair, triggered by a uracil DNA glycosylase (UDG), is the mechanistic paradigm adopted, as it seems, by all bacteria and eukaryotes and a large fraction of archaea. However, members of the UDG superfamily of enzymes are absent from the extremely thermophilic archaeon Methanothermobacter thermautotrophicus Delta H. This organism, as a hitherto unique case, initiates repair by direct strand incision next to the DNA-U residue, a reaction catalyzed by the DNA uridine endonuclease Mth212, an ExoIII homologue. To elucidate the detailed mechanism, in particular to identify the molecular partners contributing to this repair process, we reconstituted DNA uracil repair in vitro from only four purified enzymes of M. thermautotrophicus Delta H. After incision at the 5-side of a ...
T. kodakarensis MNase digestion. T. kodakarensis strain KOD1 [22] was cultivated under anaerobic conditions at 85 °C and an insoluble unfixed chromatin fraction prepared from cells at the late‐log/stationary‐phase transition [10]. Chromatin was digested with 1 unit/ml of MNase, or 0.1 units/ml of DNase I for 1 h at 37 °C in the presence of 10 μg/μl RNase A. De‐proteinized genomic DNA was digested with 0.03 units/ml of MNase [10].. S. cerevisiae MNase digestion. EUROSCARF wild‐type reference strain BY4742 was grown and chromatin digestion (pooled triplicate samples) performed as described [11], with chromatin in unfixed detergent‐permeabilised yeast spheroplasts incubated with 600 units/ml of MNase for 3 min at 37 °C. Illumina DNA sequencing. NEBNext DNA sample prep master mix set 1 was used for Illumina adaptor ligation. Adaptor ligates were size selected on polyacrylamide gels to preserve the size distribution of the fragments before sequencing in 100 nucleotide paired end mode ...
RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative
The coordinated activities of AlaAT and GDH have been proposed to play an important role in the maintenance of the redox balance during fermentative growth of P. furiosus(19). These activities result in a change in the relative flux of pyruvate to acetate formation toward alanine formation. Pyruvate is therefore used as a catabolic electron sink. Due to the important role AlaAT plays in this pathway, this enzyme was purified from P. furiosus and represents the first AlaAT purified from either an archaeon or a hyperthermophile.. Similar to the AlaAT from mesophilic sources, the active form of the enzyme was found to be a homodimer with a subunit molecular mass of 43.5 kDa (22, 34, 36). It has been reported that the AlaATs have a high substrate specificity and are only able to transaminate alanine or glutamate (22, 34, 36). The P. furiosus enzyme, however, was capable of utilizing aspartate and, to a much lesser extent, the branched-chain amino acids with α-ketoglutarate as the amino acceptor, ...
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts extremozymes for utilization in White Biotechnology. Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012 ...
Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts extremozymes for utilization in White Biotechnology. Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012 ...
Living organisms rely on many different mechanisms to adapt to changes within their environment. Protein phosphorylation and dephosphorylation events are one such way cells can communicate to generate a response to environmental changes. In the Kennelly laboratory we hope to gain insight on phosphorylation events in the domain Archaea through the study of the acidothermophilic organism Sulfolobus solfataricus. Such findings may provide answers into evolutionary relationships and facilitate an understanding of phosphate transfer via proteins in more elaborate systems where pathway disturbances can lead to disease processes. A λ-phage expression library was generated from S. solfataricus genomic DNA. The immobilized expression products were probed with a purified protein kinase, SsoPK4, and radiolabeled ATP to identify potential native substrates. A protein fragment of the ORF sso0563, the catalytic A-type ATPase subunit A (AtpA), was phosphorylated by SsoPK4. Full length and truncated forms of ...
Archaea is a peer-reviewed, Open Access journal that publishes original research articles as well as review articles dealing with all aspects of archaea, including environmental adaptation, enzymology, genetics and genomics, metabolism, molecular biology, molecular ecology, phylogeny, and ultrastructure. Published since 2002, Archaea provides a unique venue for exchanging information about these extraordinary prokaryotes.
cytosol, phosphoribosylamine-glycine ligase activity, phosphoribosylformylglycinamidine cyclo-ligase activity, purine nucleotide biosynthetic process
1. Godfroy, A., Meunier, J., Guezennec, J., Lesongeur, F., Raguenes, G., Rimbault, A., and Barbier, G. 1996. Thermococcus fumicolans sp. nov., a New Hyperthermophilic Archaeon Isolated from a Deep-Sea Hydrothermal Vent in the North Fiji Basin. Int. J. Systematic Bacteriology 46: 1113-1119 2. Thermococcus fumicolans genome sequence. http://www.ncbi.nlm.nih.gov/ 3. Cambon-Bonavita, M., Schmitt, P., Zieger, M., Flaman, J., Lesongeur, F., Raguenes, G., Bindel, D., Frisch, N., Lakkis, Z., Dupret, D., Barbier, G., and Querellou, J. 2000. Cloning, expression and characterization of DNA polymerase I from the hyperthermophilic archaea Thermococcus fumicolans. Extremophiles 4: 215-225 4. Raffin, J., Henneke, G., and Dietrich, J. 2000. Purification and characterization of a new DNA polymerase modulator from the hyperthermophilic archaeon Thermococcus fumicolans. Comp. Bioc. & Physiol. Part B 127: 299-308 5. Lloyd, K. G., Edgcomb, V. P., Molyneaux, S. J., Boer, S., Wirsen, C. O., Atkins, M. S., and Teske, ...
Methanosarcina mazei ATCC ® BAA-159D-5™ Designation: Genomic DNA from Methanosarcina mazei strain DSM 3647 TypeStrain=False Application:
Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the SSV type and pNOB8 type. The former carries a smaller N-terminal and a larger C-terminal integrase gene fragment, and the latter an intact integrase gene. All integrated elements overlap tRNA genes that were target sites for integration. It has been demonstrated that SSV (Sulfolobus spindle virus) viruses, carrying an SSV-type integrase gene, and conjugative plasmids, carrying a pNOB8-type integrase, are integrative elements. Two mechanisms have been proposed for stably maintaining an integrated element within archaeal chromosomes. There is also evidence for changes having occurred in the captured integrated elements present in archaeal genomes. Thus we infer that site-specific integration constitutes an important mechanism for horizontal gene transfer and genome evolution.. ...
View Notes - 22 from BIOL 4125 at LSU. PROKARYOTIC DIVERSITY BIOL 4125 SPRING 2009 LECTURE 22 Hyperthermophilic Archaea Part II The early overview of archaeal diversity was exemplified by a
Our division studies the Biology of Archaea as well as bacterial symbioses with a focus on ecological, physiological and evolutionary aspects to shed light on the diversity and fundamental distinctions between these two prokaryotic groups. In particular we are interested in: - The ecological distribution of archaea from terrestrial, aquatic and hot environments - The phylogeny of archaea - The metabolism and genomes of ammonia oxidizing thaumarchaeota - virus-defense (CRISPR-) systems of hyperthermophilic archaea - physiology and biotechnological application of methanogenic archaea - bacterium-nematode symbioses ...
Our division studies the Biology of Archaea as well as bacterial symbioses with a focus on ecological, physiological and evolutionary aspects to shed light on the diversity and fundamental distinctions between these two prokaryotic groups. In particular we are interested in: - The ecological distribution of archaea from terrestrial, aquatic and hot environments - The phylogeny of archaea - The metabolism and genomes of ammonia oxidizing thaumarchaeota - virus-defense (CRISPR-) systems of hyperthermophilic archaea - physiology and biotechnological application of methanogenic archaea - bacterium-nematode symbioses ...
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Prosser , J I & Nicol , G W 2012 , Archaeal and bacterial ammonia-oxidisers in soil : the quest for niche specialisation and differentiation Trends in Microbiology , vol 20 , no. 11 , pp. 523-531 . DOI: 10.1016/j.tim.2012.08. ...
Eight of Fourteen gvp Genes Are Sufficient for Formation of Gas Vesicles in Halophilic Archaea: The minimal number of genes required for the formation of gas ve
A long-standing question is how chromosomal DNA is packaged in Crenarchaeota, a major group of archaea, which synthesize large amounts of unique small DNA-binding proteins but in general contain no archaeal histones. In the present work, we tested our hypothesis that the two well-studied crenarchaeal chromatin proteins Cren7 and Sul7d compact DNA by both DNA bending and bridging. We show that the two proteins are capable of compacting... ...
Nunoura, T.; Takaki, Y.; Kakuta, J.; Nishi, S.; Sugahara, J.; Kazama, H.; Chee, G.J.; Hattori, M.; Kanai, A.; Aatomi, H.; Takai, K. and akami, H. 2011: Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res., 39, 3204-3223. doi: doi: 10.1093/nar/gkq1228 ...
Typical growth inhibition of S. solfataricus on plates due to infectious virus. Lawns of S. solfataricus strain GΘ were prepared as in Stedman et al. (2003). T
Thermococcus pacificus ATCC ® 700653D™ Designation: Genomic DNA from Thermococcus pacificus DSM 10394 TypeStrain=True Application:
Structure of a two-domain N-terminal fragment of ribosomal protein L10 from Methanococcus jannaschii reveals a specific piece of the archaeal ribosomal ...
Human ferritins have been extensively studied to be used as nanocarriers for diverse applications and could represent a convenient alternative for targeted delivery of anticancer drugs and imaging agents. However, the most relevant limitation to their applications is the need for highly acidic experimental c
I m looking for any info avaliable concerning maintenance of S. solfataricus. Please e-mail : dhatzini at orfeas.chemeng.ntua.gr ...
Some Archaea thrive in extreme places such as in thermal pools, hot vents at the bottom of the sea, extremely salty water, and even in underground oil reserves. This book examines the diverse Archaea kingdom and the division of these organisms by their unusual biology into three main groups. It also explains why little in general is known about them, and why further classification of Archaea is so difficult.
Read about how mammalian plasmids differ from their bacterial counterparts, including how replication occurs and whether selection is necessary for transfected cells.
Angelika works as a budtender in a medical dispensary and is her customers favorite. She loves to spend time with her dog Coco. In her free time she likes to cook with cannabis products and also give talks in the local communities about the benefits of medical cannabis.. ...
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قَالَ سَعْدُ بْنُ عُبَادَةَ : لَوْ رَأَيْتُ رَجُلاً مَعَ امْرَأَتِي لَضَرَبْتُهُ بِالسّيْفِ غَيْرُ مُصْفِحٍ عَنْهُ ، فَبَلَغَ ذَلِكَ رَسُولَ اللّهِ صلى الله عليه على آله وسلم فَقَالَ : أَتَعْجَبُونَ مِنْ غَيْرَةِ سَعْدٍ ؟ فَوَ الله لأَنَا أَغْيَرُ مِنْهُ ، وَالله أَغْيَرُ مِنّي ، مِنْ أَجْلِ غَيْرَةِ الله حَرّمَ الْفَوَاحِشَ مَا ظَهَرَ مِنْهَا وَمَا بَطَن. ...
The genes encoding the three subunits of the primary ABC transporter Ota of the methanogenic archaeon Methanosarcina mazei Gö1 were cloned in an expression vector (pBAD24) and transformed into the glycine betaine transport-negative mutant Escherichia coli MKH13. Ota was produced as demonstrated by Western blotting. Uptake studies revealed that Ota catalyzed the transport of glycine betaine in E. coli MKH13(pBAD-Ota) with a Km of 10±5 μM and a maximal velocity of 1.5±0.5 nmol min⁻¹ mg protein⁻¹. Transport was ATP dependent. Ota was activated by salinity gradients, but only marginally by sugar gradients across the membrane. Glycine betaine transport was inhibited to a small extent by an excess of dimethylglycin or proline betaine, but not by sarcosine or glycine ...
TY - JOUR. T1 - Recombinant superoxide dismutase from a hyperthermophilic archaeon, Pyrobaculum aerophilum. AU - Whittaker, Mei M.. AU - Whittaker, James W.. PY - 2000/6/1. Y1 - 2000/6/1. N2 - Superoxide dismutase (SOD) from the hyperthermophilic archaeon Pyrobaculum aerophilum (a facultative aerobe) has been cloned and expressed in a mesophilic host (Escherichia coli) as a soluble tetrameric apoprotein. The purified apoprotein can be reconstituted with either Mn or Fe by heating the protein with the appropriate metal salt at an elevated temperature (95 °C). Both Mn- and Fe-reconstituted P. aerophilum SOD exhibit superoxide dismutase activity, with the Mn-containing enzyme having the higher activity. P. aerophilum SOD is extremely thermostable and the reconstitution with Mn(II) can be performed in an autoclave (122 °C, 18 psi). The Mn(III) optical absorption spectrum of Mn-reconstituted P. aerophilum SOD is distinct from that of most other MnSODs and is unchanged upon addition of NAN3. The ...
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The central metabolic pathways are a glycolytic pathway, a pentose phosphate pathway, and the citric acid cycle (Fig. 1). Conversion of glucose to pyruvate via the nonphosphorylating Entner-Doudoroff pathway produces no net energy (19). Genes for most enzymes, except gluconate dehydratase, are present (Sso3204, 3197, 3194, 0666, 0913, 0981). Conversion of pentose substrates (xylose, arabinose) is predicted to proceed via the pentose phosphate pathway, or a variant thereof. However, only genes encoding ribose-5-P isomerase (Sso0978) and transketolase (Sso0297 and 0299) are assigned. In contrast, all citric acid cycle genes are present (Sso1077, 1095, 2182, 2356 to 2359, 2482, 2483, 2585, 2589, 2815, 2816, 2863).. It is striking that NAD+ is used rarely as an electron acceptor in some central metabolic redox reactions. Both glucose dehydrogenase and glyceraldehyde dehydrogenase are reported to reduce NADP+ specifically. Moreover, glyceraldehyde-3-phosphate dehydrogenase, isocitrate dehydrogenase, ...
Homologous recombination plays a central role in the repair of double-strand DNA breaks, the restart of stalled replication forks and the generation of genetic diversity. Regulation of recombination is essential since defects can lead to genome instability and chromosomal rearrangements. Strand exchange is a key step of recombination - it is catalysed by RecA in bacteria, Rad51/Dmc1 in eukaryotes and RadA in archaea. RadB, a paralogue of RadA, is present in many archaeal species. RadB has previously been proposed to function as a recombination mediator, assisting in RadA-mediated strand exchange. In this study, we use the archaeon Haloferax volcanii to provide evidence to support this hypothesis. We show that RadB is required for efficient recombination and survival following treatment with DNA-damaging agents, and we identify two point mutations in radA that suppress the ΔradB phenotype. Analysis of these point mutations leads us to propose that the role of RadB is to act as a recombination ...
The two transducers in the phototaxis system of the archaeon Halobacterium salinarum, HtrI and HtrII, are methyl-accepting proteins homologous to the chemotaxis transducers in eubacteria. Consensus sequences predict three glutamate pairs containing potential methylation sites in HtrI and one in HtrII. Mutagenic substitution of an alanine pair for one of these, Glu265-Glu266, in HtrI and for the homologous Glu513-Glu514 in HtrII eliminated methylation of these two transducers, as demonstrated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis autofluorography. Photostimulation of the repellent receptor sensory rhodopsin II (SRII) induced reversible demethylation of HtrII, while no detectable change in the extent of methylation of HtrI was observed in response to stimulation of its cognate sensory rhodopsin, the attractant receptor SRI. Cells containing HtrI or HtrII with all consensus sites replaced by alanine still exhibited phototaxis responses and behavioral adaptation, and methanol ...
Empadinhas, N., Marugg, J.D., Borges, N., Santos, H. and da Costa, M.S. (2001). "Pathway for the synthesis of mannosylglycerate in the hyperthermophilic archaeon Pyrococcus horikoshii. Biochemical and genetic characterization of key-enzymes". J. Biol. Chem. 276: 43580-43588. PMID 11562374. ...
The single cubane cluster ferredoxin (Fd) from the hyperthermophilic archaeon Pyrococcus furiosus (Pf) possesses several unique properties when compared even to Fds from other hyperthermophilic archaea or bacteria. These include an equilibrium molecular heterogeneity, a six- to seven-residue increase in size, an Asp rather than the Cys as one cluster ligand, and a readily reducible disulfide bond. NMR assignments and determination of both secondary structure and tertiary contacts remote from the paramagnetic oxidized cluster of Pf 3Fe Fd with an intact disulfide bond reported previously (Teng Q., Zhou, Z. H., Smith, E. T., Busse, S.C., Howard, J. B. Adams, M. W. W., and La Mar, G. (1994) Biochemistry 33, 6316-6328) are extended here to the 4Fe oxidized cluster WT (1H and 15N) and D14C (1H only) Fds with an intact disulfide bond and to the 4Fe oxidized WT Fd (1H and 15N) with a cleaved disulfide bond. All forms are shown to possess a long (13-member) α-helix, two β-sheets (one double-, one triple
2W8L: Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts.
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated overexpression of native genes, allowed for the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and permitted the introduction of sequences encoding new proteins in these fast growing fermentative heterotrophs. Tightly controlled and easily manipulated systems permitting regulated gene expression are however limited for these hosts. Here we describe an alternative method for regulatory control reliant on a cis-encoded functional riboswitch in the model archaeon Thermococcus kodakarensis Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria, and similarly functions to regulate a component conserved fluoride export pathway ...
Author: Kliefoth, Michael et al.; Genre: Journal Article; Published in Print: 2012-02; Keywords: Methanosarcina acetivoran; Carbon monoxide; Acclimation; Aldehyde dehydrogenase; Sensing; Regulation; Title: Genetic analysis of MA4079, an aldehyde dehydrogenase homolog, in Methanosarcina acetivorans
Enzymatic Degradation of PrPSc by a Protease Secreted from Aeropyrum pernix K1. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Persister cells are phenotypic variants within a microbial population, which are dormant and transiently tolerant to stress. Persistence has been studied extensively in bacteria, and in eukaryotes to a limited extent, however, it has never been observed in archaea. Using the model haloarchaeon, Haloferax volcanii DS2, we demonstrated persister cell formation in this domain, with time-kill curves exhibiting a characteristic biphasic pattern following starvation or exposure to lethal concentrations of various biocidal compounds. Repeated challenges of surviving cells showed that, as with bacteria, persister formation in H. volcanii was not heritable. Additionally, as previously shown with bacteria, persister formation in H. volcanii was suppressed by exogenous indole. The addition of spent culture media to assays conducted on planktonic cells showed that H. volcanii-conditioned media stimulated persistence, whereas conditioned media of other haloarchaea or halophilic bacteria did not, suggesting the
The archaeon Halobacterium NRC-1 is an extreme halophile that thrives in saturated brine environments such as the Dead Sea and solar salterns. It offers a versatile and easily assayed system for an array of well-coordinated physiologies that are necessary for survival in its harsh environment [1]. It has robust DNA repair systems that can efficiently reverse the damages caused by a variety of mutagens including UV radiation and desiccation/re-hydration cycles [2, 3]. Halobacterium NRC-1 adapts its metabolism to anaerobic conditions with the synthesis of bacterorhodopsin, which facilitates the conversion of energy from light into ATP. The completely sequenced genome of Halobacterium NRC-1 (containing ~2,600 genes) has provided insights into many of its physiological capabilities, however nearly half of all genes encoded in the halobacterial genome have no known function [4-7].. This work is intended to be a prototype for the development of a biological data integration system with a focus on ...
In constrast to bacteria, all archaea possess cell walls lacking peptidoglycan and a number of different cell envelope components have also been described. A paracrystalline protein surface layer, commonly referred to as S-layer, is present in nearly all archaea described to date. S-layers are composed of only one or two proteins and form different lattice structures. In this review, we summarise current understanding of archaeal S-layer proteins, discussing topics such as structure, lattice type distribution among archaeal phyla and glycosylation. The hexagonal lattice type is dominant within the phylum Euryarchaeota, while in the Crenarchaeota this feature is mainly associated with specific orders. S-layers exclusive to the Crenarchaeota have also been described, which are composed of two proteins. Information regarding S-layers in the remaining archaeal phyla is limited, mainly due to organism description through only culture-independent methods. Despite the numerous applied studies using bacterial S
A flavoprotein. The enzyme catalyses the reduction of bound ferric iron in a variety of iron chelators (siderophores), resulting in the release of ferrous iron. The enzyme from the hyperthermophilic archaeon Archaeoglobus fulgidus is not active with uncomplexed Fe(III). cf. EC 1.16.1.7, ferric-chelate reductase (NADH) and EC 1.16.1.9, ferric-chelate reductase (NADPH ...
Sako, Y., Nomura, N., Uchida, A., Ishida, Y., Morii, H., Koga, Y., Hoaki, T., and Maruyama, T. 1996. Aeropyrum pernix gen. nov., sp. nov., a novel aerobic hyperthermophilic archaeon growing at temperatures up to 100 degrees C. Int. J. Syst. Bacteriol. 46:1070-1077 ...
Archaea are nowadays known as the third domain of life. Before 1970 archaea were thought to belong to the domain bacteria, since archaeal cells have similar sizes as bacterial cells and like bacteria possess neither a nucleus nor cell organelles. In the 1970s Carl Woese sequenced ribosomal RNAs of prokaryotic organisms and discovered two different types of rRNA sequences. Because of this discovery Woese proposed that the prokaryotic domain has to be subdivided into two separate domains, namely Bacteria and Archaea. Since then more and more data accumulated which show that Archaea indeed belong to a separate domain. Initially people thought that archaea are freaks living only at sites with extreme living conditions like f.i. hot geysers in Yellowstone National Park and Black Smokers at the bottom of the ocean. But nowadays it is known that archaea also constitute a big part of the biomass in normal environments. Asgard archaea: Close relatives to the first eukaryotic cell? ...
PDCD5蛋白質是個最早被發現在人類體內細胞用來上調節的細胞凋亡蛋白。PDCD5蛋白質可從細胞質向細胞核迅速的通過並與Tip60蛋白結合於DNA造成乙醯化,進而傳遞細胞凋亡訊息,其重要性為調節第五型賴氨酸乙酰轉化酶抑制其蛋白酶體相關的降解(參與轉錄、DNA損傷反應和細胞週期控制蛋白)。我們從KEGG數據分析庫確定了SSO0352基因為PDCD5蛋白在古生菌Sulfolobus solfataricus的同源基因,由於目前在古生菌Sulfolobus solfataricus的功能仍然還是未知,為了研究是否有相似的作用及結構。我們表現在質體pET-21a上和找到適合生產PDCD5蛋白質的方法,並表現於大腸桿菌(RIL)菌株,找到其純化條件。利用陽離子交換樹脂和膠體交換法純化出蛋白並使用X-ray繞射與單重原子異常散射(SAD)得知PDCD5蛋白的結構。Sso-PDCD5晶體在X-ray的繞射數據為Space group=C2, a = 100.34 Å, b = 39.71 Å, c = 77.57 ...
Lübben, M. , Güldenhaupt, J. , Zoltner, M. , Deigweiher, K. , Haebel, P. , Urbanke, C. and Scheidig, A. J. (2007): Sulfate Acts as Phosphate Analog on the Monomeric Catalytic Fragment of the CPx-ATPase CopB from Sulfolobus solfataricus , Journal of Molecular Biology ...
So, first a bit of biology. This will make more sense to you if you are not a creationist. Somewhere back in the mists of time -- long before the universe was created 6,000 years ago -- actually somewhere around 2 billion years ago, it seems that 2 (or possibly 3) simple prokaryotic cells entered into an endosymbiotic relationship. We dont know exactly how this happened. Prokaryotic cells dont have a nucleus and are otherwise relatively simple in their internal structure. There are two major kinds, called archaea and bacteria. The most straightforward explanation of the origin of the eukaryotes is that an archaeal cell somehow engulfed a bacterium, but didnt digest it. Instead, the bacterium reproduced and its progeny started living happily within the cytoplasm of the archaea and its descendants. The endosymbiotic bacteria gradually lost most of their DNA -- they didnt need it because their environment was properly managed by the archaeal DNA, which is now our nuclear DNA -- and they settled ...
Their phytanyl tails are primarily hooked to their glycerols using ether, not ester, linkages (see 2, above), which resist destruction better than esters. And their glycerols have opposite handedness to the glycerols in our membrane lipids (note mirror orientation in the bacterial and archaeal lipids in figure).. Molecular handedness -- chirality in chemistry-speak -- is not a thing changed easily by evolution. For instance, the vast majority of protein building blocks called amino acids used by life on Earth are exclusively "left-handed". Why? No one really knows, although some have guesses. Once lefty amino acids took over, though, there was no going back biochemically -- the enzymes were set up a certain way and that was that. Thus, that archaeal and bacterial enzymes use glycerols with opposite handedness implies that bacteria and archaea parted ways long, long ago.. Some archaeal lipids have a property that is rarely or never seen in bacteria or eukaryotes. Bacteria and eukaryotes have ...
Jung J-H, Seo D-H, Holden JF, Park C-S. 2014. Maltose-forming α-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04.. Appl Microbiol Biotechnol. 98(5):2121-31. ...
Archaeal flagellum. The flagellum of Archaea is a long hair-like cell surface appendage made of polymerized flagellin with an attached hook. This rotating structure with switches propels the cell through a liquid medium. The archaeal flagellum is distinct from its bacterial equivalent in terms of architecture, composition and mechanism of assembly. Thinner (10-15 nm) compared to the bacterial flagellum (18-24 nm), it is usually composed of several types of flagellins and is glycosylated. The archeal flagellum is considered as a type IV pilus-like structure.. Category: Cellular component ...
Biohazard level, growth media and temperature, gram stain, industrial applications and more information for Methanothermobacter wolfeii.
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InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
Sodium/calcium exchanger 1 (Na+/Ca2+-exchange protein 1). The cardiac isoform, CAX1.1, like the archaeal homologues for which high resolution 3-d structures are available (TC#s 2.A.19.5.3 and 2.A.19.8.2), have two aqueous ion permeation channels with cavities that can face the cytoplasm or the external medium (John et al. 2013). It exchanges one Ca2+ ion against three to four Na+ ions, and thereby contributes to the regulation of cytoplasmic Ca2+ levels and Ca2+-dependent cellular processes (Komuro et al. 1992; , Van Eylen et al. 2001; Kofuji et al. 1992). It also contributes to Ca2+ transport during excitation-contraction coupling in muscle. In a first phase, voltage-gated channels mediate the rapid increase of cytoplasmic Ca2+ levels due to release of Ca2+ stores from the endoplasmic reticulum. SLC8A1 mediates the export of Ca2+ from the cell during the next phase, so that cytoplasmic Ca2+ levels rapidly return to baseline. It is also required for normal embryonic heart development and the ...
Sodium/calcium exchanger 1 (Na+/Ca2+-exchange protein 1). The cardiac isoform, CAX1.1, like the archaeal homologues for which high resolution 3-d structures are available (TC#s 2.A.19.5.3 and 2.A.19.8.2), have two aqueous ion permeation channels with cavities that can face the cytoplasm or the external medium (John et al. 2013). It exchanges one Ca2+ ion against three to four Na+ ions, and thereby contributes to the regulation of cytoplasmic Ca2+ levels and Ca2+-dependent cellular processes (Komuro et al. 1992; , Van Eylen et al. 2001; Kofuji et al. 1992). It also contributes to Ca2+ transport during excitation-contraction coupling in muscle. In a first phase, voltage-gated channels mediate the rapid increase of cytoplasmic Ca2+ levels due to release of Ca2+ stores from the endoplasmic reticulum. SLC8A1 mediates the export of Ca2+ from the cell during the next phase, so that cytoplasmic Ca2+ levels rapidly return to baseline. It is also required for normal embryonic heart development and the ...
This archaeal enzyme differs from EC 2.7.1.26, riboflavin kinase, in using CTP as the donor nucleotide. UTP, but not ATP or GTP, can also act as a phosphate donor but it is at least an order of magnitude less efficient than CTP ...
Introduction: Archaea comes from the greek word, archaio, meaning ancient (billions of years, and if you dont call that old, then I dont know what is). In order to fully understand the origins of Archaea, we must look at evolutionary history. From what we understand, all living forms have descended from a Universal ancestor, which appeared through spontaneous generation. The term spontaneous generation is generally used to explain what Europeans before 1668 believed to be the cause of life, indicating that every day, living organisms were created by non living things (such as mud). This should not be confused with the modern theory of the origin of life, that abiotic amino acids were generated in the primordial soup and spontaneously joined together to form LUCA ...
This model describes the bacterial and organellar branch of the ribosomal protein S7 family (includes prokaroytic S7 and eukaryotic S5). The eukaryotic and archaeal branch is described by model TIGR01028 ...
Genetic information processingProtein fateProtein and peptide secretion and traffickingprotein translocase SEC61 complex gamma subunit, archaeal and eukaryotic (TIGR00327; HMM-score: 8.1) ...
Archea (or Ancient) Messene was the most fascinating place we saw, even more than the Acropolis. Its huge, there are lots of remains, especially columns. and the stadium area is simply marvellous.
CRP se određuje kada postoji sumnja na zapaljenje, kod praćenja efikasnosti terapije i kod praćenja napredovanja nekih bolesti.
TY - JOUR. T1 - The hyperthermophilic cystathionine c-synthase from the aerobic crenarchaeon Sulfolobus tokodaii. T2 - Expression, purification, crystallization and structural insights. AU - Sato, Dan. AU - Shiba, Tomoo. AU - Mizuno, Sae. AU - Kawamura, Ayaka. AU - Hanada, Shoko. AU - Yamada, Tetsuya. AU - Shinozaki, Mai. AU - Yanagitani, Masahiko. AU - Tamura, Takashi. AU - Inagaki, Kenji. AU - Harada, Shigeharu. PY - 2017. Y1 - 2017. N2 - Cystathionine γ-synthase (CGS; EC 2.5.1.48), a pyridoxal 5′-phosphate (PLP)-dependent enzyme, catalyzes the formation of cystathionine from an l-homoserine derivative and l-cysteine in the first step of the transsulfuration pathway. Recombinant CGS from the thermoacidophilic archaeon Sulfolobus tokodaii (StCGS) was overexpressed in Escherichia coli and purified to homogeneity by heat treatment followed by hydroxyapatite and gel-filtration column chromatography. The purified enzyme shows higher enzymatic activity at 353 K under basic pH conditions compared ...
43] Kouril T, Wieloch P, Reimann J, Wagner M, Zaparty M, Albers SV, Schomburg D, Ruoff P, Siebers B (2012). Unraveling the function of the two Entner-Doudoroff branches in the thermoacidophilic Crenarchaeon Sulfolobus solfataricus P2. FEBS J. 2012 Dec 24. doi: 10.1111/febs.12106. PMID:23279921. [42] Peetsch A, Greulich C, Braun D, Stroetges C, Rehage H, Siebers B, Köller M, Epple M (2012). Silver-doped calcium phosphate nanoparticles: Synthesis, characterization, and toxic effects toward mammalian and prokaryotic cells. Colloids Surf B Biointerfaces. 2013 Feb 1;102:724-9. doi: 10.1016/j.colsurfb.2012.09.040. Epub 2012 Oct 6. PMID:23107950. [41] Ulas T, Riemer SA, Zaparty M, Siebers B, Schomburg D (2012). Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One. 2012;7(8):e43401. doi: 10.1371/journal.pone.0043401. Epub 2012 Aug 31. PMID:22952675. [40] Esser D, Pham TK, Reimann J, Albers SV, Siebers B, Wright PC (2012). ...
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TY - JOUR. T1 - Influence of temperature on the production of archaeal thermoactive alcohol dehydrogenases from Pyrococcus furiosus with recombinant E. coli. AU - Kube, J.. AU - Brokamp, C.. AU - Machielsen, M.P.. AU - van der Oost, J.. AU - Markl, H.. PY - 2006. Y1 - 2006. N2 - The heterologous production of a thermoactive alcohol dehydrogenase (AdhC) from Pyrococcus furiosus in Escherichia coli was investigated. E. coli was grown in a fed-batch bioreactor in minimal medium to high cell densities (cell dry weight 76 g/l, OD600 of 150). Different cultivation strategies were applied to optimize the production of active AdhC, such as lowering the cultivation temperature from 37 to 28°C, heat shock of the culture from 37 to 42°C and from 37 to 45°C, and variation of time of induction (induction at an OD600 of 40, 80 and 120). In addition to the production of active intracellular protein, inclusion bodies were always observed. The maximal activity of 30 U/l (corresponding to 6 mg/l active ...
Project 1: Bipolar Tetraether Lipid Membranes: Physical Properties, and Technological Applications. The long-term goals of this research are to understand how the Archaea live in extreme environments and to use the Archaeal bipolar tetraether lipids for technological applications. The Archaea are curious and remarkable organisms; and, their lipids are structurally distinctly different from their bacterial and eukaryotic counterparts. The native habitat of the thermoacidophilic archaeon Sulfolobus acidocaldarius, which is the focus of this research, is hot (65-80 oC) and acidic (pH 2-3) sulfur springs. The plasma membrane of S. acidocaldarius not only serves as a barrier between the low pH extracellular environment and the neutral pH intracellular compartment (pH 6.5), but also performs proton pumping and other cellular activities at high temperatures. The ability of the plasma membrane to achieve these goals in extreme environments is not clearly understood, although there is evidence suggesting ...
The ribosome consists of small and large subunits each composed of dozens of proteins and RNA molecules. However, the functions of many of the individual protomers within the ribosome are still unknown. In this article, we describe the solution NMR structure of the ribosomal protein RP-L35Ae from the archaeon Pyrococcus furiosus. RP-L35Ae is buried within the large subunit of the ribosome and belongs to Pfam protein domain family PF01247, which is highly conserved in eukaryotes, present in a few archaeal genomes, but absent in bacteria. The protein adopts a six-stranded anti-parallel β-barrel analogous to the tRNA binding motif fold. The structure of the P. furiosus RP-L35Ae presented in this article constitutes the first structural representative from this protein domain family.
Reproduction among Haloferax volcanii occurs when two cells fuse, establish cytoplasmic bridges, and exchange genetic information, forming two daughter cells. While this practice may sound similar to the mating habits of eukaryotes, Haloferax volcanii appears to be indiscriminatory when it comes to choosing prospective reproductive partner cells. They appear to be capable of fusing with the cells of any species within the Haloferax genus; their methods of specificity are virtually unknown. Haloferax volcanii processes carbohydrates for energy. Their cell wall S-layer, like all halobacteria, is made up of a glycoprotein. And in keeping with their halophilic categorization, Haloferax volcanii cells contain proteins to allow them to maintain balance between the cell material and the hypersaline environment. ...
XPB helicase is an integral part of transcription factor TFIIH, required for both transcription initiation and nucleotide excision repair (NER). Along with the XPD helicase, XPB plays a crucial but only partly understood role in defining and extending the DNA repair bubble around lesions in NER. Archaea encode clear homologues of XPB and XPD, and structural studies of these proteins have yielded key insights relevant to the eukaryal system. Here we show that archaeal XPB functions with a structure-specific nuclease, Bax1, as a helicase-nuclease machine that unwinds and cleaves model NER substrates. DNA bubbles are extended by XPB and cleaved by Bax1 at a position equivalent to that cut by the XPG nuclease in eukaryal NER. The helicase activity of archaeal XPB is dependent on the conserved Thumb domain, which may act as the helix breaker. The N-terminal damage recognition domain of XPB is shown to be crucial for XPB-Bax1 activity and may be unique to the archaea. These findings have implications ...
Phylogenetic distribution analyses of the trm5 genes revealed that three Trm5 subfamilies exist in archaea, and they are subsequently named Trm5a, Trm5b, and Trm5c. Recently, Trm5a from the archaeon Pyrococcus abyssi (PaTrm5a) has been identified and characterized (9). PaTrm5a, but not PaTrm5b, is a unique enzyme in that it catalyzes two methyltransfer reactions on G37 for the tRNAPhe hypermodifications: In the first reaction, it transfers a methyl group to the N1 atom of G37 to produce m1G, whereas in the second reaction, it further methylates the C7 atom of imG-14 to generate imG2, an intermediate along the pathway (Fig. 1A) (12). Therefore, PaTrm5a replaces the enzyme Tyw2 in eukarya and plays double roles in the mimG biosynthesis. The structural basis of the bifunctional substrate specificity of PaTrm5a is of interest but unclear at present.. The first crystal structures of Trm5 were of the Trm5b subfamily, from the methanogenic archaeon Methanococcus jannaschii (MjTrm5b). MjTrm5b in complex ...
A new type of metal centre was detected in the membranes of the thermoacidophilic archaeon Sulfolobus metallicus. This centre has an S = 1/2 ground state in the oxidised form, yielding an axial EPR signal with g values at 2.035 (g(parallel)) and 1.97
Pyrococcus furiosus PfuCP carboxypeptidase: metallocarboxypeptidase isolated from Pyrococcus furiosus; activated by cobalt; amino acid sequence in first source
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Hyperthermophiles grow optimally at 80 ºC and above, and many of them have the ability to utilize various carbohydrates as carbon source and produce ethanol as an end product. Alcohol dehydrogenase (ADH) is a key enzyme responsible for alcohol production, catalyzing interconversions between alcohols and corresponding ketones or aldehydes. ADHs from hyperthermophiles are of great interests due to their thermostability, high activity and enantioselectivity. The gene encoding ADH from hyperthermophilic archaeon Thermococcus guaymasensis was cloned, sequenced and over-expressed. DNA fragments of the genes encoding the ADHs were amplified directly from the corresponding genomic DNA by combining the use of conventional and inverse PCRs. The entire gene was detected to be 1092 bp and the deduced amino acid sequence had a total of 364 amino acids with a calculated molecular mass of 39463 Dalton. The enzyme belonged to the family of zinc-containing ADHs with catalytic zinc only. It was verified that the ...
"RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange". Genes & Development. 12 (9): 1248-1253. ... protein C-terminus binding. • protein binding. • four-way junction DNA binding. • identical protein binding. • ... RAD51 family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51.[5][6] The protein is highly conserved ... This protein can interact with the ssDNA-binding protein RPA, BRCA2, PALB2[10] and RAD52. ...
Krupovic M, Cvirkaite-Krupovic V, Prangishvili D, Koonin EV (2015). "Evolution of an archaeal virus nucleocapsid protein from ... The TTV1 virion contains four virus-encoded proteins, TP1-4. The proteins do not display any sequence similarity to structural ... Interestingly, nucleocapsid protein TP1 has apparently evolved from a Cas4 endonuclease, a conserved component of the adaptive ... "Identification and characterization of the genes encoding three structural proteins of the Thermoproteus tenax virus TTV1". MGG ...
"Protein adaptations in archaeal extremophiles". Archaea. 2013: 373275. doi:10.1155/2013/373275. PMC 3787623. PMID 24151449.. ... Even one extra disulfide bond can raise the temperature at which the protein folds by 6 °C. These adapted proteins allow ... thermophilic proteins have adapted their proteins to cope with these conditions. They have a higher amount of cysteine amino ... that interact with each other to increase how rigid the protein is. When proteins become more rigid they are less likely to ...
... as well as the bacterial protein TubZ, the archaeal protein CetZ, and the FtsZ protein family widespread in Bacteria and ... Nearly all bacterial and archaeal cells use FtsZ to divide. It was the first prokaryotic cytoskeletal protein identified. TubZ ... Tubulin in molecular biology can refer either to the tubulin protein superfamily of globular proteins, or one of the member ... Tubulin is characterized by the evolutionarily conserved Tubulin/FtsZ family, GTPase protein domain. This GTPase protein domain ...
Another quarter encodes proteins unique to the archaeal domain. One observation about the genome is that there are many gene ... However, the possibility that the shared presence of these signature proteins in these archaeal lineages is due to lateral gene ... Additionally, 18 proteins which are uniquely found in members of Thermococci, Archaeoglobus and methanogens have been ... A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons ...
Related regions are found also in archaeal and eukaryotic proteins. They have sizes that vary considerably from 311 residues ... These proteins are capable of transporting Mg2+ and Co2+ but not Ni2+. Multiple alignments contain two highly conserved ... The transport reaction catalyzed by MgtE proteins is: Mg2+ (or Co2+) (out) → Mg2+ (or Co2+) (in) Hattori, M.; Iwase, N.; Furuya ... Kehres and Maguire suggest that the MgtE proteins are secondary carriers with inwardly directed polarity. Hattori et al. have ...
The conjugation machinery of some bacteria (and archaeal flagella) is capable of transporting both DNA and proteins. It was ... It is a simple system, which consists of only three protein subunits: the ABC protein, membrane fusion protein (MFP), and outer ... Protein digestion. Protein digestion occurs in the stomach and duodenum in which 3 main enzymes, pepsin secreted by the stomach ... It serves primarily as a site for acid hydrolysis of microbial and dietary protein, preparing these protein sources for further ...
The table "40S ribosomal proteins" crossreferences the human ribosomal protein names with yeast, bacterial and archaeal ... 40S ribosomal proteins[edit]. The table "40S ribosomal proteins" shows the individual protein folds of the 40S subunit colored ... Proteins shared only between eukaryotes and archaea are shown as orange ribbons and proteins specific to eukaryotes are shown ... Proteins which have homologs in eukaryotes, archaea and bacteria (EAB) are shown as blue ribbons. Proteins shared only between ...
Gurha, P.; Gupta, R. (2008). "Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA". RNA. 14: 2521-2527. ... of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain ... ". Protein Sci. 14: 2201-2206. doi:10.1110/ps.051493605. PMC 2279332 . PMID 15987897. ...
The bacterial and archaeal proteins are in general smaller than the eukaryotic proteins. They have been suggested to traverse ... Two clusters consist exclusively of animal proteins, a third contains several bacterial and archaeal proteins, a fourth ... and prevents protein unfolding. All of the characterized animal proteins catalyze Ca2+:Na+ exchange although some also ... TMS 7 may be close to TMSs 2 and 3 in the 3-D structure of the protein. The Na+:Ca2+ exchanger plays a central role in cardiac ...
The larger eukaryotic and archaeal proteins possess N- and C-terminal hydrophilic extensions. Some animal proteins, for example ... The smaller proteins are generally of prokaryotic origin while the larger ones are of eukaryotic origin. Most of them possess ... They are members of the rBAT family of mammalian proteins (TC #8.A.9). Two APC family members, LAT1 and LAT2 (TC #2.A.3.8.7), ... Subfamilies of the APC family, and the proteins in these families, can be found in the Transporter Classification Database: 2.A ...
... the archaeal LSm proteins are more similar to the eukaryote LSm proteins than either are to bacterial LSm proteins. The LSm ... The three archaeal LSm proteins (Sm1, Sm2 and Sm3) also cluster as a group, distinct from the eukaryote LSm proteins. Both the ... and consisted of seven proteins clearly homologous to the Sm proteins. These proteins were denoted LSm (like Sm) proteins (LSm1 ... Other proteins with very similar structures were subsequently discovered and named LSm proteins. New members of the LSm protein ...
Guo FB, Ou HY, Zhang CT (2003). "ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes". ... Zhang R, Zhang CT (2005). "Identification of replication origins in archaeal genomes based on the Z-curve method". Archaea. 1 ( ... such as in locating replication origins of bacterial and archaeal genomes. Similar methods of visually representing genomic ...
"A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters". Nucleic Acids Res. 34 (17): 4837-4845 ... Protein SvtR was the first crenarchaeal RHH regulator characterized in details and also the first viral coded transcriptional ... regulators within the Archaeal domain. It strongly represses the transcription of the minor structural protein and, to a lesser ... In contrast, at least 10% of its genes were predicted to have of different DNA binding motifs in the proteins they code and ...
"Activation of archaeal transcription by recruitment of the TATA-binding protein". Proc. Natl. Acad. Sci. U.S.A. 100 (9): 5097- ... Protein interference is the process where in some signaling protein interacts, either with the promoter or with some stage of ... It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. RNA ... In humans RNAP II consists of seventeen protein molecules (gene products encoded by POLR2A-L, where the proteins synthesized ...
O'Connor EM, Shand RF (2002). "Halocins and sulfolobicins: the emerging story of archaeal protein and peptide antibiotics". J. ... 1997). ""Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and ... "Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group ... Lipps, G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends (en inglés). Caister Academic Press. ISBN ...
Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack ... Archaeal histones may well resemble the evolutionary precursors to eukaryotic histones.[12] Histone proteins are among the most ... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ... Nuclear protein Ataxia-Telangiectasia (NPAT), also known as nuclear protein coactivator of histone transcription, is a ...
ISBN 978-1-904455-27-1. O'Connor EM; Shand RF (2002). "Halocins and sulfolobicins: the emerging story of archaeal protein and ... It is a 31 kDa protein that is heat-labile, loses activity when desalted, and exhibits a broad range of inhibition within the ... Production of these archaeal proteinaceous antimicrobials is a nearly universal feature of the rod-shaped haloarchaea. The ... The molecular mass of the mature HalH4 protein is 34.9 kDa (359 amino acids), processed from a preprotein of 39.6 kDa; the ...
O'Connor EM, Shand RF (2002). "Halocins and sulfolobicins: the emerging story of archaeal protein and peptide antibiotics". ... "Protein-protein interaction between halocin H7 and halobacterial membrane protein". Nippon Yakugakkai Nenkai Koen Yoshishu. 121 ... Some are large proteins, some small polypeptides (microhalocins). This diversity is surprising for a number of reasons, ... Rdest U, Sturm M (1987). "Bacteriocins from halobacteria". In Burgess R. Protein Purification: Micro to Macro. New York, New ...
Rather than originating from archaeal histones, it probably evolved from a bacterial protein. Unlike core histones featuring a ... Individual H1 proteins are often referred to as isoforms or variants. The discovery of H1 variants in calf thymus preceded the ... The linker histone H1 is a protein family forming a critical component of eukaryotic chromatin. H1 histones bind to the linker ... At the same time H1 orthologs among mammals are highly conserved across the whole protein sequence, for example human and mouse ...
"Affinity transfer to the archaeal extremophilic Sac7d protein by insertion of a CDR". Protein Engineering Design and Selection ... By randomizing the amino acids on the binding surface of Sac7d and subjecting the resulting protein library to rounds of ... 27 (10): 431-8. doi:10.1093/protein/gzu042. PMID 25301962. Mouratou, B; Schaeffer, F; Guilvout, I; Tello-Manigne, D; Pugsley, ... Krehenbrink, M; Chami, M; Guilvout, I; Alzari, PM; Pécorari, F; Pugsley, AP (2008). "Artificial binding proteins (Affitins) as ...
Haseltine CA, Kowalczykowski SC (May 2009). "An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA ... RecA protein binds to this strand and is either aided by the RecF, RecO, and RecR proteins or stabilized by them. The RecA ... The proteins of the RecA recombinase family of proteins are thought to be descended from a common ancestral recombinase. The ... The proteins generally share a long conserved region known as the RecA/Rad51 domain. Within this protein domain are two ...
Hall TA, Brown JW (2002). "Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins". ... Five of these protein subunits exhibit homology to archaeal counterparts. These protein subunits of RNase P are shared with ... The structures of protein subunits of archaeal RNase P have been resolved by x-ray crystallography and NMR, thus revealing new ... Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the eubacterial ones, the RNA cores ...
... s in nuclear and archaeal transfer RNA genes that are removed by proteins (tRNA introns) ... including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron- ... Group I and group II introns are found in genes encoding proteins (messenger RNA), transfer RNA and ribosomal RNA in a very ... Introns were first discovered in protein-coding genes of adenovirus,[4][5] and were subsequently identified in genes encoding ...
Archaeosortase A recognizes the signal PGF-CTERM, found at the C-terminus of some archaeal S-layer proteins. Haft, DH; Paulsen ... Exosortase refers to a family of integral membrane proteins that occur in Gram-negative bacteria and that recognize and cleave ... IT; Ward, N; Selengut, JD (2006). "Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH ...
Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA ... Orsay virus utilizes ribosomal frameshifting to express a novel protein that is incorporated into virions, in: Virology 450-451 ...
Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. Structure. 2011 May 11;19(5):622-632. ... Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. In: Structure. 2011 ; Vol. 19, No. 5. pp ... Structure and activity of a novel archaeal β-CASP protein with N-terminal KH domains. / Silva, Ana P G; Chechik, Maria; Byrne, ... We hypothesize that this nuclease degrades mRNAs of proteins targeted for degradation and so regulates archaeal RNA turnover, ...
Archaeal Proteins/genetics. MESH. Cell Adhesion. MESH. Cell Surface Extensions/physiology. MESH. ... The first detailed characterization of archaeal fimbriae, namely those of Methanothermobacter thermoautotrophicus, allowed us ...
... Christopher J. Reed,1 Hunter Lewis,1 Eric Trejo,1,2 Vern Winston,2 and Caryn ... Christopher J. Reed, Hunter Lewis, Eric Trejo, Vern Winston, and Caryn Evilia, "Protein Adaptations in Archaeal Extremophiles ...
By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins ... Protein Adaptations in Archaeal Extremophiles. Christopher J. Reed,1 Hunter Lewis,1 Eric Trejo,1,2 Vern Winston,2 and Caryn ... Psychrophilic proteins have a reduced hydrophobic core and a less charged protein surface to maintain flexibility and activity ... Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and ...
By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins ... Another way proteins can cope with pressure is to form multimeric proteins. The piezophlic protein, TET3 peptidase (TET3) from ... "Archaeal cold-adapted proteins: structural and evolutionary analysis of the elongation factor 2 proteins from psychrophilic, ... Protein Adaptations in Archaeal Extremophiles. Christopher J. Reed,1 Hunter Lewis,1 Eric Trejo,1,2 Vern Winston,2 and Caryn ...
... proteins for archaeal adaptation. This alignment was constructed from a larger alignment, which used 3 examples of each protein ... Protein Adaptations in Archaeal Extremophiles. Christopher J. Reed,1 Hunter Lewis,1 Eric Trejo,1,2 Vern Winston,2 and Caryn ... Supplementary Figure: Protein sequence alignment for the archaeal cysteinyl-tRNA synthetases. The sequences represented above ...
... Christopher J. Reed,1 Hunter Lewis,1 Eric Trejo,1,2 Vern Winston,2 and Caryn ... "Archaeal cold-adapted proteins: structural and evolutionary analysis of the elongation factor 2 proteins from psychrophilic, ... Z. S. Hendsch and B. Tidor, "Do salt bridges stabilize proteins? A continuum electrostatic analysis," Protein Science, vol. 3, ... G. Zhang and H. Ge, "Protein hypersaline adaptation: insight from amino acids with machine learning algorithms," The Protein ...
Crystallographic analysis of archaeal ribosomal protein L11.. Mitroshin I1, Garber M1, Gabdulkhakov A1. ... Crystallographic analysis of archaeal ribosomal protein L11. Acta Crystallogr F Struct Biol Commun. 2015 Aug 1;71(Pt 8):1083- ... Crystallographic analysis of archaeal ribosomal protein L11. Acta Crystallogr F Struct Biol Commun. 2015 Aug 1;71(Pt 8):1083- ... Crystallographic analysis of archaeal ribosomal protein L11. Acta Crystallogr F Struct Biol Commun. 2015 Aug 1;71(Pt 8):1083- ...
Archaeal promoters consist of an A+T-rich TATA-like element recognized by archaeal TATA-binding protein (TBP); the TFIIB- ... Activation of archaeal transcription by recruitment of the TATA-binding protein. Mohamed Ouhammouch, Robert E. Dewhurst, ... Activation of archaeal transcription by recruitment of the TATA-binding protein. Mohamed Ouhammouch, Robert E. Dewhurst, ... Activation of archaeal transcription by recruitment of the TATA-binding protein Message Subject (Your Name) has sent you a ...
Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. Using the ... Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form ... Nutrient transport suggests an evolutionary basis for charged archaeal surface layer proteins. *Po-Nan Li ORCID: orcid.org/0000 ... a Amino-acid sequence identity matrix for putative S-layer proteins from all known archaeal clades. Color codes indicate the % ...
4). These proteins may belong to a transmembrane protein similar to P16 in PRD1. Minor capsid proteins surrounding the base of ... Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Reza Khayat, Liang ... Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses ... Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses ...
A eukaryotic protein, NOP-1, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment.. Bieszke JA1, ... obtaining a relatively high yield of 2.2 mg of NOP-1 protein/L of cell culture. The expressed protein is membrane-associated ... The nop-1 gene from Neurospora crassa is predicted to encode a seven-helix protein exhibiting conservation with the rhodopsins ... The results demonstrate a photochemically reactive member of the archaeal rhodopsin family in a eukaryotic cell. ...
... but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on ... All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The ... Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the ... Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. ...
Stabilization of an archaeal DNA-sliding clamp protein, PCNA, by proteasome-activating nucleotidase gene knockout in Haloferax ... Kirkland, P. A. and Maupin-Furlow, J. A. (2009), Stabilization of an archaeal DNA-sliding clamp protein, PCNA, by proteasome- ... Baumann A, Lange C & Soppa J (2007) Transcriptome changes and cAMP oscillations in an archaeal cell cycle. BMC Cell Biol 8: 21 ... 2006) Tyrosine phosphorylation controls PCNA function through protein stability. Nat Cell Biol 8: 1359-1368. ...
As co-chaperones of Hsp90 (heat-shock protein 90), FKBP51 (FK506-binding protein of 51 kDa) and FKBP52 (FK506-binding protein ... The article presents hydration studies on the archaeal protein Sso7d using nuclear magnetic resonance (NMR) measurements and ... Home » Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations ... Sti1/Hop is a modular protein required for the transfer of client proteins from the Hsp70 to the Hsp90 chaperone system in ...
Protein-protein interactions in the archaeal core replisome. Stuart A. MacNeill. Biochemical Society Transactions Jan 19, 2011 ... Protein-protein interactions in the archaeal core replisome Message Subject (Your Name) has forwarded a page to you from ... Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity ... PCNA-interacting protein; PolB, DNA polymerase B; PolD, DNA polymerase D; RFC, replication factor C; RPA, replication protein A ...
PROSITE; a protein domain and family database. More...PROSITEi. View protein in PROSITE. PS50011. PROTEIN_KINASE_DOM. 1 hit. ... PROSITE; a protein domain and family database. More...PROSITEi. View protein in PROSITE. PS50011. PROTEIN_KINASE_DOM. 1 hit. ... Protein. Similar proteins. Organisms. Length. Cluster ID. Cluster name. Size. Q4JA53. C3NM99. C3MK59. C3N8M8. F0NJ35. F0NBB9. ... Protein. Similar proteins. Organisms. Length. Cluster ID. Cluster name. Size. Q4JA53. V9S894. A0A0U2Y7G8. M1J121. M1I3Y8. ...
... a DNA-binding protein acquired from bacteria via horizontal gene transfer mediates histone-like chromatin architecture. ... Protein purity was confirmed both by denaturing protein gel electrophoresis and by mass-spectrometry. Protein concentration was ... The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog. ... a) Predicted secondary structures of HTa (T. acidophilum), the bacterial HU protein HupA (E. coli), and the archaeal histone ...
We reveal that an archaeal Sir2 homolog interacts specifically with the major archaeal chromatin protein, Alba, and that Alba ... The Interaction of Alba, a Conserved Archaeal Chromatin Protein, with Sir2 and Its Regulation by Acetylation ... The Interaction of Alba, a Conserved Archaeal Chromatin Protein, with Sir2 and Its Regulation by Acetylation ... The Interaction of Alba, a Conserved Archaeal Chromatin Protein, with Sir2 and Its Regulation by Acetylation ...
Functional characterization of archaeal homologs of human nuclear ribonuclease P proteins Rpp21 and Rpp29Functional ... characterization of archaeal homologs of human nuclear ribonuclease P proteins Rpp21 and Rpp29. ヒト核リボヌクレアーゼP構成タンパク質Rpp21とRpp29の ...
A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral ... A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral ... A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral ... A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral ...
Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins. Isabelle ... Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins ... Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins ... Characterization of an archaeal family 4 uracil DNA glycosylase and its interaction with PCNA and chromatin proteins ...
Study of archaeal surface-layer (glyco)proteins has thus offered insight into the strategies employed by these proteins to ... The protein-based surface layer that envelopes many archaeal strains must thus correctly assemble and maintain its structural ... In this mini-review, recent advances in the study of archaeal surface-layer (glyco)proteins are discussed. ... yet has also served to elucidate other aspects of archaeal protein biosynthesis, including glycosylation, lipid modification ...
Although genome analyses have suggested parallels between archaeal and eukaryotic replication systems, little is known about ... In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin Proc Natl Acad ... Our data suggest that archaeal and eukaryotic Cdc6 and MCM proteins function similarly in replication initiation and imply that ... Cdc6 protein stayed bound to the replication origin after de novo protein synthesis was inhibited. ...
3D-structural models of archaeal THI4 family proteins compared to the X-ray structure ofNeurospora crassa(Nc) THI4p (PDB: 3JSK ... Fig2: 3D-structural models of archaeal THI4 family proteins compared to the X-ray structure ofNeurospora crassa(Nc) THI4p (PDB ... Fig2: 3D-structural models of archaeal THI4 family proteins compared to the X-ray structure ofNeurospora crassa(Nc) THI4p (PDB ... Thus, archaeal members of IPR002922 THI4 family that have a conserved cysteine active site should be reexamined for a function ...
  • A eukaryotic protein, NOP-1, binds retinal to form an archaeal rhodopsin-like photochemically reactive pigment. (nih.gov)
  • HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. (elifesciences.org)
  • Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. (cnrs-orleans.fr)
  • We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. (pasteur.fr)
  • Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. (pasteur.fr)
  • Leucine-rich repeat kinase 2 binds to neuronal vesicles through protein interactions mediated by its C-terminal WD40 domain. (nih.gov)
  • Tau is a brain microtubule-associated protein that directly binds to a microtubule and dynamically regulates its structure and function. (mdpi.com)
  • The mRNA binds in the cleft between the head and the body, and there are three binding sites for tRNA , the A-site, P-site and E-site (see article on protein translation for details). (wikipedia.org)
  • The singular archaeal ORC protein recognizes the AT-rich tracts and binds DNA in an ATP-dependent fashion. (wikipedia.org)
  • A structure of amino acids 675-790 of FANCM reveal how the protein binds duplex DNA through a remodeling of the MHF1:MHF2 histone-like protein complex. (wikipedia.org)
  • FetP binds Cu2+ and Mn2+ at two different sites, 1.3 Å apart, in this homodimeric protein. (wikipedia.org)
  • Individual LSm proteins assemble into a six or seven member doughnut ring (more properly termed a torus), which usually binds to a small RNA molecule to form a ribonucleoprotein complex. (wikipedia.org)
  • The RecA protein binds strongly and in long clusters to ssDNA to form a nucleoprotein filament. (wikipedia.org)
  • As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. (wikipedia.org)
  • Importers require a Solute Binding Protein (SBP) that recognizes and binds the substrate. (wikipedia.org)
  • In order to solve such a problem, phage viruses synthesize another protein called holin which binds to the cell membrane and makes holes in it (hence its name), allowing lysins to reach the peptidoglycan matrix. (wikipedia.org)
  • We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and to detect cases of functional diversification between orthologous proteins. (duhnnae.com)
  • However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation that is consistent with an acceleration of the rate of amino-acid substitution, which may be due to functional diversification. (duhnnae.com)
  • Thus, two chaperoning systems that are designed to interact with a compatible partner, e.g. , the bacterial chaperone machine physiologically interacts with the bacterial but not with the eucaryal chaperonins, coexist in archaeal cells in spite of their apparent functional incompatibility. (genetics.org)
  • Surface layer proteins efficiently crystallize to continuously coat the cell, and this trait has been utilized to design functional macromolecular nanomaterials. (pnas.org)
  • His team is currently exploring the role of structure and organization in the coevolution of proteins and functional RNA (e.g., ribosomal and transfer RNA), including the origin and history of translation and the genetic code. (wikipedia.org)
  • Phylogenomic analysis of RNA and protein molecules that make up the massive ribosomal ensemble shows that the most ancient ribosomal RNA structure interacted with the most ancient ribosomal protein and that this triggered a coordinated accretion process that ultimately resulted in a functional ribosomal core, half-way in evolution of life and prior to cellular diversification. (wikipedia.org)
  • This novel tRNA-aaRS pair ("orthogonal pair") is independent of other synthetases and tRNAs in Escherichia coli, and further possesses some flexibility in the range of amino acids processed, making it an attractive tool to allow the placement of a possibly wide range of functional chemical groups at arbitrarily specified locations in modified proteins. (wikipedia.org)
  • Functional annotation is provided to proteins from multiple resources. (wikipedia.org)
  • These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (human-curated molecular function and biological process classifications and pathway diagrams), as well as inference of amino acids important for functional specificity. (wikipedia.org)
  • The IIa sodium phosphate symporter isoform is a functional monomer, but it interacts with PDZ proteins which probably mediate apical sorting, parathyroid hormone-controlled endocytosis and/or lysosomal sorting of internalized transporters. (wikipedia.org)
  • In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [ PMID: 11290319 , PMID: 11114498 ]. (ebi.ac.uk)
  • The crystal structure of the Alba protein (PhoAlba) from a hyperthermophilic archaeon, Pyrococcus horikoshii OT3, was determined at a resolution of 2.8 Å. (elsevier.com)
  • All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. (mdpi.com)
  • Understanding the assembly pathway and creating an interaction map of the molecular players in the archaeal flagellum will shed light on the details of the assembly and also the evolutionary relationship to the bacterial type IV pili-assembly systems. (nih.gov)
  • BackgroundDetection of changes in a protein-s evolutionary rate may reveal cases of change in that protein-s function. (duhnnae.com)
  • Here, we provide an updated analysis of the evolutionary relationships between CRISPR-Cas systems and Cas proteins. (nih.gov)
  • We demonstrate that a specific domain is responsible for enhancing the rate of self-assembly, unveiling possible evolutionary mechanisms to enhance the kinetics of 2D protein crystallization. (pnas.org)
  • Analysis of the evolutionary intermediates shows that negative mutations are effectively removed while beneficial mutations accumulate and illustrates how a protein has evolved over the course of the evolution experiments. (pnas.org)
  • His insightful mind is responsible for the discovery of the archaeal domain and for transforming comparative views of microbial diversity into an overarching evolutionary framework. (hindawi.com)
  • While it is becoming clear that the archaeal domain may have an independent evolutionary history, its origin and links to the other two domains of cellular complexity remain contentious, as well as its placement in the tree of life. (hindawi.com)
  • Evolutionary relationships among proteins probed by an iterative neighborhood cluster analysis (INCA). (wikipedia.org)
  • PIRSF protein classification system is a network with multiple levels of sequence diversity from superfamilies to subfamilies that reflects the evolutionary relationship of full-length proteins and domains. (wikipedia.org)
  • Archaeal cell surface proteins undergo a variety of post-translational modifications. (duhnnae.com)
  • γ-Secretase was originally defined by its role in APP processing, but deeper study revealed it to be an enzymatic "hub" that processes scores of different cell surface proteins ( 4 , 5 ). (pnas.org)
  • The S-layer is made of a cell-surface glycoprotein, which accounts for approximately 50% of the cell surface proteins. (wikipedia.org)
  • By understanding the protein adaptations used by archaeal extremophiles, we hope to be able to engineer and utilize proteins for industrial, environmental, and biotechnological applications where function in extreme conditions is required for activity. (hindawi.com)
  • E. T. Powers and W. E. Balch, "Diversity in the origins of proteostasis networks-a driver for protein function in evolution," Nature Reviews Molecular Cell Biology , vol. 14, no. 4, pp. 237-248, 2013. (hindawi.com)
  • Taken together, our results offer important insights into archaeal SSB function and establish the haloarchaea as a valuable model for further studies. (st-andrews.ac.uk)
  • This entry contains archaeal and bacterial proteins of unknown function. (ebi.ac.uk)
  • The data suggest that the MA1715 protein is particularly important to sustaining robust physiological function when ambient sulfide concentrations are low. (asm.org)
  • Interestingly, nucleocapsid protein TP1 has apparently evolved from a Cas4 endonuclease, a conserved component of the adaptive CRISPR-Cas immunity, presenting the first described case of exaptation of an enzyme for a virus capsid protein function. (wikipedia.org)
  • Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. (wikipedia.org)
  • In cystinotic renal proximal tubules (RPTs), diminished cystinosin function appears to result in reduced reabsorption of solutes by other secondary transporters such as the Na+/Phosphate cotransporter, due to decreased expression of these other transport proteins. (wikipedia.org)
  • The FA core complex is composed of eight proteins (FANCA, -B, -C, -E, -F, -G, -L and -M). FANCF stabilizes the interaction between the FANCC/FANCE subcomplex and the FANCA/FANCG subcomplex and locks the whole FA core complex in a conformation that is essential to perform its function in DNA repair. (wikipedia.org)
  • All these proteins function together to facilitate DNA interstrand cross-link repair. (wikipedia.org)
  • TC# 2.A.20.2.7) have been reported to function as viral receptors, but they undoubtedly function as transport proteins as well. (wikipedia.org)
  • Several proteins in the exosome are the target of autoantibodies in patients with specific autoimmune diseases (especially the PM/Scl overlap syndrome) and some antimetabolic chemotherapies for cancer function by blocking the activity of the exosome. (wikipedia.org)
  • The repeat has been found in proteins of diverse function such as transcriptional initiators, cell cycle regulators, cytoskeletal, ion transporters, and signal transducers. (wikipedia.org)
  • The association of sensory rhodopsins with their transducer proteins appears to determine whether they function as transporters or receptors. (wikipedia.org)
  • In a further essay on the function of the RecA protein, Cox summarized data demonstrating that "RecA protein evolved as the central component of a recombinational DNA repair system, with the generation of genetic diversity as a sometimes useful byproduct. (wikipedia.org)
  • A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. (wikipedia.org)
  • In a multidomain protein, each domain may fulfill its own function independently, or in a concerted manner with its neighbours. (wikipedia.org)
  • 1997). CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in E. coli (Spiers and Bergquist, 1992). (wikipedia.org)
  • In molecular biology, YqeY is a type of protein domain of unknown function. (wikipedia.org)
  • In eukarya however, prefoldins have acquired a more specific function: they are used to establish correct tubular assembly for many tubular proteins, such as actin. (wikipedia.org)
  • Chaperonins undergo large conformational changes during a folding reaction as a function of the enzymatic hydrolysis of ATP as well as binding of substrate proteins and cochaperonins, such as GroES. (wikipedia.org)
  • The C-terminal end of Channelrhodopsin-2 extends into the intracellular space and can be replaced by fluorescent proteins without affecting channel function. (wikipedia.org)
  • Halophilic proteins are characterized by increased negative surface charge due to increased acidic amino acid content and peptide insertions, which compensates for the extreme ionic conditions. (hindawi.com)
  • In contrast, the larger halocin proteins are heat-labile and typically obligately halophilic as they lose their activity (or activity is reduced) when desalted. (wikipedia.org)
  • For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments, and in the human receptor SorCS2. (wikipedia.org)
  • Here, we describe an efficient strategy for heterologous production of membrane transport proteins in E. coli. (univ-grenoble-alpes.fr)
  • Bioassay for the detection of Cby synthesized in vitro by cell-free extract of E. coli cells overproducing CbiZ protein. (nih.gov)
  • Opnå en forståelse hvordan phosphonat kan udnyttes som kilde til phosphat via carbon-phosphorus lyase-pathway'en i E. coli. (au.dk)
  • The E. coli ChaA (TC# 2.A.19.1.1) protein catalyzes Ca2+:H+ antiport but may also catalyze Na+:H+ antiport slowly. (wikipedia.org)