Proteins found in any species of archaeon.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
The small subunit of archaeal RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 28 different RIBOSOMAL PROTEINS.
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.
Deoxyribonucleic acid that makes up the genetic material of archaea.
The functional genetic units of ARCHAEA.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
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.
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.
Viruses whose hosts are in the domain ARCHAEA.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.
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.
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)
A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.
Structures within the nucleus of archaeal cells consisting of or containing DNA, which carry genetic information essential to the cell.
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.
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.
A species of halophilic archaea found in the Dead Sea.
A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.
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.
A species of gram-negative hyperthermophilic ARCHAEA found in deep ocean hydrothermal vents. It is an obligate anaerobe and obligate chemoorganotroph.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
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.
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.
Anaerobic hyperthermophilic species of ARCHAEA, isolated from hydrothermal fluid samples. It is obligately heterotrophic with coccoid cells that require TRYPTOPHAN for growth.
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 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.
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.
A class of enzymes that catalyze the conversion of a nucleotide and water to a nucleoside and orthophosphate. EC 3.1.3.-.
A species of halophilic archaea found in the Mediterranean Sea. It produces bacteriocins active against a range of other halobacteria.
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.
Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
The protein components that constitute the common core of small nuclear ribonucleoprotein particles. These proteins are commonly referred as Sm nuclear antigens due to their antigenic nature.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
The portion of an interactive computer program that issues messages to and receives commands from a user.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
An enzyme that catalyzes the HYDROLYSIS of the N-glycosidic bond between sugar phosphate backbone and URACIL residue during DNA synthesis.
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.
A class of enzymes involved in the hydrolysis of the N-glycosidic bond of nitrogen-linked sugars.
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.
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.
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.
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).
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.
Proteins conjugated with deoxyribonucleic acids (DNA) or specific DNA.

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-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 radA genes from ...
Archaeal enzymes have great potential for industrial use; however, expressing them in their natural hosts has proven challenging. Growth conditions for many archaea are beyond typical fermentation capabilities, and to compound the problem, archaea generally achieve much lower biomass yields than Esc …
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 ...
Immunoglobulin alignments in Sulfolobus tokodaii str. 7. Alignments can be refined by adding alignments from other genomes, adding your own sequences and/or aligning to other models from the same superfamily. The display of alignments can also be customised.
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 ...
In publishing the research results obtained by use of the BIOLOGICAL RESOURCE, the USER is expected to cite the literature specified by the DEPOSITOR ...
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.
ID THKOD1_1_PE557 STANDARD; PRT; 356 AA. AC THKOD1_1_PE557; Q5JF43; DT 00-JAN-0000 (Rel. 1, Created) DT 00-JAN-0000 (Rel. 2, Last sequence update) DT 00-JAN-0000 (Rel. 3, Last annotation update) DE SubName: Full=Translation initiation factor eIF-2B, beta subunit; DE (THKOD1_1.PE557). GN OrderedLocusNames=TK0556; OS THERMOCOCCUS KODAKARENSIS KOD1. OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; OC Thermococcus. OX NCBI_TaxID=69014; RN [0] RP -.; RG -.; RL -.; CC -!- SEQ. DATA ORIGIN: Translated from the HOGENOM CDS THKOD1_1.PE557. CC Thermococcus kodakarensis KOD1, complete genome. CC genome. CC -!- ANNOTATIONS ORIGIN:Q5JF43_PYRKO CC -!- SIMILARITY: Belongs to the eIF-2B alpha/beta/delta subunits CC family. CC -!- GENE_FAMILY: HOG000224730 [ FAMILY / ALN / TREE ] DR UniProtKB/Swiss-Prot; Q5JF43; -. DR EMBL; AP006878; BAD84745.1; -; Genomic_DNA. DR RefSeq; YP_182969.1; NC_006624.1. DR ProteinModelPortal; Q5JF43; -. DR EnsemblBacteria; EBPYRT00000006558; EBPYRP00000006339; ...
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
ID THEAC_1_PE790 STANDARD; PRT; 352 AA. AC THEAC_1_PE790; DT 00-JAN-0000 (Rel. 1, Created) DT 00-JAN-0000 (Rel. 2, Last sequence update) DT 00-JAN-0000 (Rel. 3, Last annotation update) DE (THEAC_1.PE790). OS THERMOPLASMA ACIDOPHILUM DSM 1728. OC Archaea; Euryarchaeota; Thermoplasmata; Thermoplasmatales; OC Thermoplasmataceae; Thermoplasma. OX NCBI_TaxID=273075; RN [0] RP -.; RG -.; RL -.; CC -!- SEQ. DATA ORIGIN: Translated from the HOGENOM CDS THEAC_1.PE790. CC Thermoplasma acidophilum DSM 1728 chromosome, complete genome. CC genome. CC -!- GENE_FAMILY: HOG000025142 [ FAMILY / ALN / TREE ] DR HOGENOMDNA; THEAC_1.PE790; -. SQ SEQUENCE 352 AA; UNKNOWN MW; UNKNOWN CRC64; MNLIDELSEY RDRGSLAYFA SFPDRISGYE YAFLGDGMIT DPERIFDGKL RPLIVTYDFV NSVFGQKVRR SGWPEMVSFD PDTVMKRRIV RSGYLTRKEV GDFSDPDLSR KIAEVRDLIR SGEVLQAVIS RDFEACIDPW EKLREFIDHD RSRYVFYYRI GKYQVVGSSP ENLVTVSGNE VFTDPIAGTV PSTVRSSVLL ESMKDANEHR MLLDLARNDL SKFADIGTLG VSKVMQIEEF SSVKHLVSQV RASFSNTPYL DILKSMFPAG TVSGSPKERA IEIIEKYEET PRGPYGGSIG ...
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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Mae testun y dudalen ar gael dan drwydded Creative Commons Attribution-ShareAlike; gall fod telerau ychwanegol perthnasol. Gweler Telerau Defnyddior Drwydded am fanylion pellach ...
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. ...
Bell SD (2012). "Archaeal orc1/cdc6 proteins". Sub-Cellular Biochemistry. Subcellular Biochemistry. 62: 59-69. doi:10.1007/978- ... Lastly, the C domain is necessary for facilitating protein-protein interactions. ARSs are found distributed across 16 ... In bacteria, the protein DnaA is the replication initiator. It gets loaded onto oriC at a DnaA box sequence where binds and ... DNA unwinding element proteins (DUE-Bs) are found in eukaryotes. They act to initiate strand separation by binding to DUE. DUE- ...
Bell SD (2012). "Archaeal orc1/cdc6 proteins". The Eukaryotic Replisome: A Guide to Protein Structure and Function. Subcellular ... Kasiviswanathan R, Shin JH, Kelman Z (2005). "Interactions between the archaeal Cdc6 and MCM proteins modulate their ... February 2013). "Specificity and function of archaeal DNA replication initiator proteins". Cell Reports. 3 (2): 485-96. doi: ... Although the evolutionary kinship of archaeal and eukaryotic initiators and replicative helicases indicates that archaeal MCM ...
Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. Eukaryotic and archaeal 7S RNAs ... The Archaeal SRP contains proteins SRP54 and SRP19. In eukaryotes, the SRP RNA combines with the imported SRP proteins SRP9/14 ... The ribosome resumes protein synthesis, but now the protein is moving through the SRP-receptor transmembrane pore. In this way ... I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein". The Journal of Cell ...
... as well as the bacterial protein TubZ, the archaeal protein CetZ, and the FtsZ protein family widespread in Bacteria and ... March 2015). "CetZ tubulin-like proteins control archaeal cell shape". Nature. 519 (7543): 362-5. Bibcode:2015Natur.519..362D. ... 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 ...
Reed, Christopher J.; Lewis, Hunter; Trejo, Eric; Winston, Vern; Evilia, Caryn (2013). "Protein Adaptations in Archaeal ... The genome of N. magadii consists of four replicons with a total sequence of 4,443,643 bp and encodes 4,212 putative proteins. ... Those harsh conditions resulted in changed composition of charged amino acids in the proteins (average isoelectric point is ... Additionally, proton-driven ATP synthase and a variety of putative cytochromes and other proteins required for aerobic ...
Reed CJ, Lewis H, Trejo E, Winston V, Evilia C (2013). "Protein adaptations in archaeal extremophiles". Archaea. 2013: 373275. ... Some acidophilic microorganisms are effective at metal remediation in acidic environments due to proteins found in their ... Chi, A. (2007). "Periplasmic proteins of the extremophile Acidithiobacillus ferrooxidans: a high throughput proteomics analysis ... affecting their protein folding ability under particular conditions. Studying extreme environments on Earth can help ...
"Protein Adaptations in Archaeal Extremophiles". Archaea. 2013: 14. doi:10.1155/2013/373275. PMC 3787623. PMID 24151449. Wong, ... and proteins (i.e. casein) as a carbon source which are oxidized to carbon dioxide via sulphur respiration. T. celer is unable ... Kam-Bo; Bycroft, Mark; Wong, Kam-Bo (March 18, 2003). "Crystal structure of ribosomal protein L30e from the extreme thermophile ... "Effects of Charge-to-Alanine Substitutions on the Stability of Ribosomal Protein L30e from Thermococcus celer". Biochemistry. ...
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 ...
Wardleworth BN, Russell RJ, Bell SD, Taylor GL, White MF (September 2002). "Structure of Alba: an archaeal chromatin protein ... Cerchia, Laura (7 August 1999). "An archaeal chaperonin-based reactor for renaturation of denatured proteins. Extremophile". ... One-third of S. solfataricus encoded proteins have no homologs in other genomes. For the remaining encoded proteins, 40% are ... Sulfolobus strains present different peculiar DNA binding proteins, such as the Sso7d protein family. They stabilize the double ...
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 N, ... Kehres and Maguire suggest that the MgtE proteins are secondary carriers with inwardly directed polarity. Hattori et al. have ...
Gurha P, Gupta R (December 2008). "Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA". RNA. 14 (12): ... of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain ... ". Protein Science. 14 (8): 2201-6. doi:10.1110/ps.051493605. PMC 2279332. PMID 15987897. ...
She is the maintainer of a database of archaeal proteins and their relations. McKay, Kathryn (January 8, 2018), "Focus on NLM ... Makarova's ongoing research involves comparative genomics, and the genetics and protein functions of archaea. ... the use of oligopeptide frequency data to classify proteins. When Makarova's husband moved to the US to work with Eugene Koonin ...
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 ...
"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 ...
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 ( ...
"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[ ... In humans, RNAP II consists of seventeen protein molecules (gene products encoded by POLR2A-L, where the proteins synthesized ...
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 (ed.). Protein Purification: Micro to Macro. New York, ...
"FlaF Is a β-Sandwich Protein that Anchors the Archaellum in the Archaeal Cell Envelope by Binding the S-Layer Protein". ... "Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases". ... In archaeal biofilms, the only proposed function is thus far during the dispersal phase of biofilm when archaeal cells escape ... "Type II protein secretion and its relationship to bacterial type IV pili and archaeal flagella". Microbiology. 149 (Pt 11): ...
Archaeal and eukaryote primases are heterodimeric proteins with one large regulatory and one small catalytic subunit. The RNA ... Archaeal and eukaryote primases are heterodimeric proteins with one large regulatory (human PRIM2, p58) and one small catalytic ... Hou L, Klug G, Evguenieva-Hackenberg E (March 2013). "The archaeal DnaG protein needs Csl4 for binding to the exosome and ... They either use them as a sole replication protein or in combination with other replication-associated proteins, such as ...
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 ...
Seitz EM, Brockman JP, Sandler SJ, Clark AJ, Kowalczykowski SC (1998). "RadA protein is an archaeal RecA protein homolog that ... Eukaryotic Rad51 and its related family members are homologous to the archaeal RadA and bacterial RecA recombinases. Rad51 is ...
"Affinity transfer to the archaeal extremophilic Sac7d protein by insertion of a CDR". Protein Engineering Design and Selection ... These have the ability to act as specific ligands for the proteins of interest that are needed when the fusion of proteins to ... Switching an anti-IgG binding site between archaeal extremophilic proteins results in Affitins with enhanced pH stability. ... which is a hyperthermostable protein. They are artificially binding proteins with high affinity, small size, and low structural ...
Haseltine CA, Kowalczykowski SC (May 2009). "An archaeal Rad54 protein remodels DNA and stimulates DNA strand exchange by RadA ... This allows a protein complex including Mre11, known as the MRX complex, to bind to DNA, and begins a series of protein-driven ... 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 ...
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 ... Nucleocapsid protein TP1 has apparently evolved from a Cas4 endonuclease, a conserved component of the adaptive CRISPR-Cas ... The structure revealed that nucleocapsid is formed from two major capsid proteins (MCP1 and MCP2). MCP1 and MCP2 form a ...
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 ...
... annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and ... List of sequenced archaeal genomes. *RefSeq - the Reference Sequence Database. *Geneious - includes a GenBank Submission Tool ...
... are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal ... In some phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more ... Connections between archaeal cells can also be found between the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) and ... Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-glycerol moiety; 4, phosphate group. Middle, a ...
... which is now known to be the sequence that interacts with the homologue of the archaeal TATA-binding protein (TBP). Also, even ... there are others that have detected notable differences between archaeal and eukaryotic TBP. The archaea protein exhibits a ... TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID.[11] When ... "TATA-binding protein recognition and bending of a consensus promoter are protein species dependent". Biochemistry. 47 (27): ...
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 ...
The protein degradation processEdit. Ribbon diagram of ubiquitin, the highly conserved protein that serves as a molecular tag ... In bacteria that express a 20S proteasome, the β subunits have high sequence identity to archaeal and eukaryotic β subunits, ... Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks ... Proteins are tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ...
23, www.pnas.org/cgi/doi/10.1073/pnas.0801980105 Guy L, Ettema TJ (2011). "The archaeal 'TACK' superphylum and the origin of ... Hansmann, S; Martin W (2000). "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is ... Barns, SM; Fundyga RE; Jeffries MW; Pace NR (1994). "Remarkable archaeal diversity detected in a Yellowstone National Park hot ... Korarchaeota is regarded as a phylum, which itself is part of the archaeal TACK superphylum which encompasses Thaumarchaeota, ...
Protein biosynthesis: translation (bacterial, archaeal, eukaryotic). Proteins. Initiation factor. Bacterial. *PIF-1 ... McClain WH (November 1993). "Rules that govern tRNA identity in protein synthesis". Journal of Molecular Biology. 234 (2): 257- ... For instance, one can start with the gene for a protein that binds a certain sequence of DNA, and, by directing an unnatural ... Both classes of aminoacyl-tRNA synthetases are multidomain proteins. In a typical scenario, an aaRS consists of a catalytic ...
A possible homolog of Dot1 was found in archaea which shows the ability to methylate archaeal histone-like protein in recent ... Advances in Protein Chemistry. 67. Amsterdam: Elsevier Academic Press. pp. 201-222. doi:10.1016/S0065-3233(04)67008-2. ISBN 0- ... McBride AE, Silver PA (July 2001). "State of the arg: protein methylation at arginine comes of age". Cell. 106 (1): 5-8. doi: ... Protein-Arginine+N-Methyltransferase at the US National Library of Medicine Medical Subject Headings (MeSH) ...
This is how the protein checks for the recognition site as it allows the DNA duplex to follow the shape of the protein. In ... The lacI gene synthesizes LacI repressor protein. The LacI repressor protein represses lacZYA by binding to the operator ... lacZYA transcribes the proteins needed for lactose breakdown.[1] lacI synthesizes the repressor of the lacZYA gene.[1] The gene ... In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by ...
Protein biosynthesis: translation (bacterial, archaeal, eukaryotic). Proteins. Initiation factor. Bacterial. *PIF-1 ... Heat shock proteins[edit]. Secondary structures formed by the RBS can affect the translational efficiency of mRNA, generally ... The ribosomal protein S1 binds to adenine sequences upstream of the RBS. Increasing the concentration of adenine upstream of ... At a higher-than-usual temperature (~42 °C), the RBS secondary structure of heat shock proteins becomes undone thus allowing ...
Eukaryotic translation initiation factor 3 subunit A (eIF3a) is a protein that in humans is encoded by the EIF3A gene.[5][6][7] ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3: 89. doi:10.1038/msb4100134 ... protein binding. • structural molecule activity. • translation initiation factor activity. • receptor tyrosine kinase binding. ... protein biosynthesis. • IRES-dependent viral translational initiation. • negative regulation of ERK1 and ERK2 cascade. • ...
"The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution". J Mol Biol. 319 (3): 791- ... Studies of proteins adapted to low pH have revealed a few general mechanisms by which proteins can achieve acid stability. In ... Therefore, intracellular proteins do not need to develop acid stability through evolution. However, other acidophiles, such as ... In a specialized case of acid stability, the NAPase protein from Nocardiopsis alba was shown to have relocated acid-sensitive ...
Protein Sci, 13: 1594-1602.. *Barsky, D. and Venclovas, Č. (2005) DNA sliding clamps: just the right twist to load onto DNA. ... and Siksnys, V. (2007) Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday ... Protein Sci, 11: 2403-2416.. *Venclovas, Č., Ginalski, K. and Kang, C. (2004) Sequence-structure mapping errors in the PDB: OB- ... Proteins, 20: 279-282.. *Venclovas, Č. and Siksnys, V. (1995) Different enzymes with similar structures involved in Mg2± ...
High-resolution structures of an archaeal S-layer protein (MA0829 from Methanosarcina acetivorans C2A) of the Methanosarcinales ... Thus, the S-layer protein can represent up to 15% of the whole protein content of a cell.[3] S-layer proteins are poorly ... protein-carbohydrate interactions and/or protein-protein interactions.[2]. *In Gram-positive bacteria whose S-layers often ... Sequence analyses of S-layer proteins have predicted that S-layer proteins have sizes of 40-200 kDa and may be composed of ...
Protein-Protein Interactions Involving the HSV Virion Host Shutoff Protein and Translation Factors eIF4H and eIF4A". J. Virol. ... "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/ ... protein binding. • nucleic acid binding. • hydrolase activity. • ATP binding. • ATP-dependent RNA helicase activity. • ATPase ... Eukaryotic initiation factor 4A-II is a protein that in humans is encoded by the EIF4A2 gene.[5][6] ...
Human proteins containing this domain[edit]. BACE1; BACE2; CTSD; CTSE; NAPSA; PGA5; PGC; REN; ... Jarrell KF, Ng SY, Chaban B (2006). "Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and ... Hartsuck JA, Koelsch G, Remington SJ (May 1992). "The high-resolution crystal structure of porcine pepsinogen". Proteins. 13 (1 ...
Ricquier D, Bouillaud F. The uncoupling protein homologues: UCP1, UCP2, UCP3, StUCP and AtUCP. „Biochem. J.". 345 Pt 2, s. 161- ... Müller V. An exceptional variability in the motor of archaeal A1A0 ATPases: from multimeric to monomeric rotors comprising 6-13 ... Plant uncoupling mitochondrial protein and alternative oxidase: energy metabolism and stress. „Biosci. Rep.". 25 (3-4), s. 271- ... Theories of biological aging: genes, proteins, and free radicals. „Free Radic. Res.". 40 (12), s. 1230-8, 2006. DOI: 10.1080/ ...
... roles of membrane structure and electrostatics in lipid-protein and protein-protein interactions". Biochimica et Biophysica ... ISBN 981-4280-06-2. Classification of ABC transporters in TCDB ABCdb Archaeal and Bacterial ABC Systems database, ABCdb ATP- ... a "2 TMS" protein has 2 transmembrane segments) to give 6 TMS proteins. ABC2 exporters evolved by intragenic duplication of a 3 ... The genome of the model plant Arabidopsis thaliana is capable of encoding 120 ABC proteins compared to 50-70 ABC proteins that ...
Dolan, Michael F.; Melnitsky, Hannah; Margulis, Lynn; Kolnicki, Robin (2002). "Motility proteins and the origin of the nucleus ... "Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life". Proceedings of the National ...
Lawrence CM, Menon S, Eilers BJ, et al.. Structural and functional studies of archaeal viruses. The Journal of Biological ... coat protein) ஒரு கூடும் (capsid) இருக்கும். சில தீநுண்மங்களில் முள் (Spikes) போன்ற அமைப்பும் உள்ளன. இவை கிளைக்கோ புரதங்களாக ...
Viral capsid proteins come together to form a precursor prohead, into which the genome enters. Once this has occurred, the ... Bacteriophages occur in over 195 bacterial or archaeal genera. They arose repeatedly in different hosts and there are at least ... The tails consist of helix based proteins with 6-fold symmetry. After maturation of virus particles, the cell is lysed by ... and is attached to a flexible tail by a connector protein.[2] The order encompasses a wide range of viruses, many containing ...
LCR can be used to diagnose tuberculosis.[17] The sequence containing protein antigen B is targeted by four oligonucleotide ... which is part of every bacterial and archaeal genome and is highly conserved, bacteria can be taxonomically classified by ... encoded by these amplicons generally increases transcription of those genes and ultimately the volume of associated proteins.[6 ...
"The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 A resolution". J Mol Biol 319 (3): 791-805 ... protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins". ...
LPSN, list of accepted bacterial and archaeal names. *Cyanobacteria, a phylum of common bacteria but poorly classified at ... Radhey Gupta's molecular taxonomy, based on conserved signature sequences of proteins, includes a monophyletic Gram negative ... in archaeal terms, and organisms that live in cooler environments appeared only later.[50] Since the Archaea and Bacteria are ... "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and ...
Protein ini menjadi komponen pembentuk tubuh organisme atau memiliki kemampuan membuat komponen pembentuk tubuh tersebut atau ... "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proc. Natl. Acad. Sci. ... urutan nukleotida komponen penyusun asam nukleat digunakan untuk membuat semua protein pada suatu organisme pada waktu dan ...
... proteins with central functions in meiosis are similar to key proteins in natural transformation in bacteria and DNA transfer ... The archaeal host transferred much of its functional genome to the virus during the evolution of cytoplasm, but retained the ... These proteins could have been transferred to the cell membrane during viral reproduction, enabling cell-to-cell fusion between ... The archaeal products of the revolution maintained recombination machinery that was essentially bacterial, whereas the ...
... s protect themselves from frost and dehydration stress with antifreeze proteins, heat-shock proteins and sugars (sucrose ... "LEA proteins prevent protein aggregation due to water stress". Biochemical Journal. 388 (Part , 1): 151-157. doi:10.1042/ ... protein expression is induced by stresses and protects other proteins from aggregation as a result of desiccation and freezing. ... "Bacterial proteins pinpoint a single eukaryotic root". Proceedings of the National Academy of Sciences. 112 (7): E693-E699. ...
... 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 ...
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 % ...
Archaeal enzymes have great potential for industrial use; however, expressing them in their natural hosts has proven ... Overexpression of an archaeal protein in yeast: secretion bottleneck at the ER Biotechnol Bioeng. 2002 Sep 30;79(7):713-23. doi ... To determine whether a eukaryotic host, S. cerevisiae, would be a suitable alternative for archaeal protein production, we ... Archaeal enzymes have great potential for industrial use; however, expressing them in their natural hosts has proven ...
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 ...
Protein predictedi ,p>This indicates the type of evidence that supports the existence of the protein. Note that the protein ... to allow unambiguous identification of a protein.,p>,a href=/help/protein_names target=_top>More...,/a>,/p>Protein namesi. ... Conserved hypothetical archaeal proteinImported. ,p>Information which has been imported from another database using automatic ... Protein-protein interaction databases. STRINGi. 267377.MMP0675. Genome annotation databases. EnsemblBacteriai. CAF30231; ...
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. ...
In archaea, two ubiquitin-like small archaeal modifier protein (SAMPs) were recently shown to be conjugated to proteins in vivo ... In archaea, two ubiquitin-like small archaeal modifier protein (SAMPs) were recently shown to be conjugated to proteins in vivo ... Solution structure and activation mechanism of ubiquitin-like small archaeal modifier proteins.. Ranjan, N., Damberger, F.F., ... Solution structure of the small archaeal modifier protein 1 (SAMP1) from Methanosarcina acetivorans. *DOI: 10.2210/pdb2L52/pdb ...
Protein-protein interaction analysis of the halobacterial Che proteins revealed that CheF1 directly interacts with CheY, CheD ... Protein concentration (mg ml−1). 10. 10. Buffer composition of protein solution. 20 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. ... Proteins from H. salinarum have been expressed recombinantly in E. coli, but primarily as unfolded proteins that rely on the ... Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation. ...
... 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. ...
The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core.. Mura, C., Cascio, D., ... We report the 1.75-A crystal structure of SmAP, an Sm-like archaeal protein that forms a heptameric ring perforated by a ... We report the 1.75-A crystal structure of SmAP, an Sm-like archaeal protein that forms a heptameric ring perforated by a ... THE CRYSTAL STRUCTURE OF A HEPTAMERIC ARCHAEAL SM PROTEIN: IMPLICATIONS FOR THE EUKARYOTIC SNRNP CORE. *DOI: 10.2210/pdb1I8F/ ...
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 ...
Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif. ... Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif ... Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif. RNA, 16(1 ...
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 ...
Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism. Research ... PCNA-binding proteins in the archaea: novel functionality beyond the conserved core. MacNeill, S. A. Aug 2016 In : Current ... Single-stranded DNA-binding proteins (SSBs) play vital roles in all aspects of DNA metabolism in all three domains of life and ... We show that genes encoding the OB fold and zinc finger-containing RpaA1 and RpaB1 proteins are individually non-essential for ...
Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex Biomolecular ... Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex ... we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a ... Protein secondary-structure description with a coarse-grained model * Rational Design of Triazololipopeptides Analogs of ...
Unlike half of the genes in SSV1, including the minor capsid protein gene vp3, the vp1 gene does not tolerate deletion or ... By analyzing these mutants we demonstrate that the N-terminus of the VP1 protein is required, but the N-terminus, or entire ... The best-studied spindle-shaped virus, SSV1, is composed mostly of the major capsid protein VP1. Similar to many other viruses ... but are common in viruses of archaeal extremophiles, possibly due to the extreme conditions in which they thrive. However, the ...
Relative rates of protein evolution are remarkably constant for the three species groups analyzed here. Deviations from this ... We developed and implemented a simple relative rates test in an attempt to assess the rate constancy of protein evolution and ... However, approximately 1% of the proteins from each group of species deviates from this pattern and instead shows variation ... Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery ...
  • Extremophiles, especially those in Archaea, have a myriad of adaptations that keep their cellular proteins stable and active under the extreme conditions in which they live. (hindawi.com)
  • Rather than having one basic set of adaptations that works for all environments, Archaea have evolved separate protein features that are customized for each environment. (hindawi.com)
  • We categorized the Archaea into three general groups to describe what is known about their protein adaptations: thermophilic, psychrophilic, and halophilic. (hindawi.com)
  • While acidophiles, alkaliphiles, and piezophiles are their own class of Archaea, their protein adaptations toward pH and pressure are less discernible. (hindawi.com)
  • In archaea, two ubiquitin-like small archaeal modifier protein (SAMPs) were recently shown to be conjugated to proteins in vivo. (rcsb.org)
  • In archaea, no homologs of FliM have been identified, and the interaction of CheY-P with different partners in bacteria and archaea has been considered to be a factor that separates the archaeal system of motility from the bacterial system of motility. (iucr.org)
  • Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity with eukaryotic replication factors, making the Archaea an excellent model system for understanding the biology of chromosome replication in eukaryotes. (biochemsoctrans.org)
  • Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea. (elifesciences.org)
  • Although genome analyses have suggested parallels between archaeal and eukaryotic replication systems, little is known about the DNA replication mechanism in Archaea. (nih.gov)
  • Our data suggest that archaeal and eukaryotic Cdc6 and MCM proteins function similarly in replication initiation and imply that an oriC association of MCM could be regulated by an unknown mechanism in Archaea. (nih.gov)
  • Archaea harbor structural homologs of both the bacterial (ThiS-ThiF) and eukaryotic (THI4) proteins that mobilize sulfur to thiazole ring precursors by distinct mechanisms. (nih.gov)
  • Usage of the eukaryotic THI4-type sulfur relay was initially considered less likely for thiamine biosynthesis in archaea, since the active-site cysteine residue of yeast THI4p that donates the sulfur to the thiazole ring by a suicide mechanism is replaced by a histidine residue in many archaeal THI4 homologs and these are described as D-ribose-1,5-bisphosphate isomerases. (nih.gov)
  • No doubt, archaea are intriguing organisms that offer an opportunity to find novel molecules and mechanisms that will, most likely, enhance our understanding of the stress response and the protein folding and refolding processes in the three phylogenetic domains. (genetics.org)
  • It is important to remark, however, that becoming acquainted with what is known for archaea is extremely useful not only for deciding what to do- and how to do it-to increase our understanding of the archaeal chaperoning systems, but also for discovering new molecules and mechanisms that will enhance research with bacteria and eukaryotes. (genetics.org)
  • In this special issue of Archaea, we present a series of articles addressing the current state of understanding of selected facets of archaeal protein biogenesis and processing. (duhnnae.com)
  • Rother and Krzycki then address proteins containing the unusual animo acids, selenocysteine, and pyrrolysine, as related to the unique energy metabolism of methanogenic archaea. (duhnnae.com)
  • Questions related to protein assembly are considered when Iwasaki addresses the iron-sulfur world in hyperthermoacidophilic archaea. (duhnnae.com)
  • In this, the first special issue of Archaea dedicated to archaeal protein biogenesis, we have tried to give the reader a sampling of the current research scene. (duhnnae.com)
  • Archaea contain many unique protein assemblies and offer fascinating insights into an exotic, largely unknown macromolecular universe that we are exploring by cryoEM and cryoET. (mpg.de)
  • Some viruses that infect archaea (archaeophages) induce the formation of large, 7-fold pyramid structures in the membrane of their archaeal hosts. (mpg.de)
  • The present invention relates to recombinant protein production, and more specifically, to methods for recovery of properly folder bioactive proteins by expressing chaperone genes from extremophilic Archaea, during recombinant protein synthesis in a host cell thereby significantly improving recovery of properly folded bioactive proteins. (patentsencyclopedia.com)
  • This book describes the structures and functions of active protein filaments, found in bacteria and archaea, and now known to perform crucial roles in cell division and intra-cellular motility, as well as being essential for controlling cell shape and growth. (springer.com)
  • The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. (pasteur.fr)
  • Archaea employ proteins homologous to those of eukaryotes to replicate DNA, whereas the organization of that DNA and its cellular context are more bacterial in nature. (frontiersin.org)
  • It also provides a route to improved genetic methods for archaea and technological applications based on archaeal proteins. (frontiersin.org)
  • Analysis by MS and comparison with databases revealed that this fraction contained two dominant proteins, representing the respective major envelope proteins of the two archaea. (biochemsoctrans.org)
  • Twenty-seven (out of 32) proteins of the eukaryotic small ribosomal subunit proteins are also present in archaea (no ribosomal subunit is exclusively found in archaea), confirming that they are more closely related to eukaryotes than to eubacteria. (wikipedia.org)
  • Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. (asm.org)
  • Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? (royalsocietypublishing.org)
  • Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. (royalsocietypublishing.org)
  • In eukaryotic cells, proteins, nucleic acids and small molecules are distributed by specific trafficking mechanisms rather than by free diffusion as is largely the case in bacteria and archaea [ 4 , 5 ]. (royalsocietypublishing.org)
  • Fifteen integral membrane transport proteins from Archaea were selected as test targets, chosen to represent two superfamilies widespread in all organisms known as the Major Facilitator Superfamily (MFS) and the 5-Helix Inverted Repeat Transporter superfamily (5HIRT). (univ-grenoble-alpes.fr)
  • A paracrystalline protein surface layer, commonly referred to as S-layer, is present in nearly all archaea described to date. (frontiersin.org)
  • In both Bacteria and Archaea , S-layers are composed of only one or, in a few cases, two different (glyco) proteins. (frontiersin.org)
  • Opnå en forståelse af samspillet mellem toxin-antitoxin-systemer og CRISPR-Cas immunitet i bakterier og archaea. (au.dk)
  • With this model, we have discovered the roles of two new families of cytoskeletal proteins from the tubulin-FtsZ superfamily in archaea (Duggin et al. (edu.au)
  • The crystal structure of an archaea homologue of presenilin (mmPSH), just published in Nature, represents a substantial advance in the structural field of membrane proteins that could shed light on the structural basis of the active site of the γ-secretase complex. (alzforum.org)
  • As arqueas ( Archaea , do grego ἀρχαῖα 'os antigos') son un grupo de microorganismos unicelulares de morfoloxía procariótica (sen núcleo nin, en xeral, orgánulos membranosos internos), que forman un dos tres grandes dominios dos seres vivos, e que son diferentes das bacterias . (wikipedia.org)
  • As Archaea divídense en cinco filos recoñecidos, pero pénsase que poden haber máis. (wikipedia.org)
  • Edgell DR, Doolittle WF (1997) Archaea and the origin(s) of DNA replication proteins. (springer.com)
  • Although it is well accepted that archaea are not only the extremists they were thought to be as they occupy nearly every habitat where also bacteria are found, it is surprising how little molecular details are known about archaeal biofilm formation. (scoop.it)
  • These results provide insights into both the molecular mechanisms that govern biofilm formation in Crenarchaea and the functionality of the Lrs14-like proteins, an archaea-specific class of transcriptional regulators. (scoop.it)
  • We report here the crystal structure of the major capsid protein (MCP) of the Sulfolobus turreted icosahedral virus, an archaeal virus isolated from an acidic hot spring (pH 2-4, 72-92°C) in Yellowstone National Park. (pnas.org)
  • However, analysis of the effects of Sulfolobus chromatin proteins on UDG1 leads us to propose a mechanistic basis for coupling UDG1 to the replication fork. (biochemj.org)
  • The reversible thermal unfolding of the archaeal histone-like protein Ssh10b from the extremophile Sulfolobus shibatae was studied using differential scanning calorimetry and circular dichroism spectroscopy. (ox.ac.uk)
  • Recently, studies on a few model archaeal viruses such as SIRV2 ( Sulfolobus islandicus rod‐shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. (st-andrews.ac.uk)
  • Furthermore, the N‐terminal domain of the protein mediates toxicity to the viral host Sulfolobus . (st-andrews.ac.uk)
  • . Sulfolobus cells are unable to survive without this protein, which works in a similar way to TFIIEβ in assisting the RNAP to start transcription. (elifesciences.org)
  • A small protein ( 15 ) may anchor the S-layer to the cell membrane, as in Sulfolobus acidocaldarius , while narrow bridges between three globular domains of the S-layer protein may allow curved surfaces to form around the cell ( 6 , 10 , 44 , 53 ). (asm.org)
  • In addition to the Pyrococcus PriS structures, the structure of the PriS protein from the crenarchaeal organism Sulfolobus solfataricus has also been determined [ 6 ]. (biomedcentral.com)
  • However, it was previously found that the ST0452 protein, a thermostable enzyme from the thermophilic archaeon Sulfolobus tokodaii, exhibited increased activity following single amino acid substitutions of Ala. In this study, ST0452 proteins exhibiting a further increase in activity were created using a site saturation mutagenesis strategy at the 97th position. (qub.ac.uk)
  • Here, such a dual domain protein, i.e. the Sulfolobus islandicus Csx1 (SisCsx1) was characterized. (bireme.br)
  • En 1970, Thomas D. Brock, da Universidade de Wisconsin, descubriu a Thermoplasma , unha arquea termoacidófila e en 1972 a Sulfolobus , unha hipertermófila . (wikipedia.org)
  • Here we provide data suggesting that the transcriptional regulators belonging to the Lrs14-like protein family constitute a key regulatory factor during Sulfolobus biofilm development. (scoop.it)
  • On the other hand, all archaeal genomes sequenced to date encode potential transcription regulators of bacterial type, underscoring the chimeric nature of the archaeal transcription apparatus ( 6 , 7 ). (pnas.org)
  • The Che proteins, encoded by genes that cluster in genomes, constitute the chemotaxis signal transduction system. (iucr.org)
  • Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. (mdpi.com)
  • The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. (asm.org)
  • In RCR, Rep proteins also catalyze closure or ligation of the newly synthesized genomes once replication is complete. (asm.org)
  • The test was performed on clusters of orthologous protein sequences from complete bacterial genomes Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae, complete archaeal genomes Pyrococcus horikoshii, P. abyssi and P. furiosus and partially sequenced mammalian genomes human, mouse and rat. (duhnnae.com)
  • Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. (asm.org)
  • Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. (asm.org)
  • The complete list of histidine kinases and response regulators encoded in the analyzed archaeal genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/TCSarchaea.html . (asm.org)
  • Finally, several genes of archaeal origin located in proximity to the reverse gyrase gene in bacterial genomes have bacterial homologues mostly in thermophiles or hyperthermophiles, raising the possibility that they were co-transferred with the reverse gyrase gene. (mendeley.com)
  • The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. (biomedcentral.com)
  • In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation. (biomedcentral.com)
  • At the time of this writing nearly 400 complete prokaryotic genomes, including 28 archaeal ones, have been deposited in the GenBank database. (biomedcentral.com)
  • Sti1/Hop is a modular protein required for the transfer of client proteins from the Hsp70 to the Hsp90 chaperone system in eukaryotes. (ebscohost.com)
  • In contrast, a single group of proteins has come to dominate chromatin in eukaryotes: histones. (elifesciences.org)
  • Another archaeal paradox is that the proteins coded by these genes are very similar to bacterial homologs, as if the genes had been received via lateral transfer from bacteria, whereas the upstream flanking regions have no bacterial markers, but instead have typical archaeal promoters, which are like those of eukaryotes. (genetics.org)
  • It is difficult to understand how these hybrid characteristics of the archaeal chaperoning system became established and work, if one bears in mind the classical ideas learned from studying bacteria and eukaryotes. (genetics.org)
  • In eukaryotes, DUEs are the binding site for DNA-unwinding element binding (DUE-B) proteins required for replication initiation. (wikipedia.org)
  • Our results suggest that archaeal TFEα/β is likely to represent the evolutionary ancestor of TFIIE-like factors in extant eukaryotes. (elifesciences.org)
  • But several recent discoveries suggest that the origin of the eukaryotes lies within the archaeal domain. (elifesciences.org)
  • Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. (pasteur.fr)
  • [5] Among the 40 proteins found in various small ribosomal subunits , 15 subunits are universally conserved across prokaryotes and eukaryotes. (wikipedia.org)
  • Among the large ribosomal subunit , 18 proteins are universal, i.e. found in both bacteria, eukaryotes, and archea. (wikipedia.org)
  • 14 proteins are only found in bacteria, while 27 proteins are only found in archea and eukaryotes. (wikipedia.org)
  • The discovery of this 'dispersed eukaryome' implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. (royalsocietypublishing.org)
  • The system is associated with a large number of Cas accessory proteins among which many contain a CARF (CRISPR-associated Rossmann fold) domain implicated in ligand binding and a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) nuclease domain. (bireme.br)
  • [5] [6] The protein is highly conserved in most eukaryotes, from yeast to humans. (wikipedia.org)
  • In eukaryotes, RAD51 protein has a central role in homologous recombinational repair. (wikipedia.org)
  • Similar proteins are found in archea, prokaryotes and eukaryotes (but not humans). (bioquest.org)
  • Guy L, Ettema TJ (2011) The archaeal 'TACK' superphylum and the origin of eukaryotes. (springer.com)
  • The protein is encoded by multiple loci in some eukaryotes and has been assigned a number of extra-ribosomal functions, some of which will require re-evaluation in the context of identification as a ribosomal protein. (jcvi.org)
  • Gopalan, V. Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P. Biomolecules 2016 , 6 , 22. (mdpi.com)
  • Samanta MP, Lai SM, Daniels CJ, Gopalan V. Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P. Biomolecules . (mdpi.com)
  • One of the eukarotyic RNAPs, termed RNAP II, works with a transcription factor that contains two protein subunits (called TFIIEα and TFIIEβ). (elifesciences.org)
  • [5] Typically 22 proteins are found in bacterial 30S subunits and 32 in yeast, human and most likely most other eukaryotic species. (wikipedia.org)
  • Despite their high conservation over billions of years of evolution, the absence of several ribosomal proteins in certain species shows that ribosomal subunits have been added and lost over the course of evolution. (wikipedia.org)
  • All of them are different with three exceptions: one protein is found in both subunits (S20 and L26), L7 and L12 are acetylated and methylated forms of the same protein, and L8 is a complex of L7/L12 and L10. (wikipedia.org)
  • However, the addition of PhoAlba to reconstituted particles composed of PhopRNA and four or five protein subunits had little influence on either the pre-tRNA processing activity or the optimum temperature for the processing activity. (elsevier.com)
  • The archaeal part of the reverse gyrase tree is congruent with recent phylogenies of the archaeal domain based on ribosomal proteins or RNA polymerase subunits. (mendeley.com)
  • This gene encodes one of the protein subunits of the small nucleolar ribonucleoprotein complexes: the endoribonuclease for mitochondrial RNA processing complex and the ribonuclease P complex. (genecards.org)
  • Crystals of the native protein and its selenomethionine derivative belonged to the orthorhombic space group I222 and were suitable for structural studies. (nih.gov)
  • Here, we offer a rationale for charged S-layer proteins in the context of the structural evolution of S-layers. (nature.com)
  • 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. (microbiologyresearch.org)
  • 3D-structural models of archaeal THI4 family proteins compared to the X-ray structure ofNeurospora crassa(Nc) THI4p (PDB: 3JSK). (nih.gov)
  • The level of information in all chapters is suitable both for active researchers and for advanced students in courses involving bacterial or archaeal physiology, molecular microbiology, structural cell biology, molecular motility or evolution. (springer.com)
  • Chandra Sanyal S, Liljas A. The end of the beginning: structural studies of ribosomal proteins. (ebi.ac.uk)
  • Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the form of a conserved structural domain comprising a three-stranded antiparallel β-sheet adjacent to an α-helix and a two-stranded β-sheet or hairpin. (biomedcentral.com)
  • Despite their importance, structural and functional characterisation of membrane proteins still remains a challenge, partially due to the difficulties in recombinant expression and purification. (univ-grenoble-alpes.fr)
  • Moreover, this work generated useful proteins for three-dimensional structural analysis clarifying the processes underlying the regulation and mechanism of enzymatic activity. (qub.ac.uk)
  • The first structure of this protein family has been determined to 2.5-Å resolution and shows the structural features of the three conserved domains C2A, C2B and vWA. (exeter.ac.uk)
  • However, there is currently no SARM1-directed therapeutic approach available because of an insufficient structural and mechanistic understanding of this protein. (exeter.ac.uk)
  • Genetic, structural, and biochemical studies have revealed the nature of archaeal origin specification. (springer.com)
  • Gaudier M, Schuwirth BS, Westcott SL, Wigley DB (2007) Structural basis of DNA replication origin recognition by an ORC protein. (springer.com)
  • Bacteria typically encode multiple small basic proteins that are dynamically expressed and fulfill a variety of architectural roles by bridging, wrapping, or bending DNA ( Dillon and Dorman, 2010 ). (elifesciences.org)
  • Outside bacteria, HU proteins are comparatively rare ( Figure 2a ). (elifesciences.org)
  • Unique amino acid composition of proteins in halophilic bacteria. (microbiologyresearch.org)
  • Two important molecular teams are involved in assisting protein folding: the chaperone machine formed by Hsp70(DnaK), Hsp40(DnaJ), and GrpE, and the chaperonin system, which in bacteria consists of the GroEL and GroES proteins, and in the eukaryotic-cell organelles is represented by homologs of GroEL and GroES. (genetics.org)
  • 1. A method of enhancing protein folding in a bacteria host, the method comprising: providing at least one expression vector comprising nucleic acid sequences encoding for a chaperone from a hyperthermophilic and/or psychrophilic archaeon and nucleic acid sequences encoding a native and/or non-native protein for expression in the host bacteria. (patentsencyclopedia.com)
  • and culturing the bacteria host under conditions sufficient for expression of the proteins and chaperones. (patentsencyclopedia.com)
  • 16. A delivery device comprising nucleotide sequences encoding chaperones from a hyperthermophilic and/or psychrophilic archaeon, in an amount to enhance the folding of expressed native and non-native proteins in a bacteria host. (patentsencyclopedia.com)
  • In bacteria, the protein DnaA is the replication initiator. (wikipedia.org)
  • Genes coding for these proteins are essential in almost all bacteria investigated thus far. (portlandpress.com)
  • [ 13 ] Brock iniciárase en 1969 no campo da bioloxía dos hipertermófilos co descubrimento de Thermus aquaticus , que non é unha arquea senón unha bacteria. (wikipedia.org)
  • Here, we elucidate primary chromatin architecture in an archaeon without histones, Thermoplasma acidophilum, which harbors a HU family protein (HTa) that protects part of the genome from micrococcal nuclease digestion. (elifesciences.org)
  • Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. (asm.org)
  • Archaeal viruses display tremendous diversity of both morphology and genome content. (asm.org)
  • Archaeal signal peptides - a comparative survey at the genome level. (microbiologyresearch.org)
  • The stability of thermophilic proteins: a study based on comprehensive genome comparison. (microbiologyresearch.org)
  • The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. (st-andrews.ac.uk)
  • Although we have genome sequences for most of the crenarchaeal viruses isolated, we have only a rudimentary understanding of archaeal virus assembly and release from cells. (asm.org)
  • N. equitans , on the other hand, has a genome of just 0.49 Mb, by far the smallest of all archaeal cells known today. (biochemsoctrans.org)
  • Taken together with previous results, 22 of the 54 E. coli ribosomal protein genes can be individually deleted from the genome. (wikipedia.org)
  • The Arabidopsis ( Arabidopsis thaliana ) genome encodes homologs of the Guided Entry of Tail (GET)-anchored protein system for the posttranslational insertion of tail-anchored ( TA ) proteins into endoplasmic reticulum (ER) membranes. (plantphysiol.org)
  • A serious case is the archaeal genome Aeropyrum pernix . (biomedcentral.com)
  • A quarter of the genome encodes preserved proteins whose functions are not yet determined, but are expressed in other archaeons such as Methanococcus jannaschii . (kenyon.edu)
  • One observation about the genome is that there are many gene duplications and the duplicated proteins are not identical. (kenyon.edu)
  • The expressed protein is membrane-associated and forms with all-trans retinal a visible light-absorbing pigment with a 534 nm absorption maximum and approximately 100 nm half-bandwidth typical of retinylidene protein absorption spectra. (nih.gov)
  • However, such proteins must first be targeted to and traverse the plasma membrane. (duhnnae.com)
  • address questions related to the biogenesis of one class of membrane proteins, namely, lipoproteins. (duhnnae.com)
  • We use cryoET and sub-tomogram averaging to elucidate this unusual structure, and have expressed and crystallized the 10 kDa membrane protein that assembles into the pyramids. (mpg.de)
  • The single-stranded RNA and ssDNA phages use an amurin type of protein that prevents cell wall synthesis ( 7 , 8 , 34 ), leaving the cell membrane unprotected and subject to lysis. (asm.org)
  • In addition, a considerable set of membrane proteins is specifically associated with these proteins. (biochemsoctrans.org)
  • An efficient strategy for small-scale screening and production of archaeal membrane transport proteins in Escherichia coli. (univ-grenoble-alpes.fr)
  • Membrane proteins play a key role in many fundamental cellular processes such as transport of nutrients, sensing of environmental signals and energy transduction, and account for over 50% of all known drug targets. (univ-grenoble-alpes.fr)
  • Here, we describe an efficient strategy for heterologous production of membrane transport proteins in E. coli. (univ-grenoble-alpes.fr)
  • The methods described in this work are simple to implement and can be easily applied to many more membrane proteins. (univ-grenoble-alpes.fr)
  • This very frequently occurring problem in membrane-protein crystallography laboratories is reported, as well as suggestions to avoid it. (iucr.org)
  • The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. (biomedsearch.com)
  • The Arabidopsis thaliana BON1 gene product is a member of the evolutionary conserved eukaryotic calcium-dependent membrane-binding protein family. (exeter.ac.uk)
  • The BON1 protein is localized on the plasma membrane, and is known to suppress the expression of immune receptor genes and to positively regulate stomatal closure. (exeter.ac.uk)
  • This molecule is an adaptor protein that localizes to the membrane in neurons undergoing guidance, in response to the activation of a guidance cue receptor on the cell surface. (bioquest.org)
  • In yeast, TA proteins are loaded onto the cytosolic targeting factor Get3 and are then delivered to the membrane-associated Get1/2 complex for insertion into ER membranes. (plantphysiol.org)
  • The role of the GET system in Arabidopsis was investigated by monitoring the membrane insertion of a tail-anchored protein, SYP72, a syntaxin. (plantphysiol.org)
  • Targeting newly made membrane proteins to their appropriate subcellular location is a complex matter because different proteins have different destinations and membrane topologies. (plantphysiol.org)
  • It has been known for over 40 years that many membrane proteins are targeted to the ER membrane by cotranslational mechanisms ( Blobel and Dobberstein, 1975 ). (plantphysiol.org)
  • In yeast, Get3 chaperones TA proteins to the ER , whereupon the Get3-TA complex interacts with the ER membrane multispanning proteins Get1 and Get2. (plantphysiol.org)
  • 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. (mdpi.com)
  • RAD51 family members are homologous to the bacterial RecA , Archaeal RadA and yeast Rad51. (wikipedia.org)
  • In humans, RAD51 is a 339- amino acid protein that plays a major role in homologous recombination of DNA during double strand break repair. (wikipedia.org)
  • We chose to align 8 sequences of homologous archaeal helicases. (bioquest.org)
  • 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)
  • This protein binds oxysterols, cholesterol, and ergosteterol (the yeast version of cholestreol). (bioquest.org)
  • The hydrophobic pocket of this protein binds sterols and the outside of this protein binds phosphatidylinositol-3-phosphate. (bioquest.org)
  • Get3, an ATPase, binds to and chaperones the TMDs of TA proteins for their delivery and insertion into the ER ( Hegde and Keenan, 2011 ). (plantphysiol.org)
  • The P. furiosus and P. horikoshii PriS proteins are composed of two distinct domains: a mixed α/β domain (the Prim domain) that includes the catalytic site of the enzyme and a smaller α-helical domain of unknown function [ 4 , 5 ]. (biomedcentral.com)
  • 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)
  • The present review summarizes current knowledge of how the core components of the archaeal chromosome replication apparatus interact with one another to perform their essential functions. (biochemsoctrans.org)
  • We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. (asm.org)
  • The implications for Rep protein function and viral replication are discussed. (asm.org)
  • RCR requires a replication initiator (Rep) protein, which nicks the circular DNA, forming a 5′ DNA adduct and releasing a free 3′ end to act as a primer for DNA synthesis. (asm.org)
  • Whereas the oriC association of MCM was specifically inhibited by stopping DNA replication with puromycin treatment, Cdc6 protein stayed bound to the replication origin after de novo protein synthesis was inhibited. (nih.gov)
  • Once bound to replicators, initiators (often with the help of co-loader proteins) deposit replicative helicases onto DNA, which subsequently drive the recruitment of additional replisome components and the assembly of the entire replication machinery. (wikipedia.org)
  • Little is known about the replication cycle of archaeal viruses. (asm.org)
  • Primase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. (biomedcentral.com)
  • Organisms within the archaeal domain of life possess a simplified version of the eukaryotic DNA replication machinery. (springer.com)
  • Dueber ELC, Corn JE, Bell SD, Berger JM (2007) Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex. (springer.com)
  • Kelman LM, Kelman Z (2014) Archaeal DNA replication. (springer.com)
  • primosomal protein N' (replication factor Y) (superfamily II helicase) [EC:3.6.4. (kegg.jp)
  • 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)
  • Viruses with spindle or lemon-shaped virions are rare in the world of viruses, but are common in viruses of archaeal extremophiles, possibly due to the extreme conditions in which they thrive. (preprints.org)
  • Although histones are one likely target for the enzymatic activity of eukaryotic Sir2 proteins, little is known about the substrates and roles of prokaryotic Sir2 homologs. (sciencemag.org)
  • Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil--coil structures, protein secondary structure or genes, extra support can be gained from homologs. (psu.edu)
  • In contrast, largely due to a lack of suitable model systems and a limited number of appropriate molecular tools, considerably less was known about archaeal proteins in terms of their biogenesis, modification, trafficking, or degradation. (duhnnae.com)
  • All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. (mdpi.com)
  • This discovery provides new insights in the evolutionary history of both the archaeal and the eukaryotic transcription machineries. (elifesciences.org)
  • The conserved core of the archaeal and eukaryotic transcription machineries encompasses a highly complex multisubunit RNAP as well as evolutionary conserved transcription factors that govern its activities through the transcription cycle. (elifesciences.org)
  • BackgroundDetection of changes in a protein-s evolutionary rate may reveal cases of change in that protein-s function. (duhnnae.com)
  • Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. (royalsocietypublishing.org)
  • The projects will involve methodological innovation and development, and the utilization of cutting-edge technology, including recombinant DNA and molecular genetics, high-resolution fluorescence or electron microscopy, and protein structure and function studies. (edu.au)
  • Makarova and Koonin rely on comparative genomic analysis to reveal functional versatility of archaeal ubiquitin-like proteins, while Humbard et al. (duhnnae.com)
  • Ribosomal protein L11 is an important part of the GTPase-associated centre in ribosomes of all organisms. (nih.gov)
  • Due to the physiological importance and the high degree of conservation of this protein, its absence in archaeal organisms has raised intriguing questions pertaining to the evolution of the chaperone machine as a whole and that of its components in particular, namely, Hsp70(DnaK), Hsp40(DnaJ), and GrpE. (genetics.org)
  • Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. (ebi.ac.uk)
  • The ABC protein ABCE1, formerly named RNase L inhibitor RLI1, is one of the most conserved proteins in evolution and is expressed in all organisms except eubacteria. (scoop.it)
  • Tyrosine phosphorylation of a small set of bacterial proteins was first linked to specialized cellular events, primarily with the synthesis and export of polysaccharides associated with lipopolysaccharide (LPS) and capsule biosynthesis ( 3 - 5 ). (asm.org)
  • While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. (ebi.ac.uk)
  • The 'genetic code' is used here as the way in which triplets of three nucleotide bases are mapped to corresponding amino acids for the purpose of protein synthesis. (antievolution.org)
  • p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (uniprot.org)
  • section shows the unique identifier assigned by the NCBI to the source organism of the protein. (uniprot.org)
  • Information regarding S-layers in the remaining archaeal phyla is limited, mainly due to organism description through only culture-independent methods. (frontiersin.org)
  • Strong interest and motivation to pursue research in discovery/fundamental science, evolution, microbial model organism development, and/or protein and structure and function. (edu.au)
  • We reveal that an archaeal Sir2 homolog interacts specifically with the major archaeal chromatin protein, Alba, and that Alba exists in acetylated and nonacetylated forms. (sciencemag.org)
  • 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)
  • We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. (st-andrews.ac.uk)
  • In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. (ebi.ac.uk)
  • Mammalian splicing factor SF1 interacts with SURP domains of U2 snRNP-associated proteins. (mpg.de)
  • The nop-1 gene from Neurospora crassa is predicted to encode a seven-helix protein exhibiting conservation with the rhodopsins of the archaeon Halobacterium salinarum. (nih.gov)
  • Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. (wikipedia.org)
  • L11 is a highly conserved two-domain ribosomal protein. (nih.gov)
  • Ribosomal proteins are among the most highly conserved proteins across all life forms. (wikipedia.org)
  • The protein is highly conserved towards the middle region and is represented by the purple and pink color schemes. (bioquest.org)
  • In this study, two new crystal forms and protein structures of CheY are reported. (iucr.org)
  • considers archaeal protein export and describes different cell surface structures, while a report by Jarrell et al. (duhnnae.com)
  • S-layers are composed of only one or two proteins and form different lattice structures. (frontiersin.org)
  • Green, T. J. Nucleocapsid protein structures from orthobunyaviruses reveal insight into ribonucleoprotein architecture and RNA polymerization . (wikipedia.org)
  • Here, the crystallization and X-ray analysis of the ribosomal protein L11 from Methanococcus jannaschii are reported. (nih.gov)
  • 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)
  • Bacterial and archaeal L11-rRNA complexes are targets for peptide antibiotics of the thiazole class. (nih.gov)
  • Phosphorylation events modify bacterial and archaeal proteomes, imparting cells with rapid and reversible responses to specific environmental stimuli or niches. (asm.org)
  • However, within the last 10 years, detailed bacterial and archaeal phosphoproteomic studies have resulted in a fresh view that compares closely to the eukaryotic condition, where tyrosine phosphorylation is a central paradigm. (asm.org)
  • nuclear human accounts was the non-propositional download Prokaryotic Cytoskeletons: Filamentous Protein Polymers Active in the Cytoplasm of Bacterial and Archaeal Cells 2017, Historical neue, possible repetition, East Baltic oxidation, and the second book. (eglindia.com)
  • In all, there are six rights in my download Prokaryotic Cytoskeletons: Filamentous Protein Polymers Active in the Cytoplasm of Bacterial and Archaeal: the 3NCERT John Lawrence Duffy, Jr. Pleasant and Sullivan's Island Municipal Courts), the Future Michael P. Duffy( US District Court), Brian C. Duffy of Duffy and Young, myself, Tim Amey and my Principal. (eglindia.com)
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  • Amino acid substitution mutants of SisCsx1 were obtained, and characterization of these mutant proteins showed that the CARF domain of the enzyme is responsible for binding to 3'-tetra-rA and the ligand binding strongly activates RNA cleavage by the HEPN domain. (bireme.br)
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics , 1868 (2), 140322-140322. (exeter.ac.uk)
  • Despite exceptional sequence diversity, S-layer proteins (SLPs) share important characteristics such as their ability to form crystalline sheets punctuated with nano-scale pores, and their propensity for charged amino acids, leading to acidic or basic isoelectric points. (nature.com)
  • By using sequence alignment and modeling techniques, this lineage was recently extended to include additional large-faceted viruses containing a double-barrel trimeric major coat protein ( 4 ). (pnas.org)
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. (uniprot.org)
  • Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. (mdpi.com)
  • providing an expression vector comprising a nucleotide sequence that encodes for an extremophilic chaperone and an indicator protein, wherein the indicator protein provides for a detectable signal. (patentsencyclopedia.com)
  • The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into final enzyme class predictions of the submitted sequence. (dtu.dk)
  • Prediction of novel archaeal enzymes from sequence-derived features. (dtu.dk)
  • The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. (pasteur.fr)
  • Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. (psu.edu)
  • ResultsAmino-acid sequence evolution rates are significantly correlated on different branches of phylogenetic trees representing the great majority of analyzed orthologous protein sets from all three domains of life. (duhnnae.com)
  • Multiple sequence alignments (data not shown) indicate that the PriS CTD is conserved in all archaeal lineages with the exception of the Thermococcales (including Pyrococcus and Thermococcus species) and the Methanobacteriales ( Methanosphaera and Methanothermobacter species), implying that these latter groups have undergone lineage-specific loss of this domain. (biomedcentral.com)
  • The first two algorithms employ an inhomogeneous Markov model for short DNA segments ( i.e. k -tuples), from which an estimate of the likelihood for the segment to belong to a protein coding sequence is derived after a training with existing gene data. (biomedcentral.com)
  • These data provide a paradigm for how Sir2 family proteins influence transcription and suggest that modulation of chromatin structure by acetylation arose before the divergence of the archaeal and eukaryotic lineages. (sciencemag.org)
  • DNA, Archaeal" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (umassmed.edu)
  • The core components of archaeal transcription closely resemble those of eukaryotic RNA polymerase II ( 1 ). (pnas.org)
  • a modest stimulatory effect of TFE, the archaeal homologue of the α subunit of the RNA polymerase II transcription factor TFIIE, is discerned under conditions of suboptimal TBP-TATA box interaction ( 4 , 5 ). (pnas.org)
  • Bound proteins were again eluted with a linear KCl gradient, and RNA polymerase-containing fractions were concentrated on Mono Q. Final purification was achieved by gel filtration on Superdex 200, preequilibrated with TMK buffer containing 300 mM KCl. (pnas.org)
  • Transcription initiation of archaeal RNA polymerase (RNAP) and eukaryotic RNAPII is assisted by conserved basal transcription factors. (elifesciences.org)
  • RNA polymerase II is a specific RNA polymerase that usually is the key part of the catalysis process that produces each RNA from the DNA gene or isoform to ultimately make a protein. (wikiversity.org)
  • Here, we report the solution structure of SAMP1 from Methanosarcina acetivorans and the activation of SAMPs by an archaeal protein with homology to eukaryotic E1 enzymes. (rcsb.org)
  • These mutant proteins might suggest clues regarding the mechanism underlying the reaction process and provide very important information for the design of synthetic improved enzymes, and they can be used as powerful biocatalysts for the production of sugar nucleotide molecules. (qub.ac.uk)
  • SET domain proteins are named after a shared motif in the Drosophila proteins Su(var)3-9, Enhancer-of-zeste and Trithorax, and they form a major branch of the protein lysine methyltransferase enzymes. (findaphd.com)
  • volcanii uses a yeast THI4-type mechanism for sulfur relay to form the thiazole ring of thiamine.Thus, archaeal members of IPR002922 THI4 family that have a conserved cysteine active site should be reexamined for a function in thiamine biosynthesis. (nih.gov)
  • Most of the information about cell lysis is based on observations of a decrease in optical density (OD) in an infected culture, plaque assays, or plate growth inhibition assays, but little is known about the actual mechanism of archaeal lysis. (asm.org)
  • Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. (asm.org)
  • The prevailing mechanism of archaeal TCS signaling appears to involve various protein-protein interactions rather than direct transcription regulation. (asm.org)
  • The binding of the C2 domains to phospholipid (PSF) has been modeled and provides an insight into the lipid-binding mechanism of the copine proteins. (exeter.ac.uk)
  • Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. (st-andrews.ac.uk)
  • In the work presented here we have expressed this gene heterologously in the yeast Pichia pastoris, obtaining a relatively high yield of 2.2 mg of NOP-1 protein/L of cell culture. (nih.gov)
  • Structure of yeast Dom34 : a protein related to translation termination factor eRF1 and involved in No-Go decay. (embl-heidelberg.de)
  • Yeast cells have 7 oxysterol-binding proteins. (bioquest.org)
  • Single-stranded DNA-binding proteins (SSBs) play vital roles in all aspects of DNA metabolism in all three domains of life and are characterized by the presence of one or more OB fold ssDNA-binding domains. (st-andrews.ac.uk)
  • Unlike other proteins involved in DNA metabolism, the RecA/Rad51 family forms a helical nucleoprotein filament on DNA. (wikipedia.org)
  • Archaeal Protein Biogenesis: Posttranslational Modification and Degradation - Descarga este documento en PDF. (duhnnae.com)
  • Protein degradation is the focus of two articles in this special issue. (duhnnae.com)
  • We hypothesize that this nuclease degrades mRNAs of proteins targeted for degradation and so regulates archaeal RNA turnover, possibly in concert with the exosome. (elsevier.com)
  • Since RNA polyadenylation is an important step in RNA decay in prokaryotes, and poly(A) RNAs can activate CARF domain proteins, the poly(A) RNA may function as an important signal in the cellular responses to viral infection and environmental stimuli, leading to degradation of both viral and host transcripts and eventually to cell dormancy or cell death. (bireme.br)
  • These proteins are important for embryonic growth and development, and IGF2R (a mannose-6-phosphate receptor) is thought to sequester IGF2 and target it for degradation. (bioquest.org)
  • PhD Studentship in the interplay between ubiquitin-proteasome degradation system and amyloid proteins, Imperial College London. (findaphd.com)
  • Accordingly, Zwieb and Bhuiyan discuss the latest findings on the archaeal signal recognition particle targeting system. (duhnnae.com)
  • report on the phosphorylation and methylation of Haloferax volcanii proteasomal proteins. (duhnnae.com)
  • Most of the putative functionally diversified proteins from all three species groups are predicted to function at the periphery of the cells and mediate their interaction with the environment. (duhnnae.com)
  • Thermophilic proteins tend to have a prominent hydrophobic core and increased electrostatic interactions to maintain activity at high temperatures. (hindawi.com)
  • A particularly intriguing case concerns the thermophilic acidophile Thermoplasma acidophilum, which lacks histone genes but instead encodes a protein named HTa ( H istone-like protein of T hermoplasma a cidophilum ). (elifesciences.org)
  • Genes and derived amino acid sequences of S-layer proteins from mesophilic, thermophilic, and extremely thermophilic methanococci. (microbiologyresearch.org)
  • Primary structure of selected archaeal mesophilic and extremely thermophilic outer surface layer proteins. (microbiologyresearch.org)
  • PhoAlba structurally belongs to the α/β proteins and is similar not only to archaeal homologues but also to RNA-binding proteins, including the C-terminal half of initiation factor 3 (IF3-C) from Bacillus stearothermophilus, an Esherichia coli protein implicated in cell division (Yhhp), and an Arabidopsis protein of unknown function. (elsevier.com)
  • This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs) and Translation Initiation Sites (TISs). (biomedcentral.com)
  • 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)
  • However, the resolution afforded by the test designed specifically for genomic-scale datasets allowed us to identify numerous cases of possible functional diversification between orthologous proteins. (duhnnae.com)
  • Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. (royalsocietypublishing.org)
  • In this review, we summarize current understanding of archaeal S-layer proteins, discussing topics such as structure, lattice type distribution among archaeal phyla and glycosylation. (frontiersin.org)
  • Previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (LGT) to the ancestors of the two bacterial hyperthermophilic phyla, Thermotogales and Aquificales. (mendeley.com)
  • Further analyses show that the TFEβ protein is actually related to a protein subunit that is unique to RNAP III, another eukarotyic RNAP. (elifesciences.org)
  • The ribosome of E. coli has about 22 proteins in the small subunit (labelled S1 to S22) and 33 proteins in the large subunit (somewhat counter-intuitively called L1 to L36). (wikipedia.org)
  • Ribosomal protein L13 is one of the proteins from the large ribosomal subunit [ PMID: 8119894 ]. (ebi.ac.uk)
  • In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit. (ebi.ac.uk)
  • The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). (ebi.ac.uk)
  • Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. (ebi.ac.uk)
  • In addition, the PriS-CTD does not appear to be present in the eukaryotic primase small subunit proteins. (biomedcentral.com)
  • The function of the non-catalytic primase subunit is less clear but experiments suggest that this protein might have a role in determining (or limiting) the length of the RNA primer synthesised by the catalytic subunit [ 7 ]. (biomedcentral.com)
  • POP4 (POP4 Homolog, Ribonuclease P/MRP Subunit) is a Protein Coding gene. (genecards.org)
  • Conserved active site cysteine residue of archaeal THI4 homolog is essential for thiamine biosynthesis in Haloferax volcanii. (nih.gov)
  • We are leading the development of Haloferax volcanii as a powerful model microorganism for molecular cell biology, and for understanding cytoskeletal protein function and evolution. (edu.au)
  • The viral particle is composed of a 37-kDa major capsid protein (MCP) and several 25-, 12.5-, and 10-kDa minor capsid proteins ( 2 ). (pnas.org)
  • Stedman, K.M. Genetic Analysis of the Major Capsid Protein of the Archaeal Fusellovirus SSV1: Mutational Flexibility and Conformational Change. (preprints.org)
  • The best-studied spindle-shaped virus, SSV1, is composed mostly of the major capsid protein VP1. (preprints.org)
  • Crystallographic analysis of archaeal ribosomal protein L11. (nih.gov)
  • a ) Photograph of a crystal of the ribosomal protein MjaL11. (nih.gov)
  • b ) Photograph of crystals of the selenomethionine derivative of the ribosomal protein MjaL11. (nih.gov)
  • A leucine zipper-like motif and a basic region-leucine zipper-like element in rat ribosomal protein L13a. (ebi.ac.uk)
  • This model finds the archaeal and eukaryotic forms of ribosomal protein uL16, previously L10.e. (jcvi.org)
  • L10.e is distantly related to eubacterial ribosomal protein L16. (jcvi.org)
  • Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. (mpg.de)
  • RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange. (umassmed.edu)
  • CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection. (iucr.org)
  • The most common types of filament are deeply related to eukaryotic cytoskeletal proteins, notably actin and tubulin that polymerise and depolymerise under the control of nucleotide hydrolysis. (springer.com)
  • Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. (elifesciences.org)
  • These studies have formed the basis of further investigations into the important role that the copine proteins play in vivo. (exeter.ac.uk)
  • The Arabidopsis GET system functioned in vivo to insert TA proteins into ER membranes as demonstrated by the fact that the YFP-tagged SYP72 localized to the ER in wild-type plants but accumulated as cytoplasmic inclusions in get1 , get3 , or get4 mutants. (plantphysiol.org)
  • This pore could be plugged in vivo either by lipid or other partner proteins. (alzforum.org)
  • To date, there is no complete structure of archaeal L11 owing to the mobility of the N-terminal domain of the protein. (nih.gov)
  • The MCP structure also provides insights into the stabilizing forces required for extracellular hyperthermophilic proteins to tolerate high-temperature hot springs. (pnas.org)
  • The MCP (an extracellular protein) structure also suggests how proteins may be able to tolerate the extreme physicochemical habitat of high-temperature hot spring environments. (pnas.org)
  • In addition to providing direct evidence for such an assembly in eukaryotic snRNPs, this structure (i) shows that SmAP homodimers are structurally similar to human Sm heterodimers, (ii) supports a gene duplication model of Sm protein evolution, and (iii) offers a model of SmAP bound to single-stranded RNA (ssRNA) that explains Sm binding-site specificity. (rcsb.org)
  • Spatial elucidation of motion in proteins by ensemble-based structure calculation using exact NOEs. (ebscohost.com)
  • Drlica and Rouviere-Yaniv, 1987 ) and predicted secondary, tertiary and quaternary structure ( Figure 1a-b ), HTa is a member of the HU family of proteins. (elifesciences.org)
  • We present here the NMR chemical shifts assignments of each partner in the complex, 1H 15N MC1 protein and 1H 13C 15N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex. (cnrs-orleans.fr)
  • Protein binding to helical junctions is important for initiating the correct tertiary fold of RNA and to organize the overall structure. (wikipedia.org)
  • In this way proteins serve to organise and stabilise the rRNA tertiary structure. (ebi.ac.uk)
  • The crystal structure of one of the four proteins, the catalytic type ThrRS from A. pernix , has successfully been solved by the Se-MAD method. (iucr.org)
  • Edwards, Thomas A. The crystal structure of the Hazara virus nucleocapsid protein . (wikipedia.org)
  • Barr, John N. Structure, Function, and Evolution of the Crimean-Congo Hemorrhagic Fever Virus Nucleocapsid Protein . (wikipedia.org)
  • The crystal structure of Arabidopsis BON1 provides insights into the copine protein family. (exeter.ac.uk)
  • The structure of the universal stress protein in Methanocaldococcus jannaschii (MJ0557) forms a dimer. (bioquest.org)
  • In The ConSurf Server, chose Amino-Acids/know protein structure - Yes and pDB ID: 1h5b / Chain Identifier: B. Here are two pictures to show the result picture and the picture with reserved residues. (bioquest.org)
  • Recent studies on archaeal motility have shown that the archaeal motility structure is unique in several aspects as, although it fulfills the same swimming function as the bacterial flagellum, it i. (scoop.it)
  • Another quarter encodes proteins unique to the archaeal domain. (kenyon.edu)
  • 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)
  • [6] A key to extremophile adaptation is their amino acid composition, affecting their protein folding ability under particular conditions. (wikipedia.org)
  • TA proteins are defined as proteins that lack other secretory signals and have a predicted TMD within 50 amino acid residues of the C-terminal tail. (plantphysiol.org)
  • Laboratory research experience in molecular biology and microbiology, particularly application of recombinant DNA technology in microorganisms, and/or protein science. (edu.au)