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 Proteins: Proteins found in any species of archaeon.Genes, Archaeal: The functional genetic units of ARCHAEA.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Genome, Archaeal: The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.Crenarchaeota: A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.Haloferax volcanii: A species of halophilic archaea found in the Dead Sea.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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)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.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.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.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.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.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.Nitrification: A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.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.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)Methanosarcinales: An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. There are two families: METHANOSARCINACEAE and Methanosaetaceae.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.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.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.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.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.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.Pyrococcus abyssi: A species of gram-negative hyperthermophilic ARCHAEA found in deep ocean hydrothermal vents. It is an obligate anaerobe and obligate chemoorganotroph.Chromosomes, Archaeal: Structures within the nucleus of archaeal cells consisting of or containing DNA, which carry genetic information essential to the cell.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.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)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)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.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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.Thermococcus: A genus of extremely thermophilic heterotrophic archaea, in the family THERMOCOCCACEAE, occurring in heated sea flows. They are anaerobic chemoorganotropic sulfidogens.Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.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.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.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.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Archaeal Viruses: Viruses whose hosts are in the domain ARCHAEA.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.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.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.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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.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.Haloferax mediterranei: A species of halophilic archaea found in the Mediterranean Sea. It produces bacteriocins active against a range of other halobacteria.Prokaryotic Cells: Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.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)Halobacterium salinarum: A species of halophilic archaea found in salt lakes. Some strains form a PURPLE MEMBRANE under anaerobic conditions.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Thermoplasmales: An order of aerobic, thermophilic archaea, in the kingdom EURYARCHAEOTA, characterized by the absence of a cell wall. Two genera have been described: THERMOPLASMA and Picrophilus.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).Methanobrevibacter: A genus of gram-positive, anaerobic, cocci to short rod-shaped ARCHAEA, in the family METHANOBACTERIACEAE, order METHANOBACTERIALES. They are found in the GASTROINTESTINAL TRACT or other anoxic environments.Bacterial Proteins: Proteins found in any species of bacterium.Haloarcula marismortui: A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.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.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.Sulfolobales: An order of CRENARCHAEOTA consisting of aerobic or facultatively aerobic, chemolithotrophic cocci which are extreme thermoacidophiles. They lack peptidoglycan in their cell walls.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)Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Methanomicrobiaceae: A family of anaerobic METHANOMICROBIALES whose cells are coccoid to straight or slightly curved rods. There are six genera.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)Archaeoglobus: A genus of extremely thermophilic, sulfate-reducing archaea, in the family Archaeoglobaceae.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)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.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.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.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.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.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.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).RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.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.Sulfolobaceae: A family of SULFOLOBALES consisting of aerobic or facultatively anaerobic chemolithotrophic cocci, usually occurring singly. They grow best at a pH of about 2.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.Hot Temperature: Presence of warmth or heat or a temperature notably higher than an accustomed norm.Hydrothermal Vents: Hot springs on the ocean floor. They are commonly found near volcanically active places such as mid-oceanic ridges.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.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.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Pacific OceanGenes, Bacterial: The functional hereditary units of BACTERIA.Deltaproteobacteria: A group of PROTEOBACTERIA represented by morphologically diverse, anaerobic sulfidogens. Some members of this group are considered bacterial predators, having bacteriolytic properties.Biota: The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.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.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.Microbial Consortia: A group of different species of microorganisms that act together as a community.Metagenomics: The genomic analysis of assemblages of organisms.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.Bacterial Physiological Phenomena: Physiological processes and properties of BACTERIA.Sulfur-Reducing Bacteria: A group of gram-negative, anaerobic bacteria that is able to oxidize acetate completely to carbon dioxide using elemental sulfur as the electron acceptor.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.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.Estuaries: A partially enclosed body of water, and its surrounding coastal habitats, where saltwater from the ocean mixes with fresh water from rivers or streams. The resulting mixture of seawater and fresh water is called brackish water and its salinity can range from 0.5 to 35 ppt. (accessed http://oceanservice.noaa.gov/education/kits/estuaries/estuaries01_whatis.html)Nanoarchaeota: A kingdom of hyperthermophilic ARCHAEA found in diverse environments.Pyrococcus horikoshii: Anaerobic hyperthermophilic species of ARCHAEA, isolated from hydrothermal fluid samples. It is obligately heterotrophic with coccoid cells that require TRYPTOPHAN for growth.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.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.Lakes: Inland bodies of still or slowly moving FRESH WATER or salt water, larger than a pond, and supplied by RIVERS and streams.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Thermoproteus: A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.Aeropyrum: A genus of anaerobic, chemolithotropic coccoid ARCHAEA, in the family DESULFUROCOCCACEAE. They live in marine environments.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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Heterotrophic Processes: The processes by which organisms utilize organic substances as their nutrient sources. Contrasts with AUTOTROPHIC PROCESSES which make use of simple inorganic substances as the nutrient supply source. Heterotrophs can be either chemoheterotrophs (or chemoorganotrophs) which also require organic substances such as glucose for their primary metabolic energy requirements, or photoheterotrophs (or photoorganotrophs) which derive their primary energy requirements 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 nutrients and energy requirements.
Taxonomia do domínio Archaea - WikipediaEsta é uma lista taxônomica do domínio Archaea. Archaea é um domínio de seres procariotas, quimiotróficos e extremófilos. A ... The Taxonomicon - Archaea (em inglês) Encyclopedia of Life - Archaea (em inglês). ... GARRITY, G. M.; LILBURN, T. G.; COLE, J. R., HARRISON, S. H.; EUZÉBY, J.; TINDALL, B. J. Archaea In Taxonomic Outline of the ... Abstract HUBER, H.; HOHN, M. J.; RACHEL, R.; FUCHS, T.; WIMMER, V.C.; STETTER, K. O. (2002). A new phylum of Archaea ...
Molecular Tools for the Detection of Nitrogen Cycling ArchaeaArchaea is a peer-reviewed, Open Access journal that publishes original research articles as well as review articles dealing ... with all aspects of research on the archaea, including bioinformatics, biotechnology, environmental adaptation, enzymology, ... Molecular Tools for the Detection of Nitrogen Cycling Archaea. Antje Rusch Department of Microbiology and Center for Ecology, ... Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic ...
Recent Articles | Archaea, Disease/Medicine And Microbiology | The Scientist Magazine®Daily News Sexual Touch Promotes Early Puberty The brains and bodies of young female rats can be accelerated into puberty by the presence of an older male or by stimulation of the genitals.. ...
ARCHEON LYRICSArcheon lyrics - Check out top lyrics like Lost Fool, Struggle With Death, Dead World ...
Recent Articles | Archaea, Cell & Molecular Biology And Immunology | The Scientist Magazine®| Page 8Asgard Archaea Hint at Eukaryotic Origins. By Joshua A. Krisch , January 18, 2017 ... A newly discovered superphylum of archaea may be related to a microbe that engulfed a bacterium to give rise to complex ... A metagenomics analysis finds Cas9 in archaea for the first time, along with two previously unknown Cas nucleases from bacteria ...
Early transport: Protein secretion pathways in Archaea - OpusEarly transport: Protein secretion pathways in Archaea. The Biochemist, 26 (3), pp. 16-18. ...
Archaea's Kansas City Blind Subwoofer Shootout 2012 - Page 28 - AVS Forum | Home Theater Discussions And ReviewsI rely on Archaea's and the KC gang's reviews of JTR products!. I have been staring at the T8-LP's in my living room and ... The owner decided to try the inuke the way Archaea had it set up for his subs. He set it up and liked it better than his dayton ... Originally Posted by Archaea Hey, look who's still alive!!!. I'm pretty decided on just adding subs and not trading or selling ... I knew nothing about the sub or amp and once it was hooked up by the owner during meet I asked Archaea "how is it being powered ...
RCSB PDB - 1KU5: Crystal Structure of recombinant histone HPhA from hyperthermophilic archaeon Pyrococcus horikoshii...Crystal Structure of recombinant histone HPhA from hyperthermophilic archaeon Pyrococcus horikoshii OT3. *DOI: 10.2210/pdb1ku5/ ...
RCSB PDB - 1NVG: N249Y MUTANT OF THE ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS-TETRAGONAL...N249Y MUTANT OF THE ALCOHOL DEHYDROGENASE FROM THE ARCHAEON SULFOLOBUS SOLFATARICUS-TETRAGONAL CRYSTAL FORM. *DOI: 10.2210/ ...
Sequence Similarity - 1CF2: THREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE...... and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon ... THREE-DIMENSIONAL STRUCTURE OF D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC ARCHAEON METHANOTHERMUS ...
How Extremophiles Work | HowStuffWorksExtremophiles are organisms that live in 'extreme' environments. Learn why extremophiles are remarkable, not only because of their habitats.
From the first living organism OOL to to the last universal common ancestor (LUCA)Guess the Evidence for Early Evolution1 Mineral evolution It is believed that biological processes started to affect Earth's surface mineralogy by 3.85-3.6 Ga F
ASMscience | Extremophiles and the OrDuring the past 2 decades, the description of a diverse assortment of prokaryotic species that thrive under extreme environments that used to be considered inhospitable has broadened our understanding of the range of conditions under which life can persist. With the exception of heat-loving prokaryotes, however, the phylogenetic distribution of other extremophiles in molecular cladograms does not provide clues to their possible antiquity. Furthermore, given the huge gap existing in current descriptions of the evolutionary transition between the prebiotic synthesis of biochemical compounds and the last common ancestor (LCA) of all extant living beings, it is probably naïve to attempt to describe the origin of life and the nature of the first living systems from molecular phylogenies. It is unlikely that data on how life originated will be provided by the geological record. The remarkable coincidence between the monomeric constituents of living organisms and those synthesized in laboratory simulations of
Eco Sys ArchaeaDet Galaktiske Pari : Archaea Archaea. Single-celled microorganisms. A single individual or species from this domain is called an archaeon (sometimes spelled 'archeon'). They have no cell nucleus or any other organelles within their cells. In the past they were viewed as an unusual group of bacteria and named archaebacteria but since the Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, they are now classified as a separate domain in the three-domain system.. Tree of Life. ...
ArchaeaMost archaeans don't look that different from bacteria under the microscope. The extreme conditions under which most species of archaea live has made them difficult to culture, so their unique place among living organisms long went unrecognized.
Archaea - HilinqwoClick here to toggle editing of individual sections of the page (if possible). Watch headings for an 'edit' link when available ...
Domain (biology): In biological taxonomy, a domain (also superregnum, superkingdom, empire, or regio) is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese, an American microbiologist and biophysicist. According to the Woese system, introduced in 1990, the tree of life consists of three domains: Archaea (a term which Woese created), Bacteria, and Eukaryota.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Atmospheric methane: Atmospheric methane is the methane present in Earth's atmosphere. Atmospheric methane concentrations are of interest due to methane's impact on climate change, as it is one of the most potent greenhouse gases in Earth's atmosphere.Exogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.Coles PhillipsMethanopyrus: In taxonomy, Methanopyrus is a genus of the Methanopyraceae.See the NCBI webpage on Methanopyrus.Warner OlandFormate-nitrite transporter: Formate-nitrite transporters are a family of evolutionarily related transmembrane bacterial and archaebacterial proteins involved in transporting formate or nitrite. They include:Ignicoccus: Ignicoccus is a genus of Archaea living in marine hydrothermal vents. They were discovered in Kolbeinsey Ridge north of Iceland and in the Pacific Ocean (at 9 degrees N, 104 degrees W) in 2000 (Huber et al.Methanosarcinales S-layer Tile Protein: The Methanosarcinales S-layer Tile Protein (MSTP) is a protein family found almost exclusively in Methanomicrobia members of the order Methanosarcinales. Typically a tandem repeat of two DUF1608 domains are contained in a single MSTP protein chain and these proteins self-assemble into the protective proteinaceous surface layer (S-layer) structure that encompasses the cell.Halobacteriales: In taxonomy, the Halobacteriales are an order of the Halobacteria,See the NCBI webpage on Halobacteriales. Data extracted from the found in water saturated or nearly saturated with salt.Thermoacidophile: A thermoacidophile (combination of thermophile and acidophile) is an extreme archeon which thrives in acidous, sulfur-rich, high temperature environments with low availability of organic material.Archease: In molecular biology, the archease superfamily of proteins are represented in all three domains of life. Archease genes are generally located adjacent to genes encoding proteins involved in DNA or RNA processing and therefore been predicted to be modulators or chaperones involved in DNA or RNA metabolism.Nankai Trough gas hydrate site: Nankai Methane Hydrate Site (or Japanese Methane Hydrate R&D Program at Nankai, Nankai Trough Methane Hydrate Site) is located in the Nankai Trough, Japan.Methanocaldococcus jannaschii: Methanocaldococcus jannaschii (formerly Methanococcus jannas chii) is a thermophilic methanogenic archaea in the class Methanococci. It was the first archaeon to have its complete genome sequenced.Archaeoglobus: Archaeoglobus is a genus of the phylum Euryarchaeota.See the NCBI webpage on Archaeoglobus.Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.Deep chlorophyll maximum: A deep chlorophyll maximum (DCM) is a subsurface maximum in the concentration of chlorophyll in the ocean or a lake. A DCM is not always present--sometimes there is more chlorophyll at the surface than at any greater depth--but it is a common feature of most aquatic ecosystems.Thermococcus kodakarensis: Thermococcus kodakarensis is a species of thermophilic archaea. The type strain T.Methylated-thiol-coenzyme M methyltransferase: Methylated-thiol-coenzyme M methyltransferase (, mtsA (gene)) is an enzyme with system name methylated-thiol:coenzyme M methyltransferase. This enzyme catalyses the following chemical reactionAmmonia transporterProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.TEX86: TEX86 is an organic paleothermometer based upon the membrane lipids of mesophilic marine Thaumarchaeota (formerly Marine Group 1 Crenarchaeota).Schouten, S.Oxymonad: The Oxymonads are a group of flagellated protozoa found exclusively in the intestines of termites and other wood-eating insects. Along with the similar parabasalid flagellates, they harbor the symbiotic bacteria that are responsible for breaking down cellulose.Thermoplasma: In taxonomy, Thermoplasma is a genus of the Thermoplasmataceae.See the NCBI webpage on Thermoplasma.CS-BLASTDNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.GvpA: GvpA is a gas vesicle structural protein found in different phyla of bacteria and archaea for example in Halobacterium salinarum or Haloferax mediterranei. Gas vesicles are small, hollow, gas filled protein structures found in several cyanobacterial and archaebacterial microorganisms.HEPN domain: In molecular biology, the HEPN domain (higher eukaryotes and prokaryotes nucleotide-binding domain) is a region of approximately 110 amino acids found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archaea proteins. There are three classes of proteins with HEPN domains:D-proline dehydrogenase: D-proline dehydrogenase (, D-Pro DH, D-Pro dehydrogenase, dye-linked D-proline dehydrogenase) is an enzyme with system name D-proline:acceptor oxidoreductase. This enzyme catalyses the following chemical reactionHalobacterium salinarum: Halobacterium salinarum is an extremely halophilic marine Gram-negative obligate aerobic archaeon. Despite its name, this microorganism is not a bacterium, but rather a member of the domain Archaea.Alliance for Zero Extinction: Formed in 2000 and launched globally in 2005, the Alliance for Zero Extinction (AZE) comprises 100 non-governmental biodiversity conservation organizations working to prevent species extinctions by identifying and safeguarding sites where species evaluated to be Endangered or Critically Endangered under International Union for Conservation of Nature (IUCN) criteria only exist at one location on earth."Zero Extinction - Home.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Acidophile: Acidophiles or acidophilic organisms are those that thrive under highly acidic conditions (usually at pH 2.0 or below).Horizontal gene transfer in evolutionMethanogen: Methanogens are microorganisms that produce methane as a metabolic byproduct in anoxic conditions. They are classified as archaea, a domain distinct from bacteria.Ferric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Global microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.Sulfolobales: In taxonomy, the Sulfolobales are an order of the Thermoprotei.See the NCBI webpage on Sulfolobales.Glucose-methanol-choline oxidoreductase family: In molecular biology, the glucose-methanol-choline oxidoreductase family (GMC oxidoreductase) is a family of enzymes with oxidoreductase activity.Reaction coordinateFecal coliform: A fecal coliform (British: faecal coliform) is a facultatively anaerobic, rod-shaped, gram-negative, non-sporulating bacterium. Coliform bacteria generally originate in the intestines of warm-blooded animals.Intramembrane protease: Intramembrane proteases (IMPs), also known as intermembrane-cleaving proteases (I-CLiPs), are enzymes that have the property of cleaving transmembrane domains of integral membrane proteins. All known intramembrane proteases are themselves integral membrane proteins with multiple transmembrane domains, and they have their active sites buried within the lipid bilayer of cellular membranes.EcosystemMcIntosh and Filde's anaerobic jar: McIntosh and Filde's anaerobic jar is an instrument used in the production of an anaerobic environment. This method of anaerobiosis as others is used to culture bacteria which die or fail to grow in presence of oxygen (anaerobes).T-box leaderSoil salinity control: Soil salinity control relates to controlling the problem of soil salinity and reclaiming salinized agricultural land.List of strains of Escherichia coli: Escherichia coli is a well studied bacterium that was first identified by Theodor Escherich, after whom it was later named.Gemmatimonadetes: The Gemmatimonadetes are a family of bacteria, given their own phylum (Gemmatimonadetes). This bacterium makes up about 2% of soil bacterial communities and has been identified as one of the top nine phyla found in soils; yet, there are currently only six cultured isolates.Continuous Plankton Recorder: The Continuous Plankton Recorder (CPR) survey is one of the longest running marine biological monitoring programmes in the world. Started in 1931 by Sir Alister Hardy, the CPR has provided marine scientists with their only measure of plankton communities on a pan-oceanic scale.Table of standard reduction potentials for half-reactions important in biochemistry: The values below are standard reduction potentials for half-reactions measured at 25°C, 1 atmosphere and a pH of 7 in aqueous solution.Transfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.BioreactorFishpaper: Fish paper or fishpaper is a strong, flexible, fibrous dielectric paper. It resists moderate heat and mechanical injury, and is often used for wrapping coils and insulating stove-top parts.Indian Ridge Hospital Open Invitational: The Indian Ridge Hospital Open Invitational was a PGA Tour satellite event that played for one year at the Indian Ridge Country Club in Andover, Massachusetts. The tournament, which was held in August 1969 and organized by Indian Ridge head club pro Ross Coon, benefited the Children's Hospital of Boston.FERM domain: In molecular biology, the FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane.Zetaproteobacteria: The class Zetaproteobacteria is the sixth and most recently described class of the Proteobacteria. Zetaproteobacteria can also refer to the group of organisms assigned to this class.Ecosystem of the North Pacific Subtropical Gyre: The North Pacific Subtropical Gyre (NPSG) is the largest contiguous ecosystem on earth. In oceanography, a subtropical gyre is a ring-like system of ocean currents rotating clockwise in the Northern Hemisphere and counterclockwise in the Southern Hemisphere caused by the Coriolis Effect.Desulfococcus oleovorans Strain Hxd3: Desulfococcus oleovorans Strain Hxd3 was isolated from the saline water phase of an oil-water separator from a northern German oil field.Aeckersberg, F.Wujing Zongyao: The Wujing Zongyao (), or the Complete Essentials for the Military Classics, is a Chinese military compendium written from around 1040 to 1044. It contains the earliest known written formulas for gunpowder, made from saltpeter, sulphur, and charcoal, along with many added ingredients.Haloarcula hispanica SH1 virus: Haloarcula hispanica SH1 virus is a double-stranded DNA virus that infects the archaeon Haloarcula hispanica.Bamford DH, Ravantti JJ, Rönnholm G, Laurinavicius S, Kukkaro P, Dyall-Smith M, Somerharju P, Kalkkinen N, Bamford JK (2005) Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica.Microbiota: A microbiota is "the ecological community of commensal, symbiotic and pathogenic microorganisms that literally share our body space". Joshua Lederberg coined the term, emphasising the importance of microorganisms inhabiting the human body in health and disease.List of hot springs: There are hot springs on all continents and in many countries around the world. Countries that are renowned for their hot springs include Honduras, Canada, Chile, Hungary, Iceland, Israel, Japan, New Zealand and United States, but there are interesting and unique hot springs in many other places as well.Sulfate-reducing bacteria: Sulfate-reducing bacteria are those bacteria and archaea that can obtain energy by oxidizing organic compounds or molecular hydrogen (H2) while reducing sulfate () to hydrogen sulfide (H2S). In a sense, these organisms "breathe" sulfate rather than oxygen in a form of anaerobic respiration.
(1/2228) Characterization of two novel haloalkaliphilic archaea Natronorubrum bangense gen. nov., sp. nov. and Natronorubrum tibetense gen. nov., sp. nov.
Two haloalkaliphilic archaea were isolated from a soda lake in Tibet. The two strains, designated A33T and GA33T, were Gram-negative, pleomorphic, flat, non-motile and strictly aerobic. Growth required at least 12% NaCl. Growth was between pH 8.0 and pH 11 with an optimum at pH 9.0-9.5. Cells were chemo-organotrophic. Polar lipids were C20-C25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate. The nucleotide sequences of the 16S rRNA genes from the two strains were obtained by the analysis of the cloned rDNAs. On 16S rRNA phylogenetic trees, the two strains formed a monophyletic cluster. They differed from their closet neighbours, Halobacterium trapanicum and Natrialba asiatica, in polar lipid composition, as well as physiological and phenotypic characteristics. DNA-DNA hybridization indicated that the two strains belonged to different species of the same genus. The results indicated that the strains A33T and GA33T should be classified in a new genus Natronorubrum gen. nov. as Natronorubrum bangense sp. nov. (strain A33T) and Natronorubrum tibetense sp. nov. (strain GA33T). (+info)
(2/2228) An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes.
Elongation factor 1 alpha (EF-1 alpha) is a highly conserved ubiquitous protein involved in translation that has been suggested to have desirable properties for phylogenetic inference. To examine the utility of EF-1 alpha as a phylogenetic marker for eukaryotes, we studied three properties of EF-1 alpha trees: congruency with other phyogenetic markers, the impact of species sampling, and the degree of substitutional saturation occurring between taxa. Our analyses indicate that the EF-1 alpha tree is congruent with some other molecular phylogenies in identifying both the deepest branches and some recent relationships in the eukaryotic line of descent. However, the topology of the intermediate portion of the EF-1 alpha tree, occupied by most of the protist lineages, differs for different phylogenetic methods, and bootstrap values for branches are low. Most problematic in this region is the failure of all phylogenetic methods to resolve the monophyly of two higher-order protistan taxa, the Ciliophora and the Alveolata. JACKMONO analyses indicated that the impact of species sampling on bootstrap support for most internal nodes of the eukaryotic EF-1 alpha tree is extreme. Furthermore, a comparison of observed versus inferred numbers of substitutions indicates that multiple overlapping substitutions have occurred, especially on the branch separating the Eukaryota from the Archaebacteria, suggesting that the rooting of the eukaryotic tree on the diplomonad lineage should be treated with caution. Overall, these results suggest that the phylogenies obtained from EF-1 alpha are congruent with other molecular phylogenies in recovering the monophyly of groups such as the Metazoa, Fungi, Magnoliophyta, and Euglenozoa. However, the interrelationships between these and other protist lineages are not well resolved. This lack of resolution may result from the combined effects of poor taxonomic sampling, relatively few informative positions, large numbers of overlapping substitutions that obscure phylogenetic signal, and lineage-specific rate increases in the EF-1 alpha data set. It is also consistent with the nearly simultaneous diversification of major eukaryotic lineages implied by the "big-bang" hypothesis of eukaryote evolution. (+info)
(3/2228) Unusual ribulose 1,5-bisphosphate carboxylase/oxygenase of anoxic Archaea.
The predominant pool of organic matter on earth is derived from the biological reduction and assimilation of carbon dioxide gas, catalyzed primarily by the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO). By virtue of its capacity to use molecular oxygen as an alternative and competing gaseous substrate, the catalytic efficiency of RubisCO and the enzyme's ability to assimilate CO2 may be severely limited, with consequent environmental and agricultural effects. Recent genomic sequencing projects, however, have identified putative RubisCO genes from anoxic Archaea. In the present study, these potential RubisCO sequences, from Methanococcus jannaschii and Archaeoglobus fulgidus, were analyzed in order to ascertain whether such sequences might encode functional proteins. We also report the isolation and properties of recombinant RubisCO using sequences obtained from the obligately anaerobic hyperthermophilic methanogen M. jannaschii. This is the first description of an archaeal RubisCO sequence; this study also represents the initial characterization of a RubisCO molecule that has evolved in the absence of molecular oxygen. The enzyme was shown to be a homodimer whose deduced sequence, along with other recently obtained archaeal RubisCO sequences, differs substantially from those of known RubisCO molecules. The recombinant M. jannaschii enzyme has a somewhat low, but reasonable kcat, however, unlike previously isolated RubisCO molecules, this enzyme is very oxygen sensitive yet it is stable to hyperthermal temperatures and catalyzes the formation of the expected carboxylation product. Despite inhibition by oxygen, this unusual RubisCO still catalyzes a weak yet demonstrable oxygenase activity, with perhaps the lowest capacity for CO2/O2 discrimination ever encountered for any RubisCO. (+info)
(4/2228) Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules.
16S rRNA-targeted in situ hybridization combined with confocal laser scanning microscopy was used to elucidate the spatial distribution of microbes within two types of methanogenic granular sludge, mesophilic (35 degrees C) and thermophilic (55 degrees C), in upflow anaerobic sludge blanket reactors fed with sucrose-, acetate-, and propionate-based artificial wastewater. The spatial organization of the microbes was visualized in thin sections of the granules by using fluorescent oligonucleotide probes specific to several phylogenetic groups of microbes. In situ hybridization with archaeal- and bacterial-domain probes within granule sections clearly showed that both mesophilic and thermophilic granules had layered structures and that the outer layer harbored mainly bacterial cells while the inner layer consisted mainly of archaeal cells. Methanosaeta-, Methanobacterium-, Methanospirillum-, and Methanosarcina-like cells were detected with oligonucleotide probes specific for the different groups of methanogens, and they were found to be localized inside the granules, in both types of which dominant methanogens were members of the genus Methanosaeta. For specific detection of bacteria which were previously detected by whole-microbial-community 16S ribosomal DNA (rDNA)-cloning analysis (Y. Sekiguchi, Y. Kamagata, K. Syutsubo, A. Ohashi, H. Harada, and K. Nakamura, Microbiology 144:2655-2665, 1998) we designed probes specific for clonal 16S rDNAs related to unidentified green nonsulfur bacteria and clones related to Syntrophobacter species. The probe designed for the cluster closely related to Syntrophobacter species hybridized with coccoid cells in the inner layer of the mesophilic granule sections. The probe for the unidentified bacteria which were clustered with the green nonsulfur bacteria detected filamentous cells in the outermost layer of the thermophilic sludge granule sections. These results revealed the spatial organizations of methanogens and uncultivated bacteria and their in situ morphologies and metabolic functions in both mesophilic and thermophilic granular sludges. (+info)
(5/2228) Universal conservation in translation initiation revealed by human and archaeal homologs of bacterial translation initiation factor IF2.
Binding of initiator methionyl-tRNA to ribosomes is catalyzed in prokaryotes by initiation factor (IF) IF2 and in eukaryotes by eIF2. The discovery of both IF2 and eIF2 homologs in yeast and archaea suggested that these microbes possess an evolutionarily intermediate protein synthesis apparatus. We describe the identification of a human IF2 homolog, and we demonstrate by using in vivo and in vitro assays that human IF2 functions as a translation factor. In addition, we show that archaea IF2 can substitute for its yeast homolog both in vivo and in vitro. We propose a universally conserved function for IF2 in facilitating the proper binding of initiator methionyl-tRNA to the ribosomal P site. (+info)
(6/2228) 10-11 bp periodicities in complete genomes reflect protein structure and DNA folding.
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)
(7/2228) The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: fact or farce?
Archaea is now recognized as the third domain of life. Since their discovery, much effort has been directed towards understanding the molecular biology and biochemistry of Archaea. The objective is to comprehend the complete structure and the depth of the phylogenetic tree of life. DNA replication is one of the most important events in living organisms and DNA polymerase is the key enzyme in the molecular machinery which drives the process. All archaeal DNA polymerases were thought to belong to family B. This was because all of the products of pol genes that had been cloned showed amino acid sequence similarities to those of this family, which includes three eukaryal DNA replicases and Escherichia coli DNA polymerase II. Recently, we found a new heterodimeric DNA polymerase from the hyperthermophilic archaeon, Pyrococcus furiosus. The genes coding for the subunits of this DNA polymerase are conserved in the euryarchaeotes whose genomes have been completely sequenced. The biochemical characteristics of the novel DNA polymerase family suggest that its members play an important role in DNA replication within euryarchaeal cells. We review here our current knowledge on DNA polymerases in Archaea with emphasis on the novel DNA polymerase discovered in Euryarchaeota. (+info)
(8/2228) Two distinct SECIS structures capable of directing selenocysteine incorporation in eukaryotes.
Translation of UGA as selenocysteine requires specific RNA secondary structures in the mRNAs of selenoproteins. These elements differ in sequence, structure, and location in the mRNA, that is, coding versus 3' untranslated region, in prokaryotes, eukaryotes, and archaea. Analyses of eukaryotic selenocysteine insertion sequence (SECIS) elements via computer folding programs, mutagenesis studies, and chemical and enzymatic probing has led to the derivation of a predicted consensus structural model for these elements. This model consists of a stem-loop or hairpin, with conserved nucleotides in the loop and in a non-Watson-Crick motif at the base of the stem. However, the sequences of a number of SECIS elements predict that they would diverge from the consensus structure in the loop region. Using site-directed mutagenesis to introduce mutations predicted to either disrupt or restore structure, or to manipulate loop size or stem length, we show that eukaryotic SECIS elements fall into two distinct classes, termed forms 1 and 2. Form 2 elements have additional secondary structures not present in form 1 elements. By either insertion or deletion of the sequences and structures distinguishing the two classes of elements while maintaining appropriate loop size, conversion of a form 1 element to a functional form 2-like element and of a form 2 to a functional form 1-like element was achieved. These results suggest commonality of function of the two classes. The information obtained regarding the existence of two classes of SECIS elements and the tolerances for manipulations of stem length and loop size should facilitate designing RNA molecules for obtaining high-resolution structural information about these elements. (+info)
- their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community. (hindawi.com)
- A metagenomics analysis finds Cas9 in archaea for the first time, along with two previously unknown Cas nucleases from bacteria. (the-scientist.com)
- In this lesson, our instructor Catherine Carpenter gives an introduction on prokaryotes: bacteria and archaea. (educator.com)
- In the past they were viewed as an unusual group of bacteria and named archaebacteria but since the Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, they are now classified as a separate domain in the three-domain system. (galaktiskeparti.no)
- They are not Bacteria, they are Archaea. (sciencepartners.info)
- Proteomics of Pyrococcus furiosus, a hyperthermophilic archaeon refractory to traditional methods. (nih.gov)
- Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. (nih.gov)
- The extreme conditions under which most species of archaea live has made them difficult to culture, so their unique place among living organisms long went unrecognized. (sciencepartners.info)
- A recent study of the microbial species diversity found in prairie, desert and rainforest soils suggests that there may be more archaea and fungi species in soils than there are bacterial species, as discussed in this article, " New Study Suggests Many Unknown Microbes in Soil ", from Science Daily. (sciencepartners.info)
- Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. (hindawi.com)
- Figure 3.20: Archaea were first detected in extreme environments, such as hot springs like Grand Prismatic Spring in Yellowstone National Park. (sciencepartners.info)
- Figure 3.21: A new group of archaea were recently discovered in acid rock drainage (sometimes referred to as acid mine drainage), like this acid drainage seen in the Rio Tinto River in Spain. (sciencepartners.info)
- By the end of the 20th century, microbiologists realized that the archaea are common in much less extreme habitats, such as soils and oceans. (sciencepartners.info)