Archaeal Proteins: Proteins found in any species of archaeon.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.Genes, Archaeal: The functional genetic units of ARCHAEA.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Archaea: One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.Archaeal Viruses: Viruses whose hosts are in the domain ARCHAEA.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.Sulfolobus: A genus of aerobic, chemolithotrophic, coccoid ARCHAEA whose organisms are thermoacidophilic. Its cells are highly irregular in shape, often lobed, but occasionally spherical. It has worldwide distribution with organisms isolated from hot acidic soils and water. Sulfur is used as an energy source.Methanobacteriaceae: A family of anaerobic, coccoid to rod-shaped METHANOBACTERIALES. Cell membranes are composed mainly of polyisoprenoid hydrocarbons ether-linked to glycerol. Its organisms are found in anaerobic habitats throughout nature.Methanococcales: An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. They are pseudosarcina, coccoid or sheathed rod-shaped and catabolize methyl groups. The cell wall is composed of protein. The order includes one family, METHANOCOCCACEAE. (From Bergey's Manual of Systemic Bacteriology, 1989)Crenarchaeota: A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.Chromosomes, Archaeal: Structures within the nucleus of archaeal cells consisting of or containing DNA, which carry genetic information essential to the cell.Methanococcus: A genus of anaerobic coccoid METHANOCOCCACEAE whose organisms are motile by means of polar tufts of flagella. These methanogens are found in salt marshes, marine and estuarine sediments, and the intestinal tract of animals.Sulfolobus solfataricus: A species of thermoacidophilic ARCHAEA in the family Sulfolobaceae, found in volcanic areas where the temperature is about 80 degrees C and SULFUR is present.Haloferax volcanii: A species of halophilic archaea found in the Dead Sea.Pyrococcus furiosus: A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.Ribosome Subunits, Large, Archaeal: The large subunit of the archaeal 70s ribosome. It is composed of the 23S RIBOSOMAL RNA, the 5S RIBOSOMAL RNA, and about 40 different RIBOSOMAL PROTEINS.Pyrococcus abyssi: A species of gram-negative hyperthermophilic ARCHAEA found in deep ocean hydrothermal vents. It is an obligate anaerobe and obligate chemoorganotroph.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Archaeoglobus fulgidus: A species of extremely thermophilic, sulfur-reducing archaea. It grows at a maximum temperature of 95 degrees C. in marine or deep-sea geothermal areas.Methanosarcina: A genus of anaerobic, irregular spheroid-shaped METHANOSARCINALES whose organisms are nonmotile. Endospores are not formed. These archaea derive energy via formation of methane from acetate, methanol, mono-, di-, and trimethylamine, and possibly, carbon monoxide. Organisms are isolated from freshwater and marine environments.Sulfolobus acidocaldarius: A species of aerobic, chemolithotrophic ARCHAEA consisting of coccoid cells that utilize sulfur as an energy source. The optimum temperature for growth is 70-75 degrees C. They are isolated from acidic fields.Pyrococcus horikoshii: Anaerobic hyperthermophilic species of ARCHAEA, isolated from hydrothermal fluid samples. It is obligately heterotrophic with coccoid cells that require TRYPTOPHAN for growth.Acidianus: 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.Methane: 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)Bacteria: 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.Nanoarchaeota: A kingdom of hyperthermophilic ARCHAEA found in diverse environments.Euryarchaeota: 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.Pyrococcus: A genus of strictly anaerobic ultrathermophilic archaea, in the family THERMOCOCCACEAE, occurring in heated seawaters. They exhibit heterotrophic growth at an optimum temperature of 100 degrees C.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Thermoplasma: 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.Glyceryl Ethers: 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.Thermoproteaceae: 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)Geologic Sediments: 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)Methanobacterium: 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.Methanosarcinales: An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. There are two families: METHANOSARCINACEAE and Methanosaetaceae.Sequence Alignment: 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.Methanobacteriales: 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.Ribosome Subunits, Small, Archaeal: The small subunit of archaeal RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 28 different RIBOSOMAL PROTEINS.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Desulfurococcaceae: 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)Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Nitrification: A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Methanococcaceae: A family of anaerobic METHANOCOCCALES whose organisms are motile by means of flagella. These methanogens use carbon dioxide as an electron acceptor.Sulfolobales: An order of CRENARCHAEOTA consisting of aerobic or facultatively aerobic, chemolithotrophic cocci which are extreme thermoacidophiles. They lack peptidoglycan in their cell walls.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Korarchaeota: 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.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Halobacterium salinarum: A species of halophilic archaea found in salt lakes. Some strains form a PURPLE MEMBRANE under anaerobic conditions.Haloarcula: 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.Methanosarcinaceae: A family of anaerobic METHANOSARCINALES whose cells are mesophilic or thermophilic and appear as irregular spheroid bodies or sheathed rods. These methanogens are found in any anaerobic environment including aquatic sediments, anaerobic sewage digesters and gastrointestinal tracts. There are four genera: METHANOSARCINA, Methanolobus, Methanothrix, and Methanococcoides.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.Halorubrum: 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.Hot Springs: 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.Protein Structure, Tertiary: 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.Thermosomes: Group II chaperonins found in species of ARCHAEA.Microbial Consortia: A group of different species of microorganisms that act together as a community.Genes, rRNA: 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.RNA, Transfer: 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.Eukaryota: 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.Methanomicrobiales: 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.Protein Subunits: 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.Halobacteriaceae: 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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Ribonuclease P: An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.Gene Transfer, Horizontal: 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).Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Conserved Sequence: 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.Pyrobaculum: 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.Archaeoglobales: An order of extremely thermophilic, sulfate-reducing archaea, in the kingdom EURYARCHAEOTA. The single family Archaeoglobaceae contains one genus ARCHAEOGLOBUS.Ecosystem: 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)Ammonia: 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.Thermoproteus: A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.Archaeoglobus: A genus of extremely thermophilic, sulfate-reducing archaea, in the family Archaeoglobaceae.Thermoproteales: 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.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.Protein Conformation: 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).Temperature: 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.Escherichia coli: 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.Prokaryotic Initiation Factors: 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.Halobacteriales: 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.Chaperonins: 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.RNA, Guide: 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.Cloning, Molecular: 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.PseudouridineBinding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.WyomingHaloarcula marismortui: A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.Protein Binding: 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.Bacterial Proteins: Proteins found in any species of bacterium.Oxidoreductases: 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)Transcription Factor TFIIB: 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.Holliday Junction Resolvases: Enzymes that recognize CRUCIFORM DNA structures and introduce paired incisions that help to resolve the structure into two DNA helices.Enzyme Stability: 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.Protein Structure, Secondary: 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.Structural Homology, Protein: 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.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Pyrodictiaceae: 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.Hydrothermal Vents: Hot springs on the ocean floor. They are commonly found near volcanically active places such as mid-oceanic ridges.Denaturing Gradient Gel Electrophoresis: 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.Salinity: Degree of saltiness, which is largely the OSMOLAR CONCENTRATION of SODIUM CHLORIDE plus any other SALTS present. It is an ecological factor of considerable importance, influencing the types of organisms that live in an ENVIRONMENT.Soil: The unconsolidated mineral or organic matter on the surface of the earth that serves as a natural medium for the growth of land plants.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Recombinant Proteins: Proteins prepared by recombinant DNA technology.RNA, Ribosomal: 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)Protein Structure, Quaternary: The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.tRNA Methyltransferases: Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.Adenosine Triphosphatases: 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.Haloferax: 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.RNA, Transfer, Trp: A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.Leucine-tRNA Ligase: An enzyme that activates leucine with its specific transfer RNA. EC 18.104.22.168.Genes, Bacterial: The functional hereditary units of BACTERIA.Galium: A genus of herbaceous annual and perennial plants in the family RUBIACEAE.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.RNA, Small Nucleolar: 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.Autotrophic Processes: 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.Oil and Gas Fields: Areas of the earth where hydrocarbon deposits of PETROLEUM and/or NATURAL GAS are located.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Amino Acyl-tRNA Synthetases: A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.Bacterial Physiological Phenomena: Physiological processes and properties of BACTERIA.Pacific OceanDNA Primers: 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.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Transfer RNA Aminoacylation: The conversion of uncharged TRANSFER RNA to AMINO ACYL TRNA.Methanomicrobiaceae: A family of anaerobic METHANOMICROBIALES whose cells are coccoid to straight or slightly curved rods. There are six genera.Group II Chaperonins: 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.Antigens, Archaeal: Substances of archaeal origin that have antigenic activity.Open Reading Frames: 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).Antibodies, Archaeal: Immunoglobulins produced in a response to ARCHAEAL ANTIGENS.Cluster Analysis: 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.Lakes: Inland bodies of still or slowly moving FRESH WATER or salt water, larger than a pond, and supplied by RIVERS and streams.Combretaceae: A plant family of the order Myrtales, subclass Rosidae, class Magnoliopsida. They are mostly trees and shrubs growing in warm areas.Plankton: 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.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Cryoelectron Microscopy: 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.TATA-Box Binding Protein: 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.Sequence Homology, Nucleic Acid: 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.Polymerase Chain Reaction: 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.CRISPR-Associated Proteins: 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.Species Specificity: 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.Oxidation-Reduction: 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 PRD1: Bacteriophage and type species in the genus Tectivirus, family TECTIVIRIDAE. They are specific for Gram-negative bacteria.DNA-Directed RNA Polymerases: 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).Hydrogensulfite Reductase: An enzyme found primarily in SULFUR-REDUCING BACTERIA where it plays an important role in the anaerobic carbon oxidation pathway.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Multigene Family: 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)Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Methanosarcina barkeri: A species of halophilic archaea whose organisms are nonmotile. Habitats include freshwater and marine mud, animal-waste lagoons, and the rumens of ungulates.Anaerobiosis: 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)Amino Acid Motifs: 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-Directed DNA Polymerase: 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.DNA-Binding Proteins: 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.Halobacterium: A genus of HALOBACTERIACEAE whose growth requires a high concentration of salt. Binary fission is by constriction.Endoribonucleases: 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.-.Serine-tRNA Ligase: An enzyme that activates serine with its specific transfer RNA. EC 22.214.171.124.Antarctic Regions: 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)DNA: 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).Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.Deltaproteobacteria: A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.RNA, Transfer, Gln: A transfer RNA which is specific for carrying glutamine to sites on the ribosomes in preparation for protein synthesis.Sequence Homology: 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.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Protein Multimerization: The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.Sulfur: 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.Sensory Rhodopsins: 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.RNA, Transfer, Tyr: A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.DNA Replication: The process by which a DNA molecule is duplicated.Gene Order: The sequential location of genes on a chromosome.Intramolecular Transferases: 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.RNA, Transfer, Asn: A transfer RNA which is specific for carrying asparagine to sites on the ribosomes in preparation for protein synthesis.Chemoautotrophic Growth: 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.Ferredoxins: 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)Ribonucleoproteins, Small Nucleolar: Nucleolar RNA-protein complexes that function in pre-ribosomal RNA processing.Thermotoga maritima: 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)Hydrogen-Ion Concentration: 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)Lysine-tRNA Ligase: An enzyme that activates lysine with its specific transfer RNA. EC 126.96.36.199.Mutation: 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.Kinetics: The rate dynamics in chemical or physical systems.Proteobacteria: 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.Rhizosphere: 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.Tyrosine-tRNA Ligase: An enzyme that activates tyrosine with its specific transfer RNA. EC 188.8.131.52.DNA Helicases: 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: 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.Biocatalysis: The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.Replication Origin: 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)Natronobacterium: 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.Bioreactors: 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.Biosynthetic Pathways: Sets of enzymatic reactions occurring in organisms and that form biochemicals by making new covalent bonds.