Proteins found in any species of archaeon.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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.
Viruses whose hosts are in the domain ARCHAEA.
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.
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.
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.
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.
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.
A genus of facultatively anaerobic coccoid ARCHAEA, in the family SULFOLOBACEAE. Cells are highly irregular in shape and thermoacidophilic. Lithotrophic growth occurs aerobically via sulfur oxidation in some species. Distribution includes solfataric springs and fields, mudholes, and geothermically heated acidic marine environments.
The simplest saturated hydrocarbon. It is a colorless, flammable gas, slightly soluble in water. It is one of the chief constituents of natural gas and is formed in the decomposition of organic matter. (Grant & Hackh's Chemical Dictionary, 5th ed)
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
A kingdom of hyperthermophilic ARCHAEA found in diverse environments.
A phylum of ARCHAEA comprising at least seven classes: Methanobacteria, Methanococci, Halobacteria (extreme halophiles), Archaeoglobi (sulfate-reducing species), Methanopyri, and the thermophiles: Thermoplasmata, and Thermococci.
A genus of strictly anaerobic ultrathermophilic archaea, in the family THERMOCOCCACEAE, occurring in heated seawaters. They exhibit heterotrophic growth at an optimum temperature of 100 degrees C.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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.
A genus of facultatively anaerobic heterotrophic archaea, in the order THERMOPLASMALES, isolated from self-heating coal refuse piles and acid hot springs. They are thermophilic and can grow both with and without sulfur.
Compounds in which one or more of the three hydroxyl groups of glycerol are in ethereal linkage with a saturated or unsaturated aliphatic alcohol; one or two of the hydroxyl groups of glycerol may be esterified. These compounds have been found in various animal tissue.
A family of THERMOPROTEALES consisting of variable length rigid rods without septa. They grow either chemolithoautotrophically or by sulfur respiration. The four genera are: PYROBACULUM; THERMOPROTEUS; Caldivirga; and Thermocladium. (From Bergey's Manual of Systematic Bacteriology, 2d ed)
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
A genus of anaerobic, rod-shaped METHANOBACTERIACEAE. Its organisms are nonmotile and use ammonia as the sole source of nitrogen. These methanogens are found in aquatic sediments, soil, sewage, and the gastrointestinal tract of animals.
An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. There are two families: METHANOSARCINACEAE and Methanosaetaceae.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
An order of anaerobic, coccoid to rod-shaped methanogens, in the kingdom EURYARCHAEOTA. They are nonmotile, do not catabolize carbohydrates, proteinaceous material, or organic compounds other than formate or carbon monoxide, and are widely distributed in nature.
The small subunit of archaeal RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 28 different RIBOSOMAL PROTEINS.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A family of archaea, in the order DESULFUROCOCCALES, consisting of anaerobic cocci which utilize peptides, proteins or carbohydrates facultatively by sulfur respiration or fermentation. There are eight genera: AEROPYRUM, Desulfurococcus, Ignicoccus, Staphylothermus, Stetteria, Sulfophoboccus, Thermodiscus, and Thermosphaera. (From Bergey's Manual of Systematic Bacteriology, 2d ed)
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A family of anaerobic METHANOCOCCALES whose organisms are motile by means of flagella. These methanogens use carbon dioxide as an electron acceptor.
An order of CRENARCHAEOTA consisting of aerobic or facultatively aerobic, chemolithotrophic cocci which are extreme thermoacidophiles. They lack peptidoglycan in their cell walls.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
A kingdom in the domain ARCHAEA, comprising thermophilic organisms from terrestrial hot springs that are among the most primitive of all life forms. They have undergone comparatively little evolutionary change since the last common ancestor of all extant life.
The variety of all native living organisms and their various forms and interrelationships.
A species of halophilic archaea found in salt lakes. Some strains form a PURPLE MEMBRANE under anaerobic conditions.
A genus of HALOBACTERIACEAE distinguished from other genera in the family by the presence of specific derivatives of TGD-2 polar lipids. Haloarcula are found in neutral saline environments such as salt lakes, marine salterns, and saline soils.
A family of anaerobic METHANOSARCINALES whose cells are mesophilic or thermophilic and appear as irregular spheroid bodies or sheathed rods. These methanogens are found in any anaerobic environment including aquatic sediments, anaerobic sewage digesters and gastrointestinal tracts. There are four genera: METHANOSARCINA, Methanolobus, Methanothrix, and Methanococcoides.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
A genus of HALOBACTERIACEAE which are chemoorganotrophic and strictly aerobic. They have been isolated from multiple hypersaline environments that vary widely in chemical and physical properties.
Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Group II chaperonins found in species of ARCHAEA.
A group of different species of microorganisms that act together as a community.
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
An order of anaerobic, highly specialized methanogens, in the kingdom EURYARCHAEOTA. Its organisms are nonmotile or motile, with cells occurring as coccoid bodies, pseudosarcina, or rods. Families include METHANOMICROBIACEAE, Methanocorpusculaceae, and Methanospirillaceae.
Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.
A family of extremely halophilic archaea found in environments with high salt concentrations, such as salt lakes, evaporated brines, or salted fish. Halobacteriaceae are either obligate aerobes or facultative anaerobes and are divided into at least twenty-six genera including: HALOARCULA; HALOBACTERIUM; HALOCOCCUS; HALOFERAX; HALORUBRUM; NATRONOBACTERIUM; and NATRONOCOCCUS.
The genetic complement of a BACTERIA as represented in its DNA.
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.
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
A genus of rod-shaped, almost rectangular ARCHAEA, in the family THERMOPROTEACEAE. Organisms are facultatively aerobic or strictly anaerobic, grow on various organic substrates, and are found in continental solfataras.
An order of extremely thermophilic, sulfate-reducing archaea, in the kingdom EURYARCHAEOTA. The single family Archaeoglobaceae contains one genus ARCHAEOGLOBUS.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
A colorless alkaline gas. It is formed in the body during decomposition of organic materials during a large number of metabolically important reactions. Note that the aqueous form of ammonia is referred to as AMMONIUM HYDROXIDE.
A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.
A genus of extremely thermophilic, sulfate-reducing archaea, in the family Archaeoglobaceae.
An order of CRENARCHAEOTA comprised of rod, disc, or spherical shaped, nonseptate, anaerobic, extreme thermophiles and found in solfataric hot waters, mud holes, and superheated submarine environments.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Peptide initiation factors from prokaryotic organisms. Only three factors are needed for translation initiation in prokaryotic organisms, which occurs by a far simpler process than in PEPTIDE CHAIN INITIATION, TRANSLATIONAL of eukaryotic organisms.
An order of extremely halophilic archaea, in the kingdom EURYARCHAEOTA. They occur ubiquitously in nature where the salt concentration is high, and are chemoorganotrophic, using amino acids or carbohydrates as a carbon source.
A family of multisubunit protein complexes that form into large cylindrical structures which bind to and encapsulate non-native proteins. Chaperonins utilize the energy of ATP hydrolysis to enhance the efficiency of PROTEIN FOLDING reactions and thereby help proteins reach their functional conformation. The family of chaperonins is split into GROUP I CHAPERONINS, and GROUP II CHAPERONINS, with each group having its own repertoire of protein subunits and subcellular preferences.
Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Proteins found in any species of bacterium.
The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)
An RNA POLYMERASE II specific transcription factor. It plays a role in assembly of the pol II transcriptional preinitiation complex and has been implicated as a target of gene-specific transcriptional activators.
Enzymes that recognize CRUCIFORM DNA structures and introduce paired incisions that help to resolve the structure into two DNA helices.
The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
A family of archaea, in the order DESULFUROCOCCALES consisting of anaerobic coccoid to disc-shaped cells. They grow either chemolithoautotrophically or by FERMENTATION. Three genera are recognized: Pyrodictium, Hyperthermus, and Pyrolobus.
Hot springs on the ocean floor. They are commonly found near volcanically active places such as mid-oceanic ridges.
Electrophoresis in which various denaturant gradients are used to induce nucleic acids to melt at various stages resulting in separation of molecules based on small sequence differences including SNPs. The denaturants used include heat, formamide, and urea.
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.
The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Proteins prepared by recombinant DNA technology.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
A genus of extremely halophilic HALOBACTERIACEAE which are chemoheterotropic and strictly aerobic. They are found in neutral saline environments such as salt lakes (especially the Dead Sea) and marine salterns.
A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.
An enzyme that activates leucine with its specific transfer RNA. EC 6.1.1.4.
The functional hereditary units of BACTERIA.
A genus of herbaceous annual and perennial plants in the family RUBIACEAE.
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
The processes by which organisms use simple inorganic substances such as gaseous or dissolved carbon dioxide and inorganic nitrogen as nutrient sources. Contrasts with heterotrophic processes which make use of organic materials as the nutrient supply source. Autotrophs can be either chemoautotrophs (or chemolithotrophs), largely ARCHAEA and BACTERIA, which also use simple inorganic substances for their metabolic energy reguirements; or photoautotrophs (or photolithotrophs), such as PLANTS and CYANOBACTERIA, which derive their energy from light. Depending on environmental conditions some organisms can switch between different nutritional modes (autotrophy; HETEROTROPHY; chemotrophy; or PHOTOTROPHY) to utilize different sources to meet their nutrient and energy requirements.
Areas of the earth where hydrocarbon deposits of PETROLEUM and/or NATURAL GAS are located.
Water containing no significant amounts of salts, such as water from RIVERS and LAKES.
A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.
Physiological processes and properties of BACTERIA.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
The conversion of uncharged TRANSFER RNA to AMINO ACYL TRNA.
A family of anaerobic METHANOMICROBIALES whose cells are coccoid to straight or slightly curved rods. There are six genera.
A subcategory of chaperonins found in ARCHAEA and the CYTOSOL of eukaryotic cells. Group II chaperonins form a barrel-shaped macromolecular structure that is distinct from GROUP I CHAPERONINS in that it does not utilize a separate lid like structure to enclose proteins.
Substances of archaeal origin that have antigenic activity.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
Immunoglobulins produced in a response to ARCHAEAL ANTIGENS.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Inland bodies of still or slowly moving FRESH WATER or salt water, larger than a pond, and supplied by RIVERS and streams.
A plant family of the order Myrtales, subclass Rosidae, class Magnoliopsida. They are mostly trees and shrubs growing in warm areas.
Community of tiny aquatic PLANTS and ANIMALS, and photosynthetic BACTERIA, that are either free-floating or suspended in the water, with little or no power of locomotion. They are divided into PHYTOPLANKTON and ZOOPLANKTON.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Electron microscopy involving rapid freezing of the samples. The imaging of frozen-hydrated molecules and organelles permits the best possible resolution closest to the living state, free of chemical fixatives or stains.
A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Protein components of the CRISPR-CAS SYSTEMS for anti-viral defense in ARCHAEA and BACTERIA. These are proteins that carry out a variety of functions during the creation and expansion of the CRISPR ARRAYS, the capture of new CRISPR SPACERS, biogenesis of SMALL INTERFERING RNA (CRISPR or crRNAs), and the targeting and silencing of invading viruses and plasmids. They include DNA HELICASES; RNA-BINDING PROTEINS; ENDONUCLEASES; and RNA and DNA POLYMERASES.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).
Bacteriophage and type species in the genus Tectivirus, family TECTIVIRIDAE. They are specific for Gram-negative bacteria.
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
An enzyme found primarily in SULFUR-REDUCING BACTERIA where it plays an important role in the anaerobic carbon oxidation pathway.
The systematic study of the complete DNA sequences (GENOME) of organisms.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
A collective genome representative of the many organisms, primarily microorganisms, existing in a community.
A species of halophilic archaea whose organisms are nonmotile. Habitats include freshwater and marine mud, animal-waste lagoons, and the rumens of ungulates.
The complete absence, or (loosely) the paucity, of gaseous or dissolved elemental oxygen in a given place or environment. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
A genus of HALOBACTERIACEAE whose growth requires a high concentration of salt. Binary fission is by constriction.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
An enzyme that activates serine with its specific transfer RNA. EC 6.1.1.11.
The continent lying around the South Pole and the southern waters of the Atlantic, Pacific, and Indian Oceans. It includes the Falkland Islands Dependencies. (From Webster's New Geographical Dictionary, 1988, p55)
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.
A transfer RNA which is specific for carrying glutamine to sites on the ribosomes in preparation for protein synthesis.
The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
An element that is a member of the chalcogen family. It has an atomic symbol S, atomic number 16, and atomic weight [32.059; 32.076]. It is found in the amino acids cysteine and methionine.
Photosensory rhodopsins found in microorganisms such as HALOBACTERIA. They convert light signals into biochemical information that regulates certain cellular functions such as flagellar motor activity.
A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.
The process by which a DNA molecule is duplicated.
The sequential location of genes on a chromosome.
Enzymes of the isomerase class that catalyze the transfer of acyl-, phospho-, amino- or other groups from one position within a molecule to another. EC 5.4.
A transfer RNA which is specific for carrying asparagine to sites on the ribosomes in preparation for protein synthesis.
Growth of organisms using AUTOTROPHIC PROCESSES for obtaining nutrients and chemotrophic processes for obtaining a primary energy supply. Chemotrophic processes are involved in deriving a primary energy supply from exogenous chemical sources. Chemotrophic autotrophs (chemoautotrophs) generally use inorganic chemicals as energy sources and as such are called chemolithoautotrophs. Most chemoautotrophs live in hostile environments, such as deep sea vents. They are mostly BACTERIA and ARCHAEA, and are the primary producers for those ecosystems.
Iron-containing proteins that transfer electrons, usually at a low potential, to flavoproteins; the iron is not present as in heme. (McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)
Nucleolar RNA-protein complexes that function in pre-ribosomal RNA processing.
A rod-shaped bacterium surrounded by a sheath-like structure which protrudes balloon-like beyond the ends of the cell. It is thermophilic, with growth occurring at temperatures as high as 90 degrees C. It is isolated from geothermally heated marine sediments or hot springs. (From Bergey's Manual of Determinative Bacteriology, 9th ed)
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
An enzyme that activates lysine with its specific transfer RNA. EC 6.1.1.6.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The rate dynamics in chemical or physical systems.
A phylum of bacteria consisting of the purple bacteria and their relatives which form a branch of the eubacterial tree. This group of predominantly gram-negative bacteria is classified based on homology of equivalent nucleotide sequences of 16S ribosomal RNA or by hybridization of ribosomal RNA or DNA with 16S and 23S ribosomal RNA.
The immediate physical zone surrounding plant roots that include the plant roots. It is an area of intense and complex biological activity involving plants, microorganisms, other soil organisms, and the soil.
An enzyme that activates tyrosine with its specific transfer RNA. EC 6.1.1.1.
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
Peptide elongation factor 1 is a multisubunit protein that is responsible for the GTP-dependent binding of aminoacyl-tRNAs to eukaryotic ribosomes. The alpha subunit (EF-1alpha) binds aminoacyl-tRNA and transfers it to the ribosome in a process linked to GTP hydrolysis. The beta and delta subunits (EF-1beta, EF-1delta) are involved in exchanging GDP for GTP. The gamma subunit (EF-1gamma) is a structural component.
The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.
A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A genus of rod-shaped, extremely halophilic HALOBACTERIACEAE which grows in alkaline conditions. They are strictly aerobic and some strains are motile. Natronobacterium is found in soda lakes, alkaline salterns, and soda soils.
Tools or devices for generating products using the synthetic or chemical conversion capacity of a biological system. They can be classical fermentors, cell culture perfusion systems, or enzyme bioreactors. For production of proteins or enzymes, recombinant microorganisms such as bacteria, mammalian cells, or insect or plant cells are usually chosen.
Sets of enzymatic reactions occurring in organisms and that form biochemicals by making new covalent bonds.
The study of the origin, structure, development, growth, function, genetics, and reproduction of organisms which inhabit the OCEANS AND SEAS.

Proposal to transfer Halococcus turkmenicus, Halobacterium trapanicum JCM 9743 and strain GSL-11 to Haloterrigena turkmenica gen. nov., comb. nov. (1/817)

The 16S rRNA gene sequences of Halococcus saccharolyticus and Halococcus salifodinae were closely related (94.5-94.7% similarity) to that of Halococcus morrhuae, the type species of the genus Halococcus. However, Halococcus turkmenicus was distinct from the other members of this genus, with low 16S rRNA similarities when compared to Halococcus morrhuae (88.7%). On the basis of phylogenetic tree reconstruction, detection of signature bases and DNA-DNA hybridization data, it is proposed to transfer Halococcus turkmenicus to a novel genus, Haloterrigena, as Haloterrigena turkmenica gen. nov., comb. nov., and to accommodate Halobacterium trapanicum JCM 9743 and strain GSL-11 in the same species. On the basis of morphological, cultural and 16S rRNA sequence data, it is also proposed that the culture collection strains of Halobacterium trapanicum NCIMB 767, ATCC 43102 and JCM 8979 should be renamed as Halococcus sp.  (+info)

An Lrp-like protein of the hyperthermophilic archaeon Sulfolobus solfataricus which binds to its own promoter. (2/817)

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)

Expression of the Methanobacterium thermoautotrophicum hpt gene, encoding hypoxanthine (Guanine) phosphoribosyltransferase, in Escherichia coli. (3/817)

The hpt gene from the archaeon Methanobacterium thermoautotrophicum, encoding hypoxanthine (guanine) phosphoribosyltransferase, was cloned by functional complementation into Escherichia coli. The hpt-encoded amino acid sequence is most similar to adenine phosphoribosyltransferases, but the encoded enzyme has activity only with hypoxanthine and guanine. The synthesis of the recombinant enzyme is apparently limited by the presence of the rare arginine codons AGA and AGG and the rare isoleucine AUA codon on the hpt gene. The recombinant enzyme was purified to apparent homogeneity.  (+info)

Halobacterial rhodopsins. (4/817)

Following the discovery of the bacteriorhodopsin proton pump in Halobacterium halobium (salinarum), not only the halorhodopsin halide pump and two photosensor rhodopsins (sensory rhodopsin and phoborhodopsin) in the same species, but also homologs of these four rhodopsins in strains of other genera of Halobacteriaceae have been reported. Twenty-eight full (and partial) sequences of the genomic DNA of these rhodopsins have been analyzed. The deduced amino acid sequences have led to new strategies and tactics for understanding bacterial rhodopsins on a comparative basis, as summarized briefly in this article. The data discussed include (i) alignment of the sequences to qualify/characterize the conserved residues; (ii) assignment of residues that cause differences in function(s)/properties; and (iii) phylogeny of the halobacterial rhodopsins to suggest their evolutionary paths. The four kinds of rhodopsin in each strain are assumed, on the basis of their genera-specific distributions, to have arisen by at least two gene-duplication processes during evolution prior to generic speciation. The first duplication of the rhodopsin ancestor gene yielded two genes, each of which was duplicated again to give four genes in the ancestor halobacterium. The bacterium carrying four rhodopsin genes, after accumulating mutations, became ready for generic speciation and the delivery of four rhodopsins to each species. The original rhodopsin ancestor is speculated to be closest to the proton pump (bacteriorhodopsin).  (+info)

Isolation and characterization of a second subunit of molecular chaperonin from Pyrococcus kodakaraensis KOD1: analysis of an ATPase-deficient mutant enzyme. (5/817)

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)

10-11 bp periodicities in complete genomes reflect protein structure and DNA folding. (6/817)

MOTIVATION: Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Two sources contribute to such signals: correlations in the corresponding protein sequences due to the amphipatic character of alpha-helices and the folding of DNA (nucleosomal patterns, DNA supercoiling). Since the topological state of genomic DNA is of importance for its replication, recombination and transcription, there is an immediate interest to obtain information about the supercoiled state from sequence periodicities. RESULTS: We show that correlations within proteins affect mainly the oscillations at distances below 35 bp. The long-ranging correlations up to 100 bp reflect primarily DNA folding. For the yeast genome these oscillations are consistent in detail with the chromatin structure. For eubacteria and archaea the periods deviate significantly from the 10.55 bp value for free DNA. These deviations suggest that while a period of 11 bp in bacteria reflects negative supercoiling, the significantly different period of thermophilic archaea close to 10 bp corresponds to positive supercoiling of thermophilic archaeal genomes. AVAILABILITY: Protein sets and C programs for the calculation of correlation functions are available on request from the authors (see http://itb.biologie.hu-berlin.de).  (+info)

Thermococcus barophilus sp. nov., a new barophilic and hyperthermophilic archaeon isolated under high hydrostatic pressure from a deep-sea hydrothermal vent. (7/817)

A novel barophilic, hyperthermophilic, anaerobic sulfur-metabolizing archaeon, strain MPT (T = type strain), was isolated from a hydrothermal vent site (Snakepit) on the Mid-Atlantic Ridge (depth, 3550 m). Enrichments and isolation were done under 40 MPa hydrostatic pressure at 95 degrees C. Strain MPT was barophilic at 75, 80, 85, 90, 95 and 98 degrees C, and was an obligate barophile between 95 and 100 degrees C (Tmax). For growth above 95 degrees C, a pressure of 15.0-17.5 MPa was required. The strain grew at 48-95 degrees C under atmospheric pressure. The optimal temperature for growth was 85 degrees C at both high (40 MPa) and low (0.3 MPa) pressures. The growth rate was twofold higher at 85 degrees C under in situ hydrostatic pressure compared to at low pressure. Strain MPT cells were motile, coccoid, 0.8-2.0 microns in diameter and covered by a hexagonal S-layer lattice. The optimum pH and NaCl concentration for growth at low pressure were 7.0 and 20-30 g l-1, respectively. The new isolate was an obligate heterotroph and utilized yeast extract, beef extract and peptone for growth. Growth was optimal in the presence of elemental sulfur. Rifampicin and chloramphenicol inhibited growth. The core lipids consisted of a major archaeol and a complex lipid pattern consisting of a major phospholipid. The DNA G + C content was 37.1 mol%. Sequencing of the 16S rRNA gene revealed that strain MPT belonged to the genus Thermococcus and it is proposed that this isolate should be designated as a new species, Thermococcus barophilus.  (+info)

Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov. (8/817)

An autotrophic, hyperthermophilic methanogen (M7T) was isolated from a deep-sea hydrothermal chimney sample collected on the East Pacific Rise at a depth of 2600 m. The coccoid-shaped cells are flagellated and exhibit a slight tumbling motility. The temperature range for growth at pH 6.5 was 49-89 degrees C, with optimum growth at 80 degrees C. The optimum pH for growth was 6.5, and the optimum NaCl concentration for growth was around 25 g l-1. The new isolate used H2 and CO2 as the only substrates for growth and methane production. Tungsten, selenium and yeast extract stimulated growth significantly. In the presence of CO2 and H2, the organism reduced elemental sulphur to hydrogen sulphide. Growth was inhibited by chloramphenicol and rifampicin, but not by ampicillin, kanamycin, penicillin and streptomycin. The G + C content of the genomic DNA was 31 mol%. As determined by 16S rDNA gene sequence analysis, this organism was closely related to Methanococcus jannaschii strain JAL-1T. However, despite the high percentage of similarity between their 16S rDNA sequences (97.1%), the DNA-DNA hybridization levels between these strains were less than 5%. On the basis of these observations and physiological traits, it is proposed that this organism should be placed in a new species, Methanococcus vulcanius. The type strain is M7T (= DSM 12094T). During the course of this study, the 16S rDNA sequence analysis placed Methanococcus sp. strain AG86T (= DSM 4213T) as a close relative of M. jannaschii strain JAL-1T. However, the weak level of DNA-DNA hybridization with this strain (< 10%) allowed the proposal that strain AG86T also constitutes a new species, Methanococcus fervens.  (+info)

Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. Full details of the specific recognition of hypoxanthine are revealed, allowing a comparison with published data that describe uracil binding. The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. Specificity for hypoxanthine (and uracil) arises from a combination of polymerase-base hydrogen bonds and shape fit between the deaminated bases and the pocket. The structure with hypoxanthine at position 2 explains the stimulation of the polymerase 3-5 proofreading exonuclease, observed with deaminated bases at this location. A beta-hairpin element, involved in partitioning the primer ...
CiteSeerX - Scientific documents that cite the following paper: Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil
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,
Two halophilic archaea, designated strains WSM-64(T) and WSM-66, were isolated from a sample taken from a borehole in the currently unexploited Barycz mining area belonging to the Wieliczka Salt Mine Company, in Poland. Strains are red pigmented and form non-motile cocci that stain Gram-negative. Strains WSM-64(T) and WSM-66 showed optimum growth at 40 °C, in 20% NaCl and at pH 6.5-7.5. The strains were facultative anaerobes. The major polar lipids of the two strains were phosphatidylglycerol (PG2), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulfated diglycosyl diether (S-DGD). Menaquinone MK-8 was the major respiratory quinone. The DNA G+C content of strain WSM-64(T) was 61.2 mol% by HPLC method; 61.0 mol% by genome sequencing. Analysis of the almost complete 16S rRNA gene sequence indicated that the strains WSM-64(T) and WSM-66 (99.7% identity) represented a member of the genus Halorhabdus in the family Halobacteriaceae. Both strains formed a distinct cluster and were most ...
A novel halophilic archaeon, strain KeC-11T, was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0-8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11T were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis GabaraT (91 % sequence similarity). The strain contained C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data
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
F. acidiphilum cells during exponential phase are pleomorphic in shape and are 0.4-0.9 um in length. They also have membrane bound electron-transport zones and no cell wall. Sulfides exposed to air and water undergo oxidative dissolution by the reaction FeS2 + 14Fe3+ + 8H2O → 15Fe2+ +2SO42- + 16H+. By producing Fe3+, Ferroplasma is able to drive this reaction forward, oxidizing FeS2. Both Ferroplasma species are heterotrophic, growing best on yeast extract. These species are also aerobic, requiring oxygen for growth. ...
F. acidiphilum cells during exponential phase are pleomorphic in shape and are 0.4-0.9 um in length. They also have membrane bound electron-transport zones and no cell wall. Sulfides exposed to air and water undergo oxidative dissolution by the reaction FeS2 + 14Fe3+ + 8H2O → 15Fe2+ +2SO42- + 16H+. By producing Fe3+, Ferroplasma is able to drive this reaction forward, oxidizing FeS2. Both Ferroplasma species are heterotrophic, growing best on yeast extract. These species are also aerobic, requiring oxygen for growth. ...
2-Carboxyphenyl phosphate methyl ester | C8H9O6P | CID 577581 - structure, chemical names, physical and chemical properties, classification, patents, literature, biological activities, safety/hazards/toxicity information, supplier lists, and more.
Gihring, Thomas M.; Bond, Philip L.; Peters, Stephen C.; Banfield, Jillian F. «Arsenic resistance in the archaeon Ferroplasma acidarmanus: new insights into the structure and evolution of the ars genes». Extremophiles. Springer-Verlag, 7, 2, 01-04-2003, pàg. 123-130. DOI: 10.1007/s00792-002-0303-6. ISSN: 1433-4909. ...
Halogeometricum borinquense ATCC ® 700274D-5™ Designation: Genomic DNA from Halogeometricum borinquense strain PR3 TypeStrain=True Application:
General Information: Environment: Lake, Fresh water; Isolation: Lake Magadi, Kenya; Temp: Mesophile. A haloalkaliphilic archaeon. ...
Strains C23T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18 % salts at around neutral pH. Mg2+ is not required. The DNA G+C content of both isolates was 46.9 mol% and DNA-DNA cross-hybridization showed a relatedness of 80 %. Their 16S rRNA gene sequences showed only 2 nucleotide differences (99.9 % identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3T (91.2 % sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S
2W8L: Versatility of Y-Family Sulfolobus Solfataricus DNA Polymerase Dpo4 in Translesion Synthesis Past Bulky N2-Alkylguanine Adducts.
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.
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 ...
Huber, R., Sthr, J., Hohenhaus, S., Rachel, R., Burggraf, S., Jannasch, H.W., and Stetter, K.O. Thermococcus chitonophagus sp. nov., a novel, chitin-degrading, hyperthermophilic archaeum from a deep-sea hydrothermal vent environment. Arch. Microbiol. (1996) 164:255-264 ...
Synonyms for crystallizer in Free Thesaurus. Antonyms for crystallizer. 29 synonyms for crystallize: take shape, form, become clear, come together, materialize, harden, solidify, coalesce, form crystals, crystallise, crystalise.... What are synonyms for crystallizer?
hjm52mar19 - single man seeking a woman in Calgary, Alberta, Canada. 68 y.o. Zodiac sign: Capricorn. Contact Alberta man hjm52mar19 for online relations. I admittedly am a little overweight but try to keep active play softball in the summer and volleybal
ID METB6_1_PE1832 STANDARD; PRT; 348 AA. AC METB6_1_PE1832; A7I9E4; 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=Putative translation initiation factor, aIF-2BI family; DE EC=5.3.1 23; (METB6_1.PE1832). GN OrderedLocusNames=Mboo_1840; OS METHANOREGULA BOONEI 6A8. OC Archaea; Euryarchaeota; Methanomicrobia; Methanomicrobiales; Genera OC incertae sedis; Methanoregula. OX NCBI_TaxID=456442; RN [0] RP -.; RG -.; RL -.; CC -!- SEQ. DATA ORIGIN: Translated from the HOGENOM CDS METB6_1.PE1832. CC Candidatus Methanoregula boonei 6A8 chromosome, complete genome. CC sequence. CC -!- ANNOTATIONS ORIGIN:A7I9E4_METB6 CC -!- SIMILARITY: Belongs to the eIF-2B alpha/beta/delta subunits CC family. CC -!- GENE_FAMILY: HOG000224730 [ FAMILY / ALN / TREE ] DR UniProtKB/Swiss-Prot; A7I9E4; -. DR EMBL; CP000780; ABS56355.1; -; Genomic_DNA. DR RefSeq; YP_001404998.1; NC_009712.1. DR ProteinModelPortal; A7I9E4; -. DR SMR; ...
ID METB6_1_PE1496 STANDARD; PRT; 813 AA. AC METB6_1_PE1496; A7I8F8; 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=Plasma-membrane proton-efflux P-type ATPase; DE (METB6_1.PE1496). GN OrderedLocusNames=Mboo_1501; OS METHANOREGULA BOONEI 6A8. OC Archaea; Euryarchaeota; Methanomicrobia; Methanomicrobiales; Genera OC incertae sedis; Methanoregula. OX NCBI_TaxID=456442; RN [0] RP -.; RG -.; RL -.; CC -!- SEQ. DATA ORIGIN: Translated from the HOGENOM CDS METB6_1.PE1496. CC Candidatus Methanoregula boonei 6A8 chromosome, complete genome. CC sequence. CC -!- ANNOTATIONS ORIGIN:A7I8F8_METB6 CC -!- GENE_FAMILY: HOG000160005 [ FAMILY / ALN / TREE ] DR UniProtKB/Swiss-Prot; A7I8F8; -. DR EMBL; CP000780; ABS56019.1; -; Genomic_DNA. DR RefSeq; YP_001404662.1; NC_009712.1. DR ProteinModelPortal; A7I8F8; -. DR GeneID; 5410875; -. DR GenomeReviews; CP000780_GR; Mboo_1501. DR KEGG; mbn:Mboo_1501; -. DR eggNOG; ...
So, first a bit of biology. This will make more sense to you if you are not a creationist. Somewhere back in the mists of time -- long before the universe was created 6,000 years ago -- actually somewhere around 2 billion years ago, it seems that 2 (or possibly 3) simple prokaryotic cells entered into an endosymbiotic relationship. We dont know exactly how this happened. Prokaryotic cells dont have a nucleus and are otherwise relatively simple in their internal structure. There are two major kinds, called archaea and bacteria. The most straightforward explanation of the origin of the eukaryotes is that an archaeal cell somehow engulfed a bacterium, but didnt digest it. Instead, the bacterium reproduced and its progeny started living happily within the cytoplasm of the archaea and its descendants. The endosymbiotic bacteria gradually lost most of their DNA -- they didnt need it because their environment was properly managed by the archaeal DNA, which is now our nuclear DNA -- and they settled ...
This website tracks Sunit Jains development as a bioinformatics professional. Im currently working as a Research Computing Specialist -- Bioinformatics at the Department of Earth and Environmental Sciences and Michigan Geomicrobiology Lab, University of Michigan. My research focuses on Environmental Meta-omics and Comparative Genomics mostly in the Great Lakes(US) and deep sea hydrothermal vent environment.
Methanoculleus marisnigri ATCC ® 35101D-5™ Designation: Genomic DNA from Methanoculleus marisnigri strain JR1 TypeStrain=True Application:
Text is available under the Creative Commons Attribution-ShareAlike License; additional terms may apply. By using this site, you agree to the Terms of Use and Privacy Policy. ...
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 ...
General Information: Temp: Mesophile. Haloterrigena turkmenica, formerly Halococcus turkmenicus, is a halophilic archaeon isolated from soil. ...
The aim of this work was to study whether feeding a methanogen inhibitor from birth of goat kids and their does has an impact on the archaeal population colonizing the rumen and to what extent the impact persists later in ...
Fingerprint Dive into the research topics of Electrophysiological characterization of the archaeal transporter NCX_Mj using solid supported membrane technology. Together they form a unique fingerprint. ...
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Dijkstra, Akkelies E.; Smolonska, J; Van Den Berge, M; Wijmenga, C; Zanen, P; Luinge, MA; Platteel, M; Lammers, JW; Dahlback, M; Tosh, K; Hiemstra, PS; Sterk, PJ; Spira, A; Vestbo, J; Nordestgaard, BG; Benn, M; Nielsen, SF; Dahl, M; Verschuren, WM; Picavet, HSJ; Smit, HA; Owsijewitsch, M; Kauczor, HU; De Koning, HJ; Nizankowska-Mogilnicka, E; Mejza, F; Nastalek, P; Van Diemen, CC; Cho, MH; Silverman, EK; Crapo, JD; Beaty, TH; Lomas, DA; Bakke, Per; Gulsvik, Amund; Bosse, Y; Obeidat, MA; Loth, DW; Lahousse, L; Rivadeneira, F; Uitterlinden, AG; Hofman, A; Stricker, BH; Brusselle, GG; Van Duijn, CM; Brouwer, U; Koppelman, GH; Vonk, JM; Nawijn, MC; Groen, HJM; Timens, W; Boezen, HM; Postma, DS; Alizadeh, BZ; De Boer, RA; Bruinenberg, M; Franke, L; Van Der Harst, P; Hillege, HL; Van Der Klauw, MM; Navis, G; Ormel, J; Rosmalen, J; Slaets, JP; Snieder, H; Stolk, RP; Wolffenbuttel, B (PLoS, 2014-04-08) ...
Dijkstra, Akkelies E.; Smolonska, J; Van Den Berge, M; Wijmenga, C; Zanen, P; Luinge, MA; Platteel, M; Lammers, JW; Dahlback, M; Tosh, K; Hiemstra, PS; Sterk, PJ; Spira, A; Vestbo, J; Nordestgaard, BG; Benn, M; Nielsen, SF; Dahl, M; Verschuren, WM; Picavet, HSJ; Smit, HA; Owsijewitsch, M; Kauczor, HU; De Koning, HJ; Nizankowska-Mogilnicka, E; Mejza, F; Nastalek, P; Van Diemen, CC; Cho, MH; Silverman, EK; Crapo, JD; Beaty, TH; Lomas, DA; Bakke, Per; Gulsvik, Amund; Bosse, Y; Obeidat, MA; Loth, DW; Lahousse, L; Rivadeneira, F; Uitterlinden, AG; Hofman, A; Stricker, BH; Brusselle, GG; Van Duijn, CM; Brouwer, U; Koppelman, GH; Vonk, JM; Nawijn, MC; Groen, HJM; Timens, W; Boezen, HM; Postma, DS; Alizadeh, BZ; De Boer, RA; Bruinenberg, M; Franke, L; Van Der Harst, P; Hillege, HL; Van Der Klauw, MM; Navis, G; Ormel, J; Rosmalen, J; Slaets, JP; Snieder, H; Stolk, RP; Wolffenbuttel, B (PLoS, 2014-04-08) ...
Euryarchaeota (es); Euryarchaeota (hu); Euryarchaeota (is); Euryarchaeota (ast); Euryarchaeota (nds); Euryarchaeota (de); Euryarchaeota (ga); پهن‌باستانیان (fa); 廣古菌門 (zh); Euryarchaeota (tr); ユリアーキオータ門 (ja); Euryarchaeota (ia); Euryarchaeota (sv); Евріархеоти (uk); Euryarchaeota (la); 유리고세균 (ko); Eŭriarkeoto (eo); Euryarchaeota (cs); Euryarchaeota (bs); Euryarchaeota (it); Euryarchaeota (fr); Euryarchaeota (jv); Euryarchaeota (et); Euryarchaeota (vi); Euriarqueotas (gl); Euryarchaeota (pt); Euryarchaeota (lt); Euryarchaeota (war); Euryarchaeota (tl); Euryarchaeota (id); Euriarqueot (ca); Euryarchaeota (ceb); Euryarchaeota (pl); Euryarchaeota (bg); Euryarchaeota (nl); эвриархеоты (ru); Euryarchaeota (sr); Euryarchaeota (ro); Euryarchaeota (nn); Euryarchaeota (en); عتائق عريضة (ar); Euryarchaeota (sq); Euryarchaeota (fi) тип архей (ru); archaea törzse, ország (hu); Stamm der Archaeen (Archaea) (de); ...
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 ...
Cold seeps in the Aleutian deep-sea trench support prolific benthic communities and generate carbonate precipitates which are dependent on carbon dioxide delivered from anaerobic methane oxidation. This process is active in the anaerobic sediments at the sulfate reduction-methane production boundary and is probably performed by archaea working in syntrophic co-operation with sulfate-reducing bacteria. Diagnostic lipid biomarkers of archaeal origin include irregular isoprenoids such as 2,6,11,15-tetramethylhexadecane (crocetane) and 2,6,10,15,19-pentamethylicosane (PMI) as well as the glycerol ether lipid archaeol (2,3-di-O-phytanyl-sn-glycerol). These biomarkers are prominent lipid constituents in the anaerobic sediments as well as in the carbonate precipitates. Carbon isotopic compositions of the biomarkers are strongly depleted in 13C with values of δ13C as low as −130.3‰ PDB. The process of anaerobic methane oxidation is also reflected in the carbon isotope composition of organic matter ...
Thermophilic bacteria and archaea that grow optimally between 50-80°C thrive in deep-sea hydrothermal vent environments. These organisms adapt and evolve unique chemosynthetic mechanisms to flourish in chemically rich vent environments in the complete absence of sunlight. This study examines one such mechanism in which microoganisms utilize Fe(III) oxides to gain energy through the metabolic process of dissimilatory iron reduction. Because the metabolism has not been studied and characterized for thermophilic bacteria and archaea, this thesis investigates the presence of such organisms in hydrothermal fluid samples collected from a diffuse vent site called Marker 113 at Axial Volcano in the northeastern Pacific Ocean. Organisms are isolated and enriched for with Fe(III) to obtain a pure isolate. Iron transformation was determined using ferrozine assays to measure Fe(II) production, and the mechanism utilized was investigated using visualization with scanning electron microscopy and transmission ...
In marine sediments archaea often constitute a considerable part of the microbial community, of which the Deep Sea Archaeal Group (DSAG) is one of the most predominant. Despite their high abundance no members from this archaeal group have so far been characterized and thus their metabolism is unknown. Here we show that the relative abundance of DSAG marker genes can be correlated with geochemical parameters, allowing prediction of both the potential electron donors and acceptors of these organisms. We estimated the abundance of 16S rRNA genes from Archaea, Bacteria, and DSAG in 52 sediment horizons from two cores collected at the slow-spreading Arctic Mid-Ocean Ridge, using qPCR. The results indicate that members of the DSAG make up the entire archaeal population in certain horizons and constitute up to ~50% of the total microbial community. The quantitative data were correlated to 30 different geophysical and geochemical parameters obtained from the same sediment horizons. We observed a significant
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 ...
Looking for Halococcus? Find out information about Halococcus. A genus of bacteria in the family Halobacteriaceae; nonmotile cocci which occur in pairs, tetrads, or clusters of tetrads Explanation of Halococcus
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 ...
original description Cui, H.-L., Sun, F.-F., Gao, X., Dong, Y., Xu, X.-W., Zhou, Y.-G., Liu, H.-C., Oren, A., and Zhou, P.-J. 2010. Haladaptatus litoreus sp. nov., an extremely halophilic archaeon from a marine solar saltern, and emended description of the genus Haladaptatus. Int. J. Syst. Evol. Microbiol. 60:1085-1089. [details] ...
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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 ...
Natura - nature Mundus - physical world;material world Naturalia Biota 3.1 Domain Archaea C.R. Woese et al., 1990 H,N,P,R,B,L; Ref:G.M. Garrity et al., 2007:6 (implicit position); Count:[*]4p;9c;15o;25f;97g;326s 1.1 Phylum Crenarchaeota G.M. Garrity & J.G. Holt, 2001 H,N,P,R,B,L; Ref:G.M. Garrity et al., 2007:6; Count:[*]1c;4o;6f;26g;54s 1.2 Phylum Thaumarchaeota H,N,P,R,B,L; Ref:J.P. Euz by, 1997-present:15 Jun 2009 (validity questionable); Count:[*]1o;1f;1g;1s 2 Phylum Euryarchaeota G.M. Garrity & J.G. Holt, 2001 H,N,P,R,B,L; Ref:G.M. Garrity et al., 2007:10; Count:[*]8c;10o;18f;69g;270s 3 Phylum Nanoarchaeota Huber et al., 2002 H,N,P,R,B,L; Ref:H. Huber et al., 2002 (new taxon); Count:[*]1g;1s ...
CiteSeerX - Scientific documents that cite the following paper: Phylogenetic diversity of the archaeal component in microbial mats on corallike structures associated with methane seeps in the Black Sea. Microbiology 71:196-201
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 ...
original description Jolivet, E., LHaridon, S., Corre, E., Forterre, P., and Prieur, D. Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation. Int. J. Syst. Evol. Microbiol. (2003) 53:847-851. [details] ...
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
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 …
The Cedars, shown here, is a small, isolated set of springs flowing out of a large patch of red rock from Earths mantle in Sonoma County, California. The
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.
Its official... Im a ttc maniac. Ive just used 2 frers at 8dpo, obviously negatives. The rational, normal part of me knows theres no way Id get
此手術只可在年輕的犬隻出現關節炎的退行性變化之前實施。手術的方法是將骨盆骨切開,矯正髖關節窩覆蓋股骨頭的角度,然後用骨板固定。這方法乃試著增加髖關節覆蓋率,避免骨頭間摩擦以減緩退行性病變及關節的脫臼 ...
I know The Courant is in favor of abolishing the sheriff system in Connecticut. I refer to the March 16 editorial ``Sheriffs Embarrass Themselves,'' along with many other one-sided editorials. What I wonder is why The Courant has taken on this task with such venom. Why are the editorials so one-sided and negative? Isn't there one thing that is good about the sheriff system?
van Wolferen M, Wagner A, van der Does C, Albers SV (2016). "The archaeal Ced system imports DNA". Proc Natl Acad Sci U S A. ... The nucleus is an organelle that houses the DNA that makes up a cell's genome. DNA (Deoxyribonucleic acid) itself is arranged ... DNA Repair: New Research. Nova Sci. Publ. pp. 1-49. ISBN 978-1-62100-808-8. Cavalier-Smith T (1 December 1993). "Kingdom ... Their genome is usually a circular bacterial chromosome - a single loop of DNA, although they can also harbor small pieces of ...
van Wolferen M, Wagner A, van der Does C, Albers SV (2016). "The archaeal Ced system imports DNA". Proc. Natl. Acad. Sci. U.S.A ... Under stressful environmental conditions that cause DNA damage, some species of archaea aggregate and transfer DNA between ... allows for efficient recombinational repair of DNA damage and a greater range of genetic diversity by combining the DNA of the ... Both organelles contain their own sets of DNA and have bacteria-like ribosomes. It is likely that modern mitochondria were once ...
"Inhibition of translesion DNA polymerase by archaeal reverse gyrase". Nucleic Acids Research. 37 (13): 4287-4295. doi:10.1093/ ... Using DNA-DNA hybridization, the total DNA-DNA relatedness of the two organisms was found to be 34.6 percent which, along with ... Analysis of this gene demonstrated that this organism shared 97.8 percent of its DNA for this gene with the related bacterium ... profundicola and this lack of external DNA is theorized to be a product of its own defense mechanisms or the lack of free DNA ...
"The archaeal Ced system imports DNA". Proc Natl Acad Sci U S A. 113 (9): 2496-501. Bibcode:2016PNAS..113.2496V. doi:10.1073/ ... "In Kimura, Sakura; Shimizu, Sora (eds.). DNA repair as the primary adaptive function of sex in bacteria and eukaryotes. DNA ... The nucleus is an organelle that houses the DNA that makes up a cell's genome. DNA (Deoxyribonucleic acid) itself is arranged ... Karner, M.B.; DeLong, E.F.; Karl, D.M. (2001). "Archaeal dominance in the mesopelagic zone of the Pacific Ocean". Nature. 409 ( ...
DNA topology is the tertiary conformations of DNA, such as supercoiling, knotting, and catenation. Topology of DNA can be ... There is limited knowledge about the archaeal genome sequences. Therefore, there is also limited knowledge about the ... Experiments have demonstrated that positive supercoiled DNA provides a sharp DNA bend in the first bound DNA segment, which ... the DNA backbone is resealed again. Since the overall chemical composition and connectivity of the DNA do not change, the DNA ...
This protein domain provides the precursors necessary for DNA synthesis. It catalyses the biosynthesis of DNA from RNA. This ... Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K (July 2000). "Crystal structure of an archaeal intein-encoded homing ... It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges ...
"RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange". Genes Dev. 12 (9): 1248-53. doi:10.1101/ ... Virus genomes (either DNA or RNA) are extremely tightly packed into the viral capsid. Many viruses are therefore little more ... In eukaryotic cells, DNA is associated with about an equal mass of histone proteins in a highly condensed nucleoprotein complex ... DNA-binding protein RNA-binding protein Nucleoproteins at the US National Library of Medicine Medical Subject Headings (MeSH) ...
"RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange". Genes Dev. 12 (9): 1248-53. doi:10.1101/ ... UvsX, like RecA, can facilitate the assimilation of linear single-stranded DNA into an homologous DNA duplex to produce a D- ... Bernstein C, Bernstein H (2001). DNA repair in bacteriophage. In: Nickoloff JA, Hoekstra MF (Eds.) DNA Damage and Repair, Vol.3 ... DNA recombinases are widely used in multicellular organisms to manipulate the structure of genomes, and to control gene ...
"Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proc Natl Acad Sci U S A. 109 ... and DNA-binding proteins. ACV does not encode any identifiable DNA or RNA polymerases, nor does it encode any proteins ... However, some other archaeal viruses also have coil-shaped virions like ACV, which may indicate such morphology is an ancient ... All but one ORF has the same directionality as the DNA strand, indicating that the genome is positive-sense. The number of ...
These peptide chains can be found in the archaeal histones, which could have come from eukaryotic H3-H4 tetramer. The archaeal ... When not in the presence of DNA, the core histones assemble into head-to-tail intermediates (H3 and H4 first assemble into ... When just looking at the histone fold motif in the Drosophila the protein-protein and the protein DNA interaction of the core ... These lead into the octamer articulated protein endoskeleton for DNA compaction. From this endoskeleton it has a central ...
"RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange". Genes & Development. 12 (9): 1248-53. doi ... DNA damage-induced oocyte apoptosis depends on the efficiency of the DNA repair machinery that in turn declines with age. ... Unlike other proteins involved in DNA metabolism, the RecA/Rad51 family forms a helical nucleoprotein filament on DNA. This ... Many cancers have epigenetic deficiencies in various DNA repair genes (see Frequencies of epimutations in DNA repair genes in ...
"Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proc Natl Acad Sci USA 109: ... Prangishvili's studies have helped to reveal that DNA viruses of Archaea constitute a distinctive part of the viral world and ... 9. Prangishvili D, and Krupovic M (2012). "A new proposed taxon for double-stranded DNA viruses, the order Ligamenvirales". ... Prangishvili D, Bamford DH, Forterre P, Iranzo J., Koonon EV, and Krupovic M (2017) "The enigmatic archaeal virosphere". Nature ...
The singular archaeal ORC protein recognizes the AT-rich tracts and binds DNA in an ATP-dependent fashion. Eukaryotes typically ... Cdc45 then recruits key components of the replisome; the replicative DNA polymerase α and its primase. DNA replication can then ... Cdc6 recruits the licensing factor Cdt1 and MCM2-7. Cdt1 binding and ATP hydrolysis by the ORC and Cdc6 load MCM2-7 onto DNA. ... After the pre-RC is formed it must be activated and the replisome assembled in order for DNA replication to occur. In ...
The DNA packaging machinery then packs DNA into each head, cutting the DNA when the head is full, attaching a tail to the head ... Different GTA types have originated independently from viruses in several bacterial and archaeal lineages. These cells produce ... However, if the incoming DNA is not closely related to DNA sequences in the cell it will be degraded, and the cell will reuse ... Particles contain 7.5 kb DNA fragments. Production of VSH-1 is stimulated by the DNA-damaging agent mitomycin C and by some ...
The binding triggers structural changes in pb5 and eventually leads to DNA release from the phage capsid. Krupovic, Mart; et al ... May 2015). "To rename all (522) existing bacterial virus and 2 archaeal virus species" (PDF). International Committee on ... The capsid contains the phage's 121,750 base pair, double-stranded DNA genome which encodes about 168 proteins (now reduced to ...
Archaeal viruses. Some viruses replicate within archaea: these are double-stranded DNA viruses with unusual and sometimes ... A virus has either a DNA or an RNA genome and is called a DNA virus or an RNA virus, respectively. The vast majority of viruses ... The escaped DNA could have come from plasmids (pieces of naked DNA that can move between cells) or transposons (molecules of ... DNA viruses The genome replication of most DNA viruses takes place in the cell's nucleus. If the cell has the appropriate ...
The DNA structure of Thermoplasma volcanium has greater flexibility than other archaeal DNA due to an increased presence of ... 2009). "The stability of the archaeal HU histone-like DNA-binding protein from Thermoplasma volcanium". Extremophiles. 13 (1): ... DNA homologies were significantly different between the two species, which is one source of uniqueness between Thermoplasma ... 2000). "Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium". Proceedings of the ...
From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the ... Mitochondria contain their own DNA, which has close structural similarities to bacterial DNA, and which encodes rRNA and tRNA ... whose DNA they had gathered from diverse environments. As the capacity to sequence DNA became easier, Banfield and team were ... In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells. These act as sex ...
... obtains score for every long-ORF generated using all the six coding DNA models and also using non-coding DNA model. If ... Glimmer supports genome annotation efforts on a wide range of bacterial, archaeal, and viral species. In a large-scale ... GLIMMER trains all the six Markov models of coding DNA from zero to eight order and also train the model for noncoding DNA ... Delcher, A. L.; Bratke, K. A.; Powers, E. C.; Salzberg, S. L. (2007). "Identifying bacterial genes and endosymbiont DNA with ...
... a large DNA virus could take control of a bacterial or archaeal cell. Instead of replicating and destroying the host cell, it ... In 2006, researchers suggested that the transition from RNA to DNA genomes first occurred in the viral world. A DNA-based virus ... Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form ... Many biologists do not consider viruses to be alive, but the hypothesis posits that viruses are the originators of the DNA ...
DNA damage[edit]. Marking sites of DNA damage is an important function for histone modifications. It also protects DNA from ... Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack ... Compacting DNA strands[edit]. Histones act as spools around which DNA winds. This enables the compaction necessary to fit the ... Farkas D (1996). DNA simplified: the hitchhiker's guide to DNA. Washington, D.C: AACC Press. ISBN 978-0-915274-84-0. .. ...
Thermodynamically the stress accumulates from the DNA-unwinding and DNA-compaction activities. Once the DNA-RNA heteroduplex is ... Archaeal RNAP subunit previously used an "RpoX" nomenclature where each subunit is assigned a letter in a way unrelated to any ... The 17-bp transcriptional complex has an 8-bp DNA-RNA hybrid, that is, 8 base-pairs involve the RNA transcript bound to the DNA ... This change involves the separation of the DNA strands to form an unwound section of DNA of approximately 13 bp, referred to as ...
Pietila, M, Laurinavicius S, Sund, J, Roine E & Bamford D (2009) The single-stranded DNA genome of novel archaeal virus ... Halorubrum pleomorphic virus 1 (HRPV-1) is a single stranded DNA virus that infects the species of the archaeal genus ... Infection appears to be productive without lysis of the host like may of the archaeal viruses. Exit is likely to be by budding ... It is unlike any other known virus infecting the archaea with a single stranded DNA genome and an external lipid envelope and ...
One of such applications is the use of archaeal enzymes, which would be better able to survive harsh conditions in vitro.[12] ... Transduction is the process by which foreign DNA is introduced into a cell by a virus or viral vector. Transduction is a common ... Both DNA and RNA viruses can undergo recombination. When two or more viruses, each containing lethal genomic damage infect the ... H. volcani forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in ...
"Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proceedings of the National ... For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular ... Although research is limited in archaeal quorum sensing, some studies have uncovered LuxR proteins in archaeal species, ... archaeal flagella are synthesized by adding subunits at the base. Archaeal membranes are made of molecules that are distinctly ...
Only some archaeal histones have tails. The distance between the spools around which eukaryotic cells wind their DNA has been ... Without histones, unwound DNA in chromosomes would be very long. For example, each human cell has about 1.8 meters of DNA if ... Histones prevent DNA from becoming tangled and protect it from DNA damage. In addition, histones play important roles in gene ... Marking sites of DNA damage is an important function for histone modifications. It also protects DNA from getting destroyed by ...
Park J, Chen L, Tockman MS, Elahi A, Lazarus P (February 2004). "The human 8-oxoguanine DNA N-glycosylase 1 (hOGG1) DNA repair ... It is found in bacterial, archaeal and eukaryotic species. OGG1 is the primary enzyme responsible for the excision of 8- ... the HPLC-EC assay suggests up to 6 fold higher levels of 8-oxo-dG in nuclear DNA and 20-fold higher in mitochondrial DNA ... "Tracing the fates of site-specifically introduced DNA adducts in the human genome". DNA Repair. 15: 11-20. doi:10.1016/j.dnarep ...
The conjugation machinery of some bacteria (and archaeal flagella) is capable of transporting both DNA and proteins. It was ... DNA and RNA are broken down into mononucleotides by the nucleases deoxyribonuclease and ribonuclease (DNase and RNase) from the ...
Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA ... 1 DNA-Viren *1.1 Doppelsträngige DNA-Viren (dsDNA: double stranded DNA). *1.2 Einzelsträngige DNA-Viren (ssDNA: single stranded ... Viren mit DNA-Genom bilden keine taxonomische Einheit. Doppelsträngige DNA-Viren (dsDNA: double stranded DNA)[Bearbeiten , ... Einzelsträngige DNA-Viren (ssDNA: single stranded DNA)[Bearbeiten , Quelltext bearbeiten]. Viren mit Einzelstrang-DNA-Genom ...
On average, archaeal DNA sequences (whole genome) show higher levels of complexity than those of Bacteria.[33] ... For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, revolutionized molecular ... "Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proceedings of the National ... Connections between archaeal cells can also be found between the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) and ...
Four phenylalanine residues(Phe57, Phe74, Phe148, Phe 165) on TBP bind to DNA and form kinks in the DNA, forcing the DNA minor ... which is now known to be the sequence that interacts with the homologue of the archaeal TATA-binding protein (TBP). Also, even ... Compounds that trap the protein-DNA intermediate could result in it being toxic to the cell once they encounter a DNA ... which distorts DNA to allow access of DNA-binding proteins in the minor groove.[45] This will destabilize the interaction ...
Lipps, G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends (en inglés). Caister Academic Press. ISBN ... Rosenshine I, Tchelet R, Mevarech M. (1989). "The mechanism of DNA transfer in the mating system of an archaebacterium". ... Gaasterland T (1999). "Archaeal genomics". Curr. Opin. Microbiol. 2 (5): 542-7. PMID 10508726. doi:10.1016/S1369-5274(99)00014- ... Allers T, Mevarech M (2005). "Archaeal genetics - the third way". Nat. Rev. Genet. 6 (1): 58-73. PMID 15630422. doi:10.1038/ ...
In bacteria that express a 20S proteasome, the β subunits have high sequence identity to archaeal and eukaryotic β subunits, ... and systemic DNA damage responses leading to malignancies.[124] ... "Quality control mechanisms in cellular and systemic DNA damage ...
"DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA". Int. J. Syst. Evol. Microbiol. 50: 1095-1102 ... 23, www.pnas.org/cgi/doi/10.1073/pnas.0801980105 Guy L, Ettema TJ (2011). "The archaeal 'TACK' superphylum and the origin of ... 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, ...
For instance, one can start with the gene for a protein that binds a certain sequence of DNA, and, by directing an unnatural ... Protein biosynthesis: translation (bacterial, archaeal, eukaryotic). Proteins. Initiation factor. Bacterial. *PIF-1 ... amino acid with a reactive side-chain into the binding site, create a new protein that cuts the DNA at the target-sequence, ...
DNA repairEdit. The methylation of histone lysine has an important role in choosing the pathway for repairing DNA double-strand ... A possible homolog of Dot1 was found in archaea which shows the ability to methylate archaeal histone-like protein in recent ... The genomic DNA of eukaryotes associates with histones to form chromatin.[8] The level of chromatin compaction depends heavily ... Wei S, Li C, Yin Z, Wen J, Meng H, Xue L, Wang J (2018). "Histone methylation in DNA repair and clinical practice: new findings ...
Within the eukaryotic genome are regions of DNA known as silencers. These DNA sequences bind to repressors to partially or ... In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by ... MetJ interacts with DNA bases via a ribbon-helix-helix (RHH) motif.[2] MetJ is a homodimer consisting of two monomers, which ... A DNA-binding repressor blocks the attachment of RNA polymerase to the promoter, thus preventing transcription of the genes ...
"DNA Research. 15 (6): 387-396. doi:10.1093/dnares/dsn027. ISSN 1340-2838. PMC 2608843 . PMID 18940874.. ... Prokaryotic ribosomes begin translation of the mRNA transcript while DNA is still being transcribed. Thus translation and ... Protein biosynthesis: translation (bacterial, archaeal, eukaryotic). Proteins. Initiation factor. Bacterial. *PIF-1 ... "DNA binding sites: representation and discovery". Bioinformatics. 16 (1): 16-23. doi:10.1093/bioinformatics/16.1.16. ISSN 1367 ...
DNA Cell Biol. 16 (4): 515-31. doi:10.1089/dna.1997.16.515. PMID 9150439.. ... The coding sequences of 40 new genes (KIAA0121-KIAA0160) deduced by analysis of cDNA clones from human cell line KG-1". DNA Res ... "Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation". Genes Dev. 13 ...
2005) DNA sliding clamps: just the right twist to load onto DNA. Curr Biol, 15: R989-992. ... and Siksnys, V. (2007) Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday ... and Lubys, A. (2007) Generation of DNA cleavage specificities of type II restriction endonucleases by reassortment of target ...
Müller V. An exceptional variability in the motor of archaeal A1A0 ATPases: from multimeric to monomeric rotors comprising 6-13 ... lipidów i wywołują mutacje w DNA. Uszkodzenia komórek prowadza do chorób i są jedną z przyczyn starzenia się[79][80]. ...
The third subgroup of ABC proteins do not function as transporters, but are rather involved in translation and DNA repair ... ISBN 981-4280-06-2. Classification of ABC transporters in TCDB ABCdb Archaeal and Bacterial ABC Systems database, ABCdb ATP- ... Some homologous ATPases function in non-transport-related processes such as translation of RNA and DNA repair. ABC transporters ... ATP-driven conformational control in DNA double-strand break repair and the ABC-ATPase superfamily". Cell. 101 (7): 789-800. ...
Lazcano, A; Guerrero, R; Margulis, L; Oró, J (1988). "The evolutionary transition from RNA to DNA in early cells". Journal of ... "Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life". Proceedings of the National ... when the genetic material of mitochondria and chloroplasts was found to be different from that of the symbiont's nuclear DNA.[ ...
Lawrence CM, Menon S, Eilers BJ, et al.. Structural and functional studies of archaeal viruses. The Journal of Biological ... டி.என்.ஏ வைரசுகள் (DNA Viruses). *ஆர்.என்.ஏ வைரசுகள் என பகுக்கப்படுகிறது. ...
"Double-Stranded DNA Bacteriophages". Boundless. 2017-11-11.. *^ Maniloff, J.; Ackermann, H.W. (1998). "Taxonomy of bacterial ... Bacteriophages occur in over 195 bacterial or archaeal genera. They arose repeatedly in different hosts and there are at least ... Upon encountering a host bacterium, the tail section of the virion binds to receptors on the cell surface and delivers the DNA ... Typically, the genome is replicated by use of concatemers, in which overlapping segments of DNA are made, and then put together ...
In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification or replication ... which is part of every bacterial and archaeal genome and is highly conserved, bacteria can be taxonomically classified by ... PCR can be used to determine sex from a human DNA sample.[15] The loci of Alu element insertion is selected, amplified and ... DNA sequencing technologies such as next-generation sequencing have made it possible to study amplicons in genome biology and ...
DNA-DNA hybridisation,[84] which corresponds to less than 97% 16S DNA sequence identity.[85] It has been noted that if this ... LPSN, list of accepted bacterial and archaeal names. *Cyanobacteria, a phylum of common bacteria but poorly classified at ... Stackebrandt, E; Goebel, B.M. (1994). "Taxonomic note: a place for DNA-DNA reassociation and 16S rDNA sequence analysis in the ... in archaeal terms, and organisms that live in cooler environments appeared only later.[50] Since the Archaea and Bacteria are ...
DNA unting ganda (double stranded, "ds") merupakan komponen pembentuk genom kebanyakan organisme dan semua sel. Namun, virus ... "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proc. Natl. Acad. Sci. ... Peta genom bakteri Carboxydothermus hydrogenoformans Z-2901 yang berupa DNA sirkuler berukuran 2.401.892 pb.[1] ... terbuat dari DNA (asam deoksiribonukleat), namun sejumlah virus memiliki genom RNA (asam ribonukleat).[5] ...
... and adaptative adjustments would have followed a course in which bacterial transformation or archaeal DNA transfer naturally ... For the advantage due to DNA repair, there is an immediate large benefit of removing DNA damage by recombinational DNA repair ... a b Bernstein H, Bernstein C, Michod RE (2011). "Meiosis as an evolutionary adaptation for DNA repair." In "DNA Repair", Intech ... While DNA is able to recombine to modify alleles, DNA is also susceptible to mutations within the sequence that can affect an ...
... and double-strand breaks in DNA can be repaired.[67] The DNA checkpoint kinase ATM has a key role in integrating progression ... Plants are capable of a DNA damage response that is a critical mechanism for maintaining genome stability.[64] The DNA damage ... The first plant genome sequenced was that of Arabidopsis thaliana which encodes about 25,500 genes.[75] In terms of sheer DNA ... DNA damage and repair. Plants are continuously exposed to a range of biotic and abiotic stresses. These stresses often cause ...
D. Bridge, B. Schierwater, C. W. Cunningham, R. DeSalle R, L. W. Buss: Mitochondrial DNA structure and the molecular phylogeny ...
In the bacteria, oxidative phosphorylation in Escherichia coli is understood in most detail, while archaeal systems are at ... as they oxidize proteins and cause mutations in DNA. This cellular damage might contribute to disease and is proposed as one ...
A provirus does not directly make new DNA copies of itself while integrated into a host genome in this way. Instead, it is ... Not only eukaryotic viruses integrate into the genomes of their hosts; many bacterial and archaeal viruses also employ this ... A provirus is a virus genome that is integrated into the DNA of a host cell. In the case of bacterial viruses (bacteriophages ... When a (nonendogenous) retrovirus invades a cell, the RNA of the retrovirus is reverse-transcribed into DNA by reverse ...
... or archaeal counterpart. This initial tRNA binding site is called the A/T site. In the A/T site, the A-site half resides in the ... These tRNA-lookalikes are also considered part of the nuclear mitochondrial DNA (genes transferred from the mitochondria to the ... the existence of the P/I site in eukaryotic or archaeal ribosomes has not yet been confirmed. The P-site protein L27 has been ...
Pada umumnya, paparan energi radiasi dapat menyebabkan mutasi gen dan putusnya rantai DNA.[45] Apabila terjadi pada intensitas ... and Other Lactic Acid Bacteria in the Human Intestine as Determined by Specific Amplification of 16S Ribosomal DNA. Appl ... DNA dan RNA) bakteri melayang-layang di daerah sitoplasma yang bernama nukleoid.[17] Salah satu struktur bakteri yang penting ... bertahan terhadap mekanisme perusakan materi genetik tersebut melalui sistem adaptasi dan adanya proses perbaikan rantai DNA ...
Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme.. Yan J1, Beattie TR2, Rojas AL3, ... Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are ... and fitted with the crystal structure of DNA PolB from Thermococcus gorgonarius in complex with a DNA primer-template (PDB ID ... Reactions contained 2.5 nM enzyme and 50 nM DNA substrate. Reactions were incubated at 75 °C for 5 min. Reaction products were ...
P45 Enhances Other Archaeal DNA Polymerases.. Because dU-DNA inhibition appears to be a property of all archaeal family B DNA ... and double-stranded dU-containing DNA. Unlike eubacterial, eukaryotic, and bacteriophage DNA polymerases, archaeal family B DNA ... Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Holly H. Hogrefe, ... 3) and related archaeal DNA polymerases (Fig. 5). dUTP was shown previously to inhibit PCRs using Pfu and Vent DNA polymerases ...
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 ... Ubiquitylation of proliferating cell nuclear antigen and recruitment of human DNA polymerase η. Biochemistry 47: 4141-4150. ...
Archaeal" by people in this website by year, and whether "DNA, Archaeal" was a major or minor topic of these publications. ... "DNA, Archaeal" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange. Genes Dev. 1998 May 1; 12(9):1248-53. ... Below are the most recent publications written about "DNA, Archaeal" by people in Profiles. ...
Archaeal histones compact DNA into nucleosome-like particles of varying sizes that contort sporadically and reorient DNA ... 2002) Archaeal histone tetramerization determines DNA affinity and the direction of DNA supercoiling Journal of Biological ... Archaeal histones were successfully expressed in E. coli cells and were found to coat bacterial DNA (Rojec et al., 2019). ... 2018) Archaeal DNA on the histone merry-go-round The FEBS Journal 285:3168-3174. ...
... a DNA-binding protein acquired from bacteria via horizontal gene transfer mediates histone-like chromatin architecture. ... The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone analog. ... The stability of the archaeal HU histone-like DNA-binding protein from Thermoplasma volcanium * F Orfaniotou ... Thank you for submitting your work entitled "The DNA-binding protein HTa from Thermoplasma acidophilum is an archaeal histone ...
The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. ... DNA packaging mutant: repression of the vaccinia virus A32 gene results in noninfectious, DNA-deficient, spherical, enveloped ... The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus. Proc. Natl. Acad. Sci. USA 99: ... Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses. Proc. Natl. Acad. ...
uracil DNA glycosylase (UDG). Abbreviations: DNA, polB1, DNA polymerase B1; Fen1, flap endonuclease-1; GST, glutathione S- ... 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 ...
Structural and functional insights into DNA-end processing by the archaeal HerA helicase-NurA nuclease complex ... Structural and functional insights into DNA-end processing by the archaeal HerA helicase-NurA nuclease complex. Nucleic Acids ... The central channel of the NurA dimer is too narrow for double-stranded DNA but appears well suited to accommodate one or two ... Here we show that HerA and NurA must interact in a complex with specific subunit stoichiometry to process DNA ends efficiently ...
A new study in this issue of BMC Biology reveals the first structure of the archaeal GINS complex. The structure reveals the ... GINS is an essential eukaryotic DNA replication factor that is found in a simplified form in Archaea. ... Model for the initial assembly of the archaeal replisome based on recent advances in the eukaryotic DNA replication field (see ... a) A double hexamer of MCM (gray) is loaded on double-stranded DNA at an archaeal replication origin. (b) The two individual ...
Single-stranded DNA-binding proteins (SSBs) play vital roles in all aspects of DNA metabolism in all three domains of life and ... Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism. Research ... Consistent with a role for RpaC in DNA repair, elevated expression of this protein leads to enhanced resistance to DNA damage. ... A type III-B CRISPR-Cas effector complex mediating massive target DNA destruction. Han, W., Li, Y., Deng, L., Feng, M., Peng, W ...
The results indicate that members of the DSAG make up the entire archaeal population in certain horizons and constitute up to ~ ... The results indicate that members of the DSAG make up the entire archaeal population in certain horizons and constitute up to ... Despite their high abundance no members from this archaeal group have so far been characterized and thus their metabolism is ... Despite their high abundance no members from this archaeal group have so far been characterized and thus their metabolism is ...
Overall, archaeal community has the capability of autogenic recovery, the process of which might be intervened by anthropogenic ... The recovery of archaeal community following disturbance is essential for maintaining the stability of ecosystem function. To ... The Nitrososphaerales was the key taxon maintaining the better recovery of the archaeal community from the disturbances due to ... The Nitrososphaerales was the key taxon maintaining the better recovery of the archaeal community from the disturbances due to ...
Archaeal" by people in this website by year, and whether "DNA, Archaeal" was a major or minor topic of these publications. ... "DNA, Archaeal" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... Below are the most recent publications written about "DNA, Archaeal" by people in Profiles. ... Below are MeSH descriptors whose meaning is more general than "DNA, Archaeal". ...
Archaeal DNA Replication: Identifying the Pieces to Solve a Puzzle. *. Control of Ribosomal Protein L1 Synthesis in Mesophilic ... The archaeal Hsp70(DnaK) is a bacterial protein: All the archaeal Hsp70(DnaK) molecules sequenced and studied thus far resemble ... Does the archaeal chaperone machine interact with the TRiC-like thermosome? Does the archaeal machine interact with another ... 1995 The archaeal dnaK-dnaJ gene cluster: organization and expression in the methanogen Methanosarcina mazei. J. Mol. Biol. 250 ...
... bifurcated nucleic acids at the junction formed between single and double-stranded DNA. The specificity and catalytic ... catalyse the exonucleolytic hydrolysis of blunt-ended duplex DNA substrates and the endonucleolytic cleavage of 5- ... extrahelical nucleotide stabilise the ground state FEN-DNA interaction, leading to stimulation of comparative reactions at DNA ... Comparison of the catalytic parameters and reaction specificities of a phage and an archaeal flap endonuclease J Mol Biol. 2007 ...
DNA Res. 5, 55-76. CrossRef CAS PubMed Google Scholar. Kinosita, Y., Uchida, N., Nakane, D. & Nishizaka, T. (2016). Nature ... Comparison of archaeal CheY from P. horikoshii (PhCheY) and M. maripaludis. CheY from M. maripaludis has recently been ... The archaeal CheY has recently been structurally determined and in its interplay with CheF has been analyzed, providing a basal ... We aimed at determining the X-ray structure of PhCheY owing to the limited structural information on archaeal CheY [the crystal ...
Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. This ... Probing the Interaction of Archaeal DNA Polymerases with Deaminated Bases Using X-ray Crystallography and Non-Hydrogen Bonding ... The two bases are recognized by the same pocket, in the N-terminal domain, and make very similar protein-DNA interactions. ... inserts between the two template bases at the extreme end of the double-stranded DNA. This denatures the two complementary ...
An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion ... An archaeal family-B DNA polymerase variant able to replicate past DNA damage: occurrence of replicative and translesion ... A mutant of the high fidelity family-B DNA polymerase from the archaeon Thermococcus gorgonarius (Tgo-Pol), able to replicate ... Tgo-Pol Z1 may also be useful for amplification of damaged DNA. ... past DNA lesions, is described. Gain of function requires ...
The reversible thermal unfolding of the archaeal histone-like protein Ssh10b from the extremophile Sulfolobus shibatae was ... Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10. Wu X., Oppermann M., Berndt KD., Bergman T., Jörnvall H., ... Amino Acid Sequence, Archaeal Proteins, Calorimetry, Differential Scanning, Circular Dichroism, DNA-Binding Proteins, Histones ... DNA vaccine protection against SARS-CoV-2 in rhesus macaques * Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human ...
All archaeal genomes sequenced so far encode a substantial number of predicted DNA-binding proteins of the helix-turn-helix and ... Identification and Functional Verification of Archaeal-Type Phosphoenolpyruvate Carboxylase, a Missing Link in Archaeal Central ... Gene orders in archaeal and bacterial genomes were compared by using the lamarck program (33). For phylogenetic analysis, ... At this step, we isolated DNA from 293 λ clones of the M. kandleri European Molecular Biology Laboratory 3 λ library (12, 16). ...
2014 DNA-guided DNA interference by a prokaryotic Argonaute. Nature 507, 258-261. (doi:10.1038/nature12971). ... 4. The scattered archaeal eukaryome. *5. The archaeal ancestor of eukaryotes: a complex, ancient group within the TACK ... 2. Burgeoning archaeal diversity, complex archaeal ancestor and origin of eukaryotes from within the archaea. As pointed out ... 2014 The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb. Perspect. Biol. 6, ...
The bacterial, archaeal and plant plastid code (translation table 11) is the DNA code used by bacteria, archaea, prokaryotic ... strain PCC6803 by amino-terminal protein sequencing". DNA Research. 3 (4): 225-32. doi:10.1093/dnares/3.4.225. PMID 8946162. ...
April 1999). "Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1". DNA Research. 6 (2 ... nov., a methane-producing archaeon, the first isolate of the lineage Rice Cluster I, and proposal of the new archaeal order ... December 2000). "Archaeal adaptation to higher temperatures revealed by genomic sequence of Thermoplasma volcanium". ... This list of sequenced archaeal genomes contains all the archaea known to have publicly available complete genome sequences ...
DNA‐Interacting characteristics of the archaeal Rudiviral protein SIRV2_Gp1. Research output: Contribution to journal › Article ... University , Research portal , Research publications , DNA‐Interacting characteristics of the archaeal Rudiviral pr... ... Archaea, Archaeal virus, Rudiviridae, SIRV2, Solfolobus, DNA binding, Helix-turn-helix doman ... It harbours a helix‐turn‐helix motif and was therefore hypothesized to bind DNA. The DNA‐binding behavior of SIRV2_Gp1 was ...
Jozwiakowski, Stanislaw and Connolly, Bernard A (2011) A modified family-B archaeal DNA polymerase with reverse transcriptase ... The high-fidelity archaeal polymerase contains a fingers domain derived from the more error prone polymerase ζ. For maximum RT ...
Eukaryotic and Archaeal Genome Replication and Expression 16. Mechanisms of Genetic Variation 17. Recombinant DNA Technology 18 ... 4. Archaeal Cell Structure 5. Eukaryotic Cell Structure 6. Viruses and Other Acellular Infectious Agents. Part Two Microbial ...
Shatters RG, Kahn ML (1989) Glutamine synthetase II in Rhizobium: Re-examination of the proposed horizontal transfer of DNA ... In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme ... Hain J, Reiter W-D, Hüdepohl U, Zillig W (1992) Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids ... Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. ...
Archaeal B‐family DNA polymerases (DNA pols) are the driving force of cutting edge biotechnological applications like next‐ ... Archaeal B‐family DNA polymerases (DNA pols) are the driving force of cutting edge biotechnological applications like next‐ ... Structure of an archaeal B‐family DNA polymerase in complex with a chemically modified nucleotide. Restricted until:. May 1, ... Structure of an archaeal B‐family DNA polymerase in complex with a chemically modified nucleotide. * Home ...
Here, we show that DNA-binding protein from starved cells (Dps) - the extremely small archaeal antioxidant nanocage - is able ... Unmodified Dps is believed to stabilize DNA through the formation of Dps-DNA complexes in archaea and bacteria (23, 24). In ... An archaeal antioxidant: characterization of a Dps-like protein from Sulfolobus solfataricus. Proc Natl Acad Sci U S A. 2005; ... The archaeal Dps nanocage targets kidney proximal tubules via glomerular filtration. Masaki Uchida,1 Bernhard Maier,2 Hitesh ...
  • The discovery of thermostable polymerase accessory factors has been reported in thermophilic bacteria ( 18 ) and archaea ( 19 ), but with the exception of single-stranded DNA binding protein ( 20 , 21 ), the potential effect of such proteins on PCR amplification is presently unknown. (pnas.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)
  • Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10. (ox.ac.uk)
  • The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. (asm.org)
  • This is a round-shaped DNA-binding protein, looks like a donut! (bioquest.org)
  • Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme. (nih.gov)
  • Two small subunits, PBP1 and PBP2, associate with distinct surfaces of the larger catalytic subunit and influence the enzymatic properties of the DNA polymerase. (nih.gov)
  • Thus, multi-subunit replicative DNA polymerase holoenzymes are present in all three domains of life. (nih.gov)
  • We discovered a thermostable enzyme from the archaeon Pyrococcus furiosus ( Pfu ), which increases yields of PCR product amplified with Pfu DNA polymerase. (pnas.org)
  • Pfu dUTPase improves the yield of products amplified with Pfu DNA polymerase by preventing dUTP incorporation and subsequent inhibition of the polymerase by dU-containing DNA. (pnas.org)
  • In the absence of dUTP inhibition, the combination of cloned Pfu DNA polymerase and Pfu dUTPase ( PfuTurbo DNA polymerase) can amplify longer targets in higher yield than Taq DNA polymerase. (pnas.org)
  • The use of high-fidelity DNA polymerases in the polymerase chain reaction (PCR) is important for minimizing amplification errors in products that will be cloned, sequenced, and expressed. (pnas.org)
  • Of the enzymes characterized to date, Pyrococcus furiosus ( Pfu ) DNA polymerase exhibits the highest fidelity, with an average error rate estimated to be 2- to 60-fold lower than other proofreading enzymes and 6- to 100-fold lower than Taq DNA polymerase ( 1 - 4 ), which lacks proofreading activity. (pnas.org)
  • Lower product yields with Pfu DNA polymerase have been attributed to the enzyme's relatively slow polymerization rate (550 vs. 2,800 nucleotides per min for Taq ) and interference from its associated 3′- to 5′-exonuclease activity ( 13 ). (pnas.org)
  • Stratagene Pfu DNA polymerase manual), incorporating additives such as DMSO ( 6 , 14 ), and mixing Pfu with Taq DNA polymerase ( 4 ). (pnas.org)
  • Although DNA polymerase mixtures synthesize higher yields of product and allow amplification of longer templates than is possible with single-enzyme formulations ( 4 ), long-range blends exhibit lower fidelity than Pfu DNA polymerase because of the relatively high proportion of Taq used ( 1 ). (pnas.org)
  • In addition to Taq , there are other proteins that might be expected to enhance the performance of Pfu DNA polymerase. (pnas.org)
  • For example, polymerase accessory proteins have been shown to dramatically increase the processivity of replicative DNA polymerases from eukaryotes, Escherichia coli , and bacteriophages ( 15 - 17 ). (pnas.org)
  • For example, pyrophosphatase facilitates DNA polymerase-catalyzed reactions by eliminating inorganic pyrophosphate (PP i ) generated during incorporation of nucleoside triphosphates ( 22 ). (pnas.org)
  • In an effort to further improve the performance of Pfu DNA polymerase, we screened Pfu extracts for factors or proteins with PCR-enhancing activity. (pnas.org)
  • It is a DNA polymerase accessory factor that, with Cdc45, binds to and activates MCM helicase. (biomedcentral.com)
  • This publication describes an X-ray crystal structure of Thermococcus gorgonarius polymerase in complex with a DNA containing hypoxanthine in the single-stranded region of the template, two bases ahead of the primer-template junction. (ncl.ac.uk)
  • A beta-hairpin element, involved in partitioning the primer strand between the polymerase and exonuclease active sites, inserts between the two template bases at the extreme end of the double-stranded DNA. (ncl.ac.uk)
  • A mutant of the high fidelity family-B DNA polymerase from the archaeon Thermococcus gorgonarius (Tgo-Pol), able to replicate past DNA lesions, is described. (sussex.ac.uk)
  • The high-fidelity archaeal polymerase contains a fingers domain derived from the more error prone polymerase ζ. (sussex.ac.uk)
  • RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. (ebi.ac.uk)
  • This heterodimer functions as a DNA-directed RNA polymerase to synthesize small RNA primers that are used to create Okazaki fragments on the lagging strand of the DNA. (nih.gov)
  • Crystal structure of the C-terminal domain of human DNA primase large subunit: implications for the mechanism of the primase-polymerase α switch. (nih.gov)
  • DNA polymerase enzymes copy DNA into new strands of identical DNA. (sciencemag.org)
  • use in vitro directed evolution and protein engineering to build an error-correcting RT from a prokaryotic DNA polymerase. (sciencemag.org)
  • To determine if the lack of proofreading is a historical coincidence or a functional limitation of reverse transcription, we attempted to evolve a high-fidelity, thermostable DNA polymerase to use RNA templates efficiently. (sciencemag.org)
  • In addition, RTX enables applications such as single-enzyme reverse transcription-polymerase chain reaction and direct RNA sequencing without complementary DNA isolation. (sciencemag.org)
  • In contrast to RTs, other DNA polymerase families have evolved exquisite proofreading mechanisms to increase DNA synthesis fidelity during genome replication ( 9 ). (sciencemag.org)
  • A specific subdomain in phi29 DNA polymerase confers both processivity and strand-displacement capacity. (semanticscholar.org)
  • Twenty of these encode proteins with recognizable functions, such as capsid proteins, a primase and a DNA polymerase. (virology.ws)
  • Eukaryotes and many archaea package their DNA with histones. (elifesciences.org)
  • Archaea also have simplified histones that help store their DNA, and studying these proteins could reveal how eukaryotic histones first evolved. (elifesciences.org)
  • The histones in Archaea don't form discrete nucleosomes, instead, they coil DNA into 'slinky-like' shapes. (elifesciences.org)
  • It's still unclear how DNA packing in archaea works and how it differs from eukaryotes. (elifesciences.org)
  • This flexibility allows the information in the genomes of Archaea to be easily accessed, so, unlike in eukaryotes, archaeal cells may not need other proteins to release the DNA from the histones. (elifesciences.org)
  • Icosahedral nontailed double-stranded DNA (dsDNA) viruses are present in all three domains of life, leading to speculation about a common viral ancestor that predates the divergence of Eukarya , Bacteria , and Archaea . (asm.org)
  • In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. (lancs.ac.uk)
  • GINS is an essential eukaryotic DNA replication factor that is found in a simplified form in Archaea. (biomedcentral.com)
  • In marine sediments archaea often constitute a considerable part of the microbial community, of which the Deep Sea Archaeal Group (DSAG) is one of the most predominant. (frontiersin.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 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)
  • Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? (royalsocietypublishing.org)
  • The bacterial, archaeal and plant plastid code (translation table 11) is the DNA code used by bacteria, archaea, prokaryotic viruses and chloroplast proteins. (wikipedia.org)
  • This list of sequenced archaeal genomes contains all the archaea known to have publicly available complete genome sequences that have been assembled, annotated and deposited in public databases. (wikipedia.org)
  • Currently in this list there are 39 genomes belonging to Crenarchaeota species, 105 belonging to the Euryarchaeota, 1 genome belonging to Korarchaeota and to the Nanoarchaeota, 3 belonging to the Thaumarchaeota and 1 genome belonging to an unclassified Archaea, totalling 150 Archaeal genomes. (wikipedia.org)
  • Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. (asm.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)
  • 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)
  • Since there are only three homologs to eukaryal general transcription factors (GTFs) present in Archaea, and because of similar promoter organisation, archaeal transcription is generally accepted to provide a simpler model of the eukaryal transcription. (uni-due.de)
  • 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. (york.ac.uk)
  • Our lab recently determined the structure of histone-based archaeal chromatin that showed striking similarities to eukaryotic nucleosomes, but crystal lattice packing and biochemical experiments suggested that archaea may form repeated stacking interactions, potentially forming long "slinky-like" extended chromatin arrangements. (aps.org)
  • Methanogenic archaea are estimated to produce one billion tons of methane per year, with an equal amount estimated to be oxidized by archaeal methanotrophs ( 1 ). (sciencemag.org)
  • Dr Daniela Barillà , Reader: the molecular mechanisms and dynamics of prokaryotic DNA segregation, partition cassettes in bacteria and archaea. (york.ac.uk)
  • Family of rod-shaped DNA viruses infecting ARCHAEA. (harvard.edu)
  • The advantages to the use of archaea as a model for studying the organization of DNA during cellular growth in humans -- and the relationship between that organization and the activation of genes that may trigger cancers -- is their relative simplicity. (newswise.com)
  • The complex is a multimer of two discrete proteins, P45 and P50, with significant similarity to bacterial dCTP deaminase/dUTPase and DNA flavoprotein, respectively. (pnas.org)
  • Eukaryotes have so much DNA that they use proteins called histones to help package and organize it inside each cell. (elifesciences.org)
  • Eukaryotic cells also contain other proteins that release pieces of DNA from histones so that their genetic information can be used. (elifesciences.org)
  • Across all domains of life, DNA is intimately associated with proteins that wrap, package, and protect it. (elifesciences.org)
  • 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)
  • Sequence analysis and structural predication of virion-associated viral proteins suggest that they may have roles in DNA packaging, penton formation, and protein-protein interaction. (asm.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)
  • 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)
  • However, genome comparisons indicate that, in both trees constructed using concatenated alignments of ribosomal proteins and trees based on gene content, M. kandleri consistently groups with other archaeal methanogens. (pnas.org)
  • Holliday junction is the universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. (elsevier.com)
  • XPF/Rad1/Mus81/Hef proteins recognize and cleave branched DNA structures. (rcsb.org)
  • These proteins all function as dimers and consist of catalytic and helix-hairpin-helix DNA binding (HhH) domains. (rcsb.org)
  • The proliferating cell nuclear antigen (PCNA) is now recognized as one of the key proteins in DNA metabolic events because of its direct interactions with many proteins involved in important cellular processes. (elsevier.com)
  • The S. solfataricus Lrp subunit is a 155-aa polypeptide that bears between 24.5 and 29% sequence identity with eubacterial regulatory proteins of the Lrp/AsnC family and 30.6% and 25.8% with the archaeal homologues of respectively Methanococcus jannaschii and Pyrococcus furiosus. (nih.gov)
  • Unlike eukaryotic proteins, several studied prokaryotic Argonautes use small DNA guides to cleave DNA, a process dubbed DNA interference 6-10 . (nature.com)
  • The mammalian Artemis proteins have important functions in the repair of DNA double-strand breaks and in the V(D)J recombination. (iscb.org)
  • During evolution, eukaryotic cells have developed a complex network of proteins that, by sensing all types of DNA-damage and inducing the appropriate response, maintain the genome s integrity. (iscb.org)
  • The molecular basis for life rests on the information flow between DNA, RNA, and proteins ( 1 ). (sciencemag.org)
  • At least 160 proteins are involved in replicating the human genome, and at least 40 diseases are caused by aberrant DNA replication, 35 by mutations in genes required for DNA replication or repair, 7 by mutations generated during mitochondrial DNA replication, and more than 40 by DNA viruses. (cshlpress.com)
  • Consequently, a growing number of therapeutic drugs are targeted to DNA replication proteins. (cshlpress.com)
  • Since their initial characterization over 30 years ago, it has been believed that the archaeal B-family DNA polymerases are single-subunit enzymes. (nih.gov)
  • dUTP was found to accumulate during PCR through dCTP deamination and to limit the efficiency of PCRs carried out with archaeal DNA polymerases. (pnas.org)
  • In vivo , archaeal dUTPases may play an essential role in preventing dUTP incorporation and inhibition of DNA synthesis by family B DNA polymerases. (pnas.org)
  • Several archaeal DNA polymerases with 3′- to 5′-exonuclease-dependent proofreading activity have been commercialized for high-fidelity PCR amplification. (pnas.org)
  • PCRs conducted with Taq are typically more efficient and require less optimization than reactions carried out with proofreading DNA polymerases. (pnas.org)
  • Archaeal family-B DNA polymerases stall replication on encountering the pro-mutagenic bases uracil and hypoxanthine. (ncl.ac.uk)
  • DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. (royalsocietypublishing.org)
  • Archaeal B‐family DNA polymerases (DNA pols) are the driving force of cutting edge biotechnological applications like next‐generation sequencing. (uni-konstanz.de)
  • The former may contribute to the thermal stability of PfuPCNA, and the latter may be the cause of the stimulatory effect of PfuPCNA on the DNA synthesizing activity of P. furiosus DNA polymerases in the absence of the clamp loader replication factor C in vitro. (elsevier.com)
  • DNA-directed RNA polymerases EC:2.7.7.6 (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. (ebi.ac.uk)
  • In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. (ebi.ac.uk)
  • Unlike many DNA polymerases, RT enzymes do not have a proofreading function that checks for errors in the newly synthesized DNA. (sciencemag.org)
  • Lateral gene transfer of family A DNA polymerases between thermophilic viruses, aquificae, and apicomplexa. (semanticscholar.org)
  • An aspartic acid residue in TPR-1, a specific region of protein-priming DNA polymerases, is required for the functional interaction with primer terminal protein. (semanticscholar.org)
  • A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil", Proc. (freepatentsonline.com)
  • However, limited information on the diversity and replication of archaeal viruses, in general, has hampered further analysis. (asm.org)
  • In eukaryotes, GINS, in conjunction with Cdc45 and additional factors, is recruited to the replicative helicase MCM(2-7) at replication origins prior to the initiation of DNA replication. (biomedcentral.com)
  • What then are the implications of this new archaeal structure for the formation and organization of the higher order macromolecular assembly at the replication fork? (biomedcentral.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)
  • This gene encodes the 58 kilodalton subunit of DNA primase, an enzyme that plays a key role in the replication of DNA. (nih.gov)
  • XRCC1 interacts with the p58 subunit of DNA Pol alpha-primase and may coordinate DNA repair and replication during S phase. (nih.gov)
  • Replicative DNA helicases are essential cellular enzymes that unwind duplex DNA in front of the replication fork during chromosomal DNA replication. (asm.org)
  • Here, we show that replication in Escherichia coli is inhibited following a challenge with hydrogen peroxide and requires manganese for the rapid recovery of DNA synthesis. (asm.org)
  • Does the Semiconservative Nature of DNA Replication Facilitate Coherent Phenotypic Diversity? (asm.org)
  • When RNA-DNA hybrids persist, cells experience an increase in mutation rate and problems with DNA replication. (asm.org)
  • Although frequently considered as independent systems or events, in recent years it has become clear that three of the most fundamental processes that support chromosome integrity and cell proliferation - DNA replication, repair, and recombination - are highly interconnected. (keystonesymposia.org)
  • This book addresses these questions by presenting a thorough analysis of the molecular events that govern DNA replication in eukaryotic cells. (cshlpress.com)
  • This authoritative volume provides a rich source of information for researchers, physicians, and teachers, and will stimulate thinking about the relevance of DNA replication to human disease. (cshlpress.com)
  • The archaeal DNA replication machinery: past, present and future. (thefreedictionary.com)
  • All three groups have genes, which are typically stored on long strands of DNA. (elifesciences.org)
  • The ability to package DNA allows cells to contain many more genes, so evolving histones was a vital step in the evolution of eukaryotic life, including the appearance of animals. (elifesciences.org)
  • Neither of these parameters correlated with the relative abundance of archaeal or bacterial 16S rRNA genes, nor did any other major electron donor or acceptor measured. (frontiersin.org)
  • In contrast, analysis of the methyl coenzyme M reductase operon of M. kandleri identified a group of genes unique to archaeal methanogens ( 15 ). (pnas.org)
  • Comparative genome analysis of M. kandleri , Methanococcus jannaschii , and Methanothermobacter thermoautotrophicum resulted in the delineation of a distinct set of genes characteristic of archaeal methanogens. (pnas.org)
  • 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)
  • Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. (royalsocietypublishing.org)
  • Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. (springer.com)
  • In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii . (springer.com)
  • Additional non-euryarchaeotal MCR-encoding genes identified in a range of environments suggest that unrecognized archaeal lineages may also contribute to global methane cycling. (sciencemag.org)
  • PCR Amplification, Clone Library Construction, and Phylogenetic Analysis of Archaeal 16S rRNA Genes. (thefreedictionary.com)
  • The similar clustering of DNA in humans and archaeal chromosomes is significant because certain genes activate or deactivate based upon how they're folded. (newswise.com)
  • These systems are widely spread in bacterial and archaeal genomes. (mdpi.com)
  • One of the most prominent archaeal lineages in marine sediments based on 16S rRNA gene surveys is the Deep Sea Archaeal Group (DSAG). (frontiersin.org)
  • The lrp gene of the extreme thermophilic archaeon Sulfolofus solfataricus, encoding a homologue of the eubacterial global leucine-responsive regulatory protein, was identified by DNA sequencing and sequence comparisons on a 6.9-kb genomic fragment cloned into Escherichia coli. (nih.gov)
  • 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)
  • 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)
  • The [alpha] subunit of ammonia monooxygenase (amoA), the enzyme which catalyses the first step in the ammonia oxidation reaction, has been used by numerous authors as a functional gene marker to detect the bacterial and archaeal ammonia-oxidising populations (for review see Junier et al. (thefreelibrary.com)
  • Due to intrinsic difficulties in constructing mammalian cell lines with more than one knockout or knockdown gene, an alternative biological model allowing the study of Artemis in DNA repair would be welcome. (iscb.org)
  • Bacterial virus phi29 DNA-packaging motor and its potential applications in gene therapy and nanotechnology. (semanticscholar.org)
  • The archaeal amoA gene copy numbers varied from 1.45 x [10.sup.6] to 5.28 x [10.sup.8] per gram of dry soil in studied soils at the beginning of incubation, being highest in the P soil and lowest in the F soil. (thefreedictionary.com)
  • In this study, with a marine picoplankton assemblage collected at eastern North Pacific, a 38.5 kbp fragment containing an archaeal 16S rRNA gene was isolated for the first time. (thefreedictionary.com)
  • Archaeal community are identified by targeting mcrA gene. (thefreedictionary.com)
  • The inaccurate bundling, or 'folding,' of DNA can lead to the wrong gene being switched on or off," Bell said. (newswise.com)
  • 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)
  • Sulfolobus turreted icosahedral virus (STIV), isolated from a hot spring in Yellowstone National Park, was the first icosahedral virus with an archaeal host to be described. (asm.org)
  • We describe the characterization of a family 4 UDG1 (uracil DNA glycosylase) from the crenarchaeote Sulfolobus solfataricus . (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)
  • A new study in this issue of BMC Biology reveals the first structure of the archaeal GINS complex. (biomedcentral.com)
  • Very early, it was realized that the structure of the archaeal cell envelope differs substantially from that of bacteria [ 1 ]. (hindawi.com)
  • Studies on the structure of STIV have revealed similarities with prokaryotic and eukaryotic viruses that suggest a common ancestry for icosahedral double-stranded DNA (dsDNA) viruses ( 30 , 38 ). (asm.org)
  • 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)
  • Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. (nature.com)
  • Yutin and Koonin, 2012 ) constitute an apparently monophyletic group of eukaryotic viruses with a large double-stranded DNA (dsDNA) genome ranging from 100 kb up to 1.26 Mb. (nature.com)
  • The Acidianus bottle-shaped virus, ABV, infects strains of the hyperthermophilic archaeal genus Acidianus and is morphologically distinct from all other known viruses. (semanticscholar.org)
  • Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs. (semanticscholar.org)
  • The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids -pieces of DNA that can move between cells-while others may have evolved from bacteria. (wikipedia.org)
  • Most of the identified archaeal and bacterial virus sequences came from the families Myoviridae and Siphoviridae (think tailed, icosahedral viruses). (virology.ws)
  • The small subunits stabilize the holoenzyme assembly and the acidic tail of one small subunit mitigates the ability of the enzyme to perform strand-displacement synthesis, with important implications for lagging strand DNA synthesis. (nih.gov)
  • Identification and Characterization of an Archaeal Kojibiose Catabolic Pathway in the Hyperthermophilic Pyrococcus sp. (asm.org)
  • Viral diversity in hot springs of Pozzuoli, Italy, and characterization of a unique archaeal virus, Acidianus bottle-shaped virus, from a new family, the Ampullaviridae. (semanticscholar.org)
  • Here, we present the first molecular characterization of fungal, bacterial, and archaeal communities in soils from different habitats within the largest Fijian island, Viti Levu. (springer.com)
  • While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form 'nucleosome-like' complexes that continuously wind between 60 and 500 base pairs of DNA ('archaeasomes'), suggested by crystal contacts and analysis of cellular chromatin. (elifesciences.org)
  • 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)
  • Archaeal chromatin and transcription. (ebi.ac.uk)
  • The aim of future work is to establish an in vitro transcription system for T. tenax (collaboration with W. Hausner) and to identify regulons and DNA binding sites, using a combination of DNA microarrays with methods like chromatin immunoprecipitation and run-off in vitro transcription with genomic DNA. (uni-due.de)
  • We utilize these data to explore how inherent dynamics of archaeal slinky chromatin may regulate transcription. (aps.org)
  • Both DNA and the nucleoproteins that compose chromatin can be irreversibly modified by these agents, resulting in chromosomal rearrangements, deletions and other genetic alterations. (iscb.org)
  • 2017. Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field. (uib.no)
  • 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)
  • used metagenomics to assemble two nearly complete archaeal genomes from deep groundwater methanogens (see the Perspective by Lloyd). (sciencemag.org)
  • In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. (pasteur.fr)
  • Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. (semanticscholar.org)
  • Overall, the archaeal complex, despite having a simplified subunit composition relative to humans, has striking similarity to the human GINS assembly, although there are some differences in the contacts observed between Gins15 and Gins23 from those seen between their eukaryotic counterparts. (biomedcentral.com)
  • A study of the domain architectures of the archaeal two-component signal transduction (TCS) machinery revealed an overall similarity of archaeal and bacterial sensory modules but substantial differences in the signal output modules. (asm.org)
  • Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs. (nih.gov)
  • The key similarity is the way in which the DNA is arranged into clusters -- or "discrete compartmentalizations" -- based upon their function. (newswise.com)
  • 2019. A glimpse of the prokaryotic diversity of the Large Aral Sea reveals novel extremophilic bacterial and archaeal groups. (uib.no)
  • At the time of this writing nearly 400 complete prokaryotic genomes, including 28 archaeal ones, have been deposited in the GenBank database. (biomedcentral.com)
  • These results identify molecular mechanisms that generate guides for DNA interference and suggest common principles of recognition of foreign nucleic acids by prokaryotic defense systems. (nature.com)
  • Here we show that HerA and NurA must interact in a complex with specific subunit stoichiometry to process DNA ends efficiently. (lancs.ac.uk)
  • Finally, M. kandleri has several unique enzymes, the most notable being type 1B DNA topoisomerase V and the two-subunit reverse gyrase ( 8 - 12 ). (pnas.org)
  • Conformation change of the two DNA-binding sites in Subunit 1 (marked with stars) will lead to the interaction between DNA and the adjacent subunit (Subunit 2) due to the helical nature of DNA. (biomedcentral.com)
  • Then, Subunit 2 completes its translocation upon ATP hydrolysis and ADP release, facilitating the interaction between Subunit 3 and the DNA target, and the cycle continues. (biomedcentral.com)
  • The NHEJ pathway contains six protein members namely Ku70, Ku80, XRCC4, DNA ligase 4 (Lig4), DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and Artemis. (iscb.org)
  • The archaeal alpha chain is a CC catalytic subunit. (univ-lyon1.fr)
  • The central channel of the NurA dimer is too narrow for double-stranded DNA but appears well suited to accommodate one or two strands of an unwound duplex. (lancs.ac.uk)
  • Flap endonucleases (FENs) catalyse the exonucleolytic hydrolysis of blunt-ended duplex DNA substrates and the endonucleolytic cleavage of 5'-bifurcated nucleic acids at the junction formed between single and double-stranded DNA. (nih.gov)
  • Its genome consists of linear double-stranded DNA, containing 23,814 bp with a G+C content of 35%, and it exhibits a 590-bp inverted terminal repeat. (semanticscholar.org)
  • The structural basis of specific base-excision repair by uracil-DNA glycosylase", Nature, vol. 373: p. 487-493, (1995). (freepatentsonline.com)
  • Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein comlex", Nature Structural Biology, vol. 2: p. 752-757, (1995). (freepatentsonline.com)
  • Recent advances in metagenomic techniques are allowing population genomes to be recovered en masse across many previously uncultivated archaeal lineages and from increasingly complex environments ( 6 , 7 ). (sciencemag.org)
  • Two previously overlooked archaeal strains fill an evolutionary gap for microbes. (the-scientist.com)
  • Helicase-nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. (lancs.ac.uk)
  • Interestingly, the Cdc45-MCM-GINS (CMG) sub-complex appears to be a highly stable assembly and has been demonstrated to have robust DNA helicase activity in vitro [ 4 ]. (biomedcentral.com)
  • 34 ] ). This type of nanobiomotor works as monomers and DNA unwinding occurs in two steps: (1) ATP binding leads to a structural change of the enzyme which pushes the two helicase domains closer. (biomedcentral.com)
  • This newly identified function of MCM to change DNA topology may imply a wider functional role for MCM in DNA metabolisms beyond helicase function. (rcsb.org)
  • This year marks the 20th anniversary of the first report on the archaeal replicative helicase, the minichromosome maintenance (MCM) protein. (asm.org)
  • In eukaryotes, groups of eight histones form a short cylinder that organizes a small section of DNA into a structure called a nucleosome. (elifesciences.org)
  • Archaeal histones may reflect early versions of histones in eukaryotes, and can be used to understand how DNA packing has evolved. (elifesciences.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 genome encodes DNA repair enzymes homologous to those in both bacteria and eukaryotes. (wikipedia.org)
  • RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange. (umassmed.edu)
  • The prevailing mechanism of archaeal TCS signaling appears to involve various protein-protein interactions rather than direct transcription regulation. (asm.org)
  • T. tenax whole genome transcription profiling is currently established and first promising results were obtained for a focused CCM DNA microarray [28]. (uni-due.de)
  • Role of DNA bubble rewinding in enzymatic transcription termination. (semanticscholar.org)
  • article{Park2006RoleOD, title={Role of DNA bubble rewinding in enzymatic transcription termination. (semanticscholar.org)
  • By using DNA heteroduplexes that inhibit rewinding of the upstream part of the transcription bubble, we show that transcript release in termination by the enzymes Mfd and Rho is facilitated by reannealing of DNA in the upstream region of the transcription bubble, as is also true for termination by intrinsic terminators. (semanticscholar.org)
  • Factor-dependent archaeal transcription termination. (semanticscholar.org)
  • The evolutionarily distinct reverse transcription xenopolymerase (RTX) actively proofreads on DNA and RNA templates, which greatly improves RT fidelity. (sciencemag.org)
  • Mechanisms of DNA Recombination and Genome Rearrangements: Methods to Study Homologous Recombination, Volume 600 , the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. (elsevier.com)
  • Homologous genetic recombination remains the most enigmatic process in DNA metabolism. (elsevier.com)
  • CbAgo induces DNA interference between homologous sequences and triggers DNA degradation at double-strand breaks in the target DNA. (nature.com)
  • We chose to align 8 sequences of homologous archaeal helicases. (bioquest.org)
  • However, in competitions of an archived strain with S . Typhimurium ATCC 14028, phage emerged that had a DNA base sequence segment of prophage ST64B but the sequence differed from the reported homologous segment in ST64B. (wiley.com)
  • Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. (elifesciences.org)
  • The same molecular machines that support genetic integrity by orchestrating accurate repair of the most deleterious DNA lesions, however, also promote survival of cancerous cells and emergence of radiation and chemotherapy resistance. (elsevier.com)
  • The extreme environments favored by many archaeal species and limited knowledge about their biochemistry and biology exacerbate this problem. (asm.org)
  • Argonautes are also present in many bacterial and archaeal species 3-5 . (nature.com)
  • Exchange of DNA in bacteria, which can occur across deep taxonomic divides, may render the concept of microbial species meaningless. (genetics.org)
  • To survive in extremely salty environments, this archaeon-as with other halophilic Archaeal species-utilizes compatible solutes (in particular potassium chloride) to reduce osmotic stress. (wikipedia.org)
  • As the archaeal cell surface is so different from that of bacteria and eukarya, unique mechanisms must exist to form and shape it. (hindawi.com)
  • Much is known about how this DNA segregation occurs in organisms such as ourselves and in bacteria. (york.ac.uk)
  • Surprisingly, this archaeal system combines components found in bacteria with those found in organisms such as ourselves, suggesting the principles of DNA segregation are conserved across all three domains of life. (york.ac.uk)
  • [9] Many common bacteria have plasmids , which are short, circular, self-replicating DNA molecules that are separate from the bacterial chromosome. (wikipedia.org)
  • We have been unable to detect any stimulation of UDG activity by PCNA, in contrast with the observed effects of PCNA on a number of DNA metabolic enzymes. (biochemj.org)
  • 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. (york.ac.uk)
  • All previously described archaeal methane-metabolizing microorganisms belong to the phylum Euryarchaeota ( 2 ) and share a core set of bidirectional enzymes responsible for their respective metabolisms ( 3 ). (sciencemag.org)
  • Reverse transcriptase (RT) enzymes copy RNA into DNA. (sciencemag.org)
  • Based upon the presented evidence, we propose alternative mechanisms of DNA end processing by the HerA-NurA complex. (lancs.ac.uk)
  • Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface structures, and the release of S-layer-coated vesicles from the archaeal membrane. (hindawi.com)
  • However, the natural functions and targets of DNA interference are poorly understood, and the mechanisms of DNA guide generation and target discrimination remain unknown. (nature.com)
  • The emergence of mechanisms for phosphorylating organic and inorganic molecules is a key step en route to the earliest living systems. (mdpi.com)
  • Hydrolytic deamination of DNA cytosine residues results in U/G mispairs, pre-mutagenic lesions threatening long-term genetic stability. (york.ac.uk)
  • To achieve this, cells must not only copy their DNA but the two copies must also be segregated accurately as a cell divides to ensure that each daughter cell has a complete copy of the genetic code. (york.ac.uk)
  • As chromosomal DNA contains most of an organism s genetic information, modifications introduced in this molecule are potentially lethal if not repaired. (iscb.org)
  • TA systems have been assigned many functions, ranging from persistence to DNA stabilization or protection against mobile genetic elements. (mdpi.com)
  • Despite their high abundance no members from this archaeal group have so far been characterized and thus their metabolism is unknown. (frontiersin.org)
  • Focused DNA microarray (central carbohydrate metabolism) Thermoproteus tenax [28]. (uni-due.de)
  • This restricted phylogenetic distribution has led to the hypothesis that archaeal methane metabolism originated within the Euryarchaeota ( 4 ), although an origin outside this phylum has also been proposed ( 5 ). (sciencemag.org)
  • Our strengths in environmental microbiology and microbial evolution are complemented with expertise in microbial DNA metabolism and synthetic biology, allowing us to develop projects pertinent to industrial biotechnology and bioenergy. (york.ac.uk)
  • Journal Article] Archaeal Type III Rubiscos function in a pathway for AMP metabolism. (nii.ac.jp)
  • This defines mechanism and minimal enzymatic requirements of DNA-U repair in this organism. (york.ac.uk)
  • High-throughput DNA sequencing of the moose rumen from different geographical location reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity. (sueishaqlab.org)
  • Soil microbial diversity was analyzed through MiSeq amplicon sequencing of 16S (for prokaryotes), ITS, LSU ribosomal DNA (for fungi). (springer.com)
  • This preliminary survey provides important baseline data on fungal, bacterial, and archaeal diversity and biogeography in the Fiji Islands. (springer.com)
  • The ratio of X-linked and autosomal DNA diversity is generally much lower than the neutral equilibrium expectations in derived populations of Drosophila melanogaster . (genetics.org)
  • Bacterial and Archaeal diversity in high altitude wetlands of the Chilean Altiplano. (thefreedictionary.com)
  • HTa preferentially binds to GC-rich sequences, exhibits invariant positioning throughout the growth cycle, and shows archaeal histone-like oligomerization behavior. (elifesciences.org)
  • Our structural and biochemical analyses also showed that each of the catalytic and HhH domains binds to distinct regions within the fork-structured DNA: each HhH domain from two separate subunits asymmetrically binds to the arm region, while the catalytic domain binds near the junction center. (rcsb.org)
  • Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. (pasteur.fr)
  • The fundamental unit of compaction is the nucleosome, which is formed by histone heteromers - two H2A-H2B dimers flanking an H3-H4 tetramer - forming an octamer that binds approximately 147 bp of DNA. (aps.org)
  • The CONSURF alignment shows a strong conservation (indicated by purple) in the area adjacent to the "hole" region, presumably where the enzyme binds the DNA. (bioquest.org)
  • Matsumiya, S , Ishino, Y & Morikawa, K 2001, ' Crystal structure of an archaeal dna sliding clamp: Proliferating cell nuclear antigen from pyrococcus furiosus ', Protein Science , vol. 10, no. 1, pp. 17-23. (elsevier.com)
  • On the other hand, if components with an origin in archaeal , bacterial, or viral membranes are chosen, they could enhance the immunogenicity of the formulation [35, 37, 46-50]. (thefreedictionary.com)
  • To provide information on the viral genomes in the oceanic basement, sequences were determined from total cellular DNA (material retained on a 0.2 micron filter) extracted from the samples. (virology.ws)
  • Most viral sequences likely had archaeal hosts. (virology.ws)
  • Some prophage sequences were identified - viral genomes integrated into host DNA - which allowed more certain identification of the infected cell. (virology.ws)
  • Each cell needs hundreds of thousands of nucleosomes to arrange its DNA. (elifesciences.org)
  • The archaeal 'slinky-like' histone structures are more flexible than nucleosomes, and can open and close like clamshells. (elifesciences.org)
  • Using PCR primers designed to specifically target archaeal amoA , we find AOA to be pervasive in areas of the ocean that are critical for the global nitrogen cycle, including the base of the euphotic zone, suboxic water columns, and estuarine and coastal sediments. (pnas.org)
  • Two chitin-degrading halophilic archaeal strains, MC-74T and MC-23, were isolated from commercial salt samples. (bireme.br)
  • Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a very deep branch, close to the root of the archaeal tree. (pnas.org)
  • A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers. (pasteur.fr)
  • Comparison of the catalytic parameters of the A. fulgidus FEN employing flap and double-flap substrates indicates that binding interactions with the 3'-extrahelical nucleotide stabilise the ground state FEN-DNA interaction, leading to stimulation of comparative reactions at DNA concentrations below saturation with the single flap substrate. (nih.gov)
  • Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA. (elsevier.com)
  • Title: Insight into the Human DNA Primase Interaction with Template-Primer. (nih.gov)
  • When we first saw the interaction patterns of the archaea's DNA, we were shocked," Bell said. (newswise.com)
  • The IU study is the first to visualize the organization of DNA in archaeal chromosomes. (newswise.com)
  • Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. (elsevier.com)
  • Loading of CbAgo with locus-specific small DNA guides depends on both its intrinsic endonuclease activity and the cellular double-strand break repair machinery. (nature.com)
  • The level of DNA-DNA relatedness between the two strains was 93 and 94 % (reciprocally), and those between the two strains and Salinarchaeumlaminariae JCM 17267T were 35-36 % and 38-39 % (reciprocally). (bireme.br)
  • UDG1 is found to have a marked preference for substrates containing a G:U base pair over either A:U or single-stranded uracil-containing DNA substrates. (biochemj.org)
  • Archaeal ammonia oxidisers are abundant in acidic, coarse-textured Australian soils. (thefreelibrary.com)
  • Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils," Microbes and Environments, vol. (thefreedictionary.com)
  • The dominant bacteriological and archaeal phyla of compounded soils sourced from a commercial farm estate located in Amukpe town and a nearby control in Adavware community both in Delta State, were evaluated with the aid of Next Generation Sequencing (NGS) protocols. (who.int)
  • Total concentrations of the extracted DNA were 6.83 and 6.65 ng/µl for the control and experimental soils. (who.int)
  • The results indicate that members of the DSAG make up the entire archaeal population in certain horizons and constitute up to ~50% of the total microbial community. (frontiersin.org)
  • Another study of arctic (Svalbard) sediment microbial communities, also based on FISH, showed that up to 5% of the cells hybridized to an archaeal probe ( 36 ). (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)
  • This approach is based on unlinking of genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and cycle sequencing directed by 2′-modified oligonucleotides (Fimers). (pnas.org)
  • We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). (sciencemag.org)
  • Omnipotent role of archaeal elongation factor 1 alpha (EF1a in translational elongation and termination and quality control of protein synthesis. (thefreedictionary.com)
  • These findings indicate that archaeal methanogens are monophyletic. (pnas.org)
  • Several analyses, based on phylogenetic trees for 16S rRNA and the presence/absence of an 11-aa insertion in EF-1α, placed M. kandleri close to the root of the Euryarchaeota and did not suggest any specific affinity with other archaeal methanogens ( 13 - 15 ). (pnas.org)
  • The study is also the first to describe the protein used to assemble archaeal DNA during cellular growth. (newswise.com)
  • Acts as DNA glycosylase that recognizes and removes damaged bases. (uniprot.org)
  • Crystal Structure of a G:T/U Mismatch-Specific DNA Glycosylase: Mismatch Recognition by Complementary-Strand Interactions", Cell, vol. 92: p. 117-129, (1998). (freepatentsonline.com)