Proteins found in any species of archaeon.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
Deoxyribonucleic acid that makes up the genetic material of archaea.
The functional genetic units of ARCHAEA.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
The genetic complement of a BACTERIA as represented in its DNA.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Viruses whose hosts are in the domain ARCHAEA.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
The genetic complement of MITOCHONDRIA as represented in their DNA.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A family of anaerobic, coccoid to rod-shaped METHANOBACTERIALES. Cell membranes are composed mainly of polyisoprenoid hydrocarbons ether-linked to glycerol. Its organisms are found in anaerobic habitats throughout nature.
An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. They are pseudosarcina, coccoid or sheathed rod-shaped and catabolize methyl groups. The cell wall is composed of protein. The order includes one family, METHANOCOCCACEAE. (From Bergey's Manual of Systemic Bacteriology, 1989)
A kingdom in the domain ARCHAEA comprised of thermoacidophilic, sulfur-dependent organisms. The two orders are SULFOLOBALES and THERMOPROTEALES.
Structures within the nucleus of archaeal cells consisting of or containing DNA, which carry genetic information essential to the cell.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
The complete gene complement contained in a set of chromosomes in a fungus.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A genus of anaerobic coccoid METHANOCOCCACEAE whose organisms are motile by means of polar tufts of flagella. These methanogens are found in salt marshes, marine and estuarine sediments, and the intestinal tract of animals.
A species of thermoacidophilic ARCHAEA in the family Sulfolobaceae, found in volcanic areas where the temperature is about 80 degrees C and SULFUR is present.
The amount of DNA (or RNA) in one copy of a genome.
A species of halophilic archaea found in the Dead Sea.
A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.
The large subunit of the archaeal 70s ribosome. It is composed of the 23S RIBOSOMAL RNA, the 5S RIBOSOMAL RNA, and about 40 different RIBOSOMAL PROTEINS.
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.
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.
The systematic study of the complete DNA sequences (GENOME) of organisms.
A species of gram-negative hyperthermophilic ARCHAEA found in deep ocean hydrothermal vents. It is an obligate anaerobe and obligate chemoorganotroph.
The genetic complement of an insect (INSECTS) as represented in its DNA.
The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.
A species of extremely thermophilic, sulfur-reducing archaea. It grows at a maximum temperature of 95 degrees C. in marine or deep-sea geothermal areas.
A genus of anaerobic, irregular spheroid-shaped METHANOSARCINALES whose organisms are nonmotile. Endospores are not formed. These archaea derive energy via formation of methane from acetate, methanol, mono-, di-, and trimethylamine, and possibly, carbon monoxide. Organisms are isolated from freshwater and marine environments.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
A species of aerobic, chemolithotrophic ARCHAEA consisting of coccoid cells that utilize sulfur as an energy source. The optimum temperature for growth is 70-75 degrees C. They are isolated from acidic fields.
Anaerobic hyperthermophilic species of ARCHAEA, isolated from hydrothermal fluid samples. It is obligately heterotrophic with coccoid cells that require TRYPTOPHAN for growth.
A 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).
The genetic complement of CHLOROPLASTS as represented in their DNA.
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.
Any method used for determining the location of and relative distances between genes on a chromosome.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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)
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
A kingdom of hyperthermophilic ARCHAEA found in diverse environments.
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.
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.
The sequential location of genes on a chromosome.
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.
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.
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).
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
The 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.
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.
Genotypic differences observed among individuals in a population.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
A 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)
The genetic complement of a helminth (HELMINTHS) as represented in its DNA.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
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)
Deoxyribonucleic acid that makes up the genetic material of bacteria.
The genetic complement of PLASTIDS as represented in their DNA.
Databases devoted to knowledge about specific genes and gene products.
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.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
Deoxyribonucleic acid that makes up the genetic material of viruses.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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.
An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. There are two families: METHANOSARCINACEAE and Methanosaetaceae.
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.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
An order of anaerobic, coccoid to rod-shaped methanogens, in the kingdom EURYARCHAEOTA. They are nonmotile, do not catabolize carbohydrates, proteinaceous material, or organic compounds other than formate or carbon monoxide, and are widely distributed in nature.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Proteins found in any species of bacterium.
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.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
The small subunit of archaeal RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 28 different RIBOSOMAL PROTEINS.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
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)
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.
The functional hereditary units of BACTERIA.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
Sequential operating programs and data which instruct the functioning of a digital computer.
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.
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.
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.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
An order of CRENARCHAEOTA consisting of aerobic or facultatively aerobic, chemolithotrophic cocci which are extreme thermoacidophiles. They lack peptidoglycan in their cell walls.
The variety of all native living organisms and their various forms and interrelationships.
A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.
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.
A family of anaerobic METHANOCOCCALES whose organisms are motile by means of flagella. These methanogens use carbon dioxide as an electron acceptor.
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).
DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
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.
Ribonucleic acid that makes up the genetic material of viruses.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
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.
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.
A species of halophilic archaea found in salt lakes. Some strains form a PURPLE MEMBRANE under anaerobic conditions.
The functional hereditary units of VIRUSES.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
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.
Proteins found in any species of virus.
Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
The process by which a DNA molecule is duplicated.
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.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A group of different species of microorganisms that act together as a community.
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.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
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.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
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.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Deoxyribonucleic acid that makes up the genetic material of plants.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
Group II chaperonins found in species of ARCHAEA.
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.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
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.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
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)
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)
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
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).
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.
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.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Viruses whose hosts are bacterial cells.
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
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.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
A 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.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
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.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
A genus of extremely thermophilic, sulfate-reducing archaea, in the family Archaeoglobaceae.
An order of CRENARCHAEOTA comprised of rod, disc, or spherical shaped, nonseptate, anaerobic, extreme thermophiles and found in solfataric hot waters, mud holes, and superheated submarine environments.
An order of extremely thermophilic, sulfate-reducing archaea, in the kingdom EURYARCHAEOTA. The single family Archaeoglobaceae contains one genus ARCHAEOGLOBUS.
An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.
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)
Proteins prepared by recombinant DNA technology.
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
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.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
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.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
The functional hereditary units of PLANTS.
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.
The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.
Established cell cultures that have the potential to propagate indefinitely.
Hot springs on the ocean floor. They are commonly found near volcanically active places such as mid-oceanic ridges.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
The portion of an interactive computer program that issues messages to and receives commands from a user.
Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
A unique DNA sequence of a replicon at which DNA REPLICATION is initiated and proceeds bidirectionally or unidirectionally. It contains the sites where the first separation of the complementary strands occurs, a primer RNA is synthesized, and the switch from primer RNA to DNA synthesis takes place. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.
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.
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.
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The genomic analysis of assemblages of organisms.
Enzymes that recognize CRUCIFORM DNA structures and introduce paired incisions that help to resolve the structure into two DNA helices.
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.

Complete genomes in WWW Entrez: data representation and analysis. (1/588)

MOTIVATION: The large amount of genome sequence data now publicly available can be accessed through the National Center for Biotechnology Information (NCBI) Entrez search and retrieval system, making it possible to explore data of a breadth and scope exceeding traditional flatfile views. RESULTS: Here we report recent improvements for completely sequenced genomes from viruses, bacteria, and yeast. Flexible web based views, precomputed relationships, and immediate access to analytical tools provide scientists with a portal into the new insights to be gained from completed genome sequences. AVAILABILITY: Entrez Genomes can be accessed on the World Wide Web at http://www.ncbi.nlm.nih.gov/Entrez/Genome/ org.html.  (+info)

Whole genome-based phylogenetic analysis of free-living microorganisms. (2/588)

A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relation-ships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.  (+info)

Novel coding regions in four complete archaeal genomes. (3/588)

In the process of analysing the four available complete archaeal genomes, we have noted that certain regions characterised as 'non-coding' exhibit significant sequence similarity to other protein sequences from Archaea and other species. Using established technology, we have identified a number of potential protein coding regions in these putative 'non-coding' regions. We have detected 524 such cases, of which 113 regions appear to code for proteins present in archaeal or other species, while the remaining 411 regions are mostly start/stop definition conflicts. Of the 113 protein coding regions, only 21 code for proteins with homologues of known function. The number of novel coding sequences identified herein amounts to 1. 5% of the total genome entries, while the conflicting cases represent an additional 5%. The observed differences between the four complete archaeal genomes seem to reflect disparate approaches to genome annotation. Genome sequence collections should be regularly checked to improve gene prediction by sequence similarity and greater effort is required to make gene definitions consistent across related species.  (+info)

The COG database: a tool for genome-scale analysis of protein functions and evolution. (4/588)

Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www. ncbi.nlm. nih.gov/COG). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56-83% of the gene products from each of the complete bacterial and archaeal genomes and approximately 35% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes.  (+info)

EMGLib: the enhanced microbial genomes library (update 2000). (5/588)

As the number of complete microbial genomes publicly available is still growing, the problem of annotation quality in these very large sequences remains unsolved. Indeed, the number of annotations associated with complete genomes is usually lower than those of the shorter entries encountered in the repository collections. Moreover, classical sequence database management systems have difficulties in handling entries of such size. In this context, the Enhanced Microbial Genomes Library (EMGLib) was developed to try to alleviate these problems. This library contains all the complete genomes from prokaryotes (bacteria and archaea) already sequenced and the yeast genome in GenBank format. The annotations are improved by the introduction of data on codon usage, gene orientation on the chromosome and gene families. It is possible to access EMGLib through two database systems set up on WWW servers: the PBIL server at http://pbil.univ-lyon1.fr/emglib.html and the MICADO server at http://locus.jouy.inra.fr/micado  (+info)

A phylogenomic study of DNA repair genes, proteins, and processes. (6/588)

The ability to recognize and repair abnormal DNA structures is common to all forms of life. Studies in a variety of species have identified an incredible diversity of DNA repair pathways. Documenting and characterizing the similarities and differences in repair between species has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of phenotypes affected by repair (e.g., mutation rates, lifespan, tumorigenesis, survival in extreme environments). Unfortunately, while repair processes have been studied in quite a few species, the ecological and evolutionary diversity of such studies has been limited. Complete genome sequences can provide potential sources of new information about repair in different species. In this paper, we present a global comparative analysis of DNA repair proteins and processes based upon the analysis of available complete genome sequences. We use a new form of analysis that combines genome sequence information and phylogenetic studies into a composite analysis we refer to as phylogenomics. We use this phylogenomic analysis to study the evolution of repair proteins and processes and to predict the repair phenotypes of those species for which we now know the complete genome sequence.  (+info)

Lessons from the Aeropyrum pernix genome. (7/588)

Aeropyrum pernix is the first crenarchaeote and first aerobic member of the Archaea for which the complete genome sequence has been determined. The sequence confirms the distinct nature of crenarchaeotes and provides new insight into the relationships between the three domains: Bacteria, Archaea and Eukaryotes.  (+info)

Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. (8/588)

Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data on archaeal transcription regulation or by analogy with known bacterial regulons, and further analysis was performed using iterative profile searches. The information content of the candidate signals detected by this method is insufficient for reliable predictions to be made. Therefore, this approach has to be complemented by examination of evolutionary conservation in different archaeal genomes. This combined strategy resulted in the prediction of a conserved heat shock regulon in all euryarchaea, a nitrogen fixation regulon in the methanogens Methanococcus jannaschii and Methanobacterium thermoautotrophicum and an aromatic amino acid regulon in M.thermoautotrophicum. Unexpectedly, the heat shock regulatory site was detected not only for genes that encode known chaperone proteins but also for archaeal histone genes. This suggests a possible function for archaeal histones in stress-related changes in DNA condensation. In addition, comparative analysis of the genomes of three Pyrococcus species resulted in the prediction of their purine metabolism and transport regulon. The results demonstrate the feasibility of prediction of at least some transcription regulatory sites by comparing poorly characterized prokaryotic genomes, particularly when several closely related genome sequences are available.  (+info)

An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for
Researchers often utilize functional genes as a proxy for the potential of microbial communities to mediate specific biochemical and nutrient cycling processes. Metabolic pathways for such processes are, in many cases, composed of multiple steps, requiring more than one protein to function. Genomic data also suggests that pathways can sometimes be incomplete, though it is not well understood what the ecological implications of incomplete pathways might be. The genes for 11 different inorganic nitrogen transformation pathways were thus investigated in 6,384 bacterial and 252 complete archaeal genomes. The analysis aimed to determine how commonly pathways were incomplete, how frequently different pathways co-occur, and how these finding relate to the evolutionary history of microbes. Results from this study indicate that the co-occurrence of different N cycling pathways is infrequent and that pathways are frequently incomplete. These data imply that many microbes specialize in specific metabolic ...
Extreme halophilic, salt-loving, Archaea are members of the third Domain of Life, thriving in hypersaline environments reaching saturating levels of sodium chloride, nine times the salinity of seawater. The unique position of Archaea in the Tree of Life makes these organisms fascinating. Archaea have characteristics of both Bacteria and Eukarya. For example, the archaeal genome structure is more similar to bacteria, while the information transfer macromolecules are eukaryotic-like. With the release of several haloarchaeal genomes I am using comparative genomics to identify haloarchaeal conserved proteins that likely play key roles in these organisms unique environmental adaptations as well as the conservation of the information transfer system of halophilic archaea. ...
The context analysis report aims at understanding drivers and obstacles to the diffusion of Photovoltaic and Building Integrated Photovoltaic solar technologies in the cities involved in the project ...
p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...
Codons consist of six bases and there are six reading frames for each DNA strand, so ... so researchers must evaluate six open reading frames.
The increasing wealth of genomic data from cultured and uncultured microorganisms provides the opportunity to develop a systematic taxonomy based on evolutionary relationships. Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy is stable under a range of phylogenetic variables, including marker genes, inference methods, and tree rooting scenarios. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. The taxonomy is based on 2,392 quality screened archaeal genomes, the great majority of which (93.3%) required one or more changes to their existing taxonomy, mostly as a result of incomplete classification. ...
The similarities between essential molecular mechanisms in Archaea and Eukarya make it possible to discover, using comparative genomics, new fundamental mechanisms conserved between these two domains. We are studying a complex of two proteins conserved in Archaea and Eukarya whose precise biological role and biochemical function remain unknown. One of them is a universal protein known as Kae1 (kinase-asociated endopeptidase 1). The second protein is a serine/threonine kinase corresponding to the proteins Bud32 in Saccharomyces cerevisiae and PRPK (p53-related protein kinase) in humans. The genes encoding the archaeal orthologues of Kae1 and PRPK are either contiguous or even fused in many archaeal genomes. In S. cerevisiae, Kae1 and Bud32 (PRPK) belong to a chromatin-associated complex [KEOPS (kinase, endopeptidase and other proteins of small size)/EKC (endopeptidase-like kinase chromatin-associated)] that is essential for telomere elongation and transcription of essential genes. Although Kae1 ...
The ATP-binding cassette (ABC) transporters form one of the largest known protein families, and are widespread in bacteria, archaea, and eukaryotes. They couple ATP hydrolysis to active transport of a wide variety of substrates such as ions, sugars, lipids, sterols, peptides, proteins, and drugs. The structure of a prokaryotic ABC transporter usually consists of three components; typically two integral membrane proteins each having six transmembrane segments, two peripheral proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. Many of the genes for the three components form operons as in fact observed in many bacterial and archaeal genomes. On the other hand, in a typical eukaryotic ABC transporter, the membrane spanning protein and the ATP-binding protein are fused, forming a multi-domain protein with the membrane-spanning domain (MSD) and the nucleotide-binding domain (NBD ...
The ATP-binding cassette (ABC) transporters form one of the largest known protein families, and are widespread in bacteria, archaea, and eukaryotes. They couple ATP hydrolysis to active transport of a wide variety of substrates such as ions, sugars, lipids, sterols, peptides, proteins, and drugs. The structure of a prokaryotic ABC transporter usually consists of three components; typically two integral membrane proteins each having six transmembrane segments, two peripheral proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. Many of the genes for the three components form operons as in fact observed in many bacterial and archaeal genomes. On the other hand, in a typical eukaryotic ABC transporter, the membrane spanning protein and the ATP-binding protein are fused, forming a multi-domain protein with the membrane-spanning domain (MSD) and the nucleotide-binding domain (NBD ...
The forkhead-associated (FHA) domain [(PUBMED:7482699)] is a phosphopeptide recognition domain found in many regulatory proteins. It displays specificity for phosphothreonine-containing epitopes but will also recognise phosphotyrosine with relatively high affinity. It spans approximately 80-100 amino acid residues folded into an 11-stranded beta sandwich, which sometimes contain small helical insertions between the loops connecting the strands [(PUBMED:11911881)]. To date, genes encoding FHA-containing proteins have been identified in eubacterial and eukaryotic but not archaeal genomes. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes - DNA repair, signal transduction, vesicular transport and protein degradation are just a few examples.. ...
© SJul 20073ISCRAM 2007 User, task, and context analysis Methodology for identifying user- and usage-centered design requirements Identifies different types and critical characteristics of target users, tasks and contexts Usually conducted at the application level
Additional calculations are performed including the search for similarities within or among genus, the search for signal sequence or transmembrane segments, predicted secondary structure and disulfide bonds, and the search for homologs with a known 3D structure in the Protein Databank. As a result, BactPepDB provides insights about candidate peptides in complete prokaryote genomes, and provides information about their conservation, together with some of their expected biological/structural features. A brief overview of the database interface and its functionalities can be found at the bottom of the Help page under the form of a step-by-step tutorial.. As of 08/08/2020, the database contains 1,747,413 Peptides from 557 Genuses, 1,226 Species and 2,240 Strains.. ...
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TY - JOUR. T1 - Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds. AU - Oh, Dickson. AU - Porter, Kate. AU - Russ, Brendan. AU - Burns, David. AU - Dyall-Smith, Mike. PY - 2010/3. Y1 - 2010/3. N2 - Haloquadratum walsbyi is frequently a dominant member of the microbial communities in hypersaline waters. 16S rRNA gene sequences indicate that divergence within this species is very low but relatively few sites have been examined, particularly in the southern hemisphere. The diversity of Haloquadratum was examined in three coastal, but geographically distant saltern crystallizer ponds in Australia, using both culture-independent and culture-dependent methods. Two 97%-OTU, comprising Haloquadratum- and Halorubrum-related sequences, were shared by all three sites, with the former OTU representing about 40% of the sequences recovered at each site. Sequences 99.5% identical to that of Hqr. walsbyi C23T were present at all three sites ...
The question of which proteins are involved in the interaction cell-cell contact and in transport between these two archaea cannot be addressed, at least presently, by genetics, such as mutagenesis or knockouts. We have therefore chosen the direct approach, by isolating a complex of membrane and membrane-associated proteins, using detergent-induced solubilization, followed by size-exclusion chromatography.. In the analysis of all proteins identified to be present in the detergent-solubilized membranes, approx. 26% of the I. hospitalis proteins, but only 4.2% of the N. equitans proteins belong to the category Transport and metabolism. This reflects the known difference between both organisms in their physiology and genome capacity: whereas I. hospitalis has the ability to grow alone and has a genome with full capacity for all biosynthetic pathways, N. equitans is not able to thrive alone and its genome is very compact and highly reduced; enzymes involved in many biosynthetic pathways cannot be ...
Citation. Ermolaeva, M. D., White, O., Salzberg, S. L.. Prediction of Operons In Microbial Genomes. Nucleic Acids Res. 2001 Mar 01; 29(5): 1216-21.. PubMed Citation. Abstract. Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P: ,/= 0.98) to belong to the same operon. The sensitivity of our method is 30-50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site www.tigr.org/tigr-scripts/operons/operons.cgi.. ...
original description Jolivet, E., LHaridon, S., Corre, E., Forterre, P., and Prieur, D. Thermococcus gammatolerans sp. nov., a hyperthermophilic archaeon from a deep-sea hydrothermal vent that resists ionizing radiation. Int. J. Syst. Evol. Microbiol. (2003) 53:847-851. [details] ...
Arrive with a DNA sample, leave with a genome Course Description This two-week course covers the process of sequencing, assembling and annotating a bacterial or archaeal genome from scratch. It then builds on these skills to train students in further analysis of microbial genomes, such as the prediction of metabolic pathways, comparative genomics, and phylogenomics. This course goes deeper than basic push-button genome assembly and annotation tools - students learn how relevant genomics software tools work and how to make intelligent, situation-dependent decisions when analysing microbial genomes. Students work on real data related to their own research by submitting DNA from an isolate of their choosing several weeks before the course begins. Illumina MiSeq sequencing is then carried out so that sequencing data is ready for students when they arrive. Is this the course for you? If you are a PhD student who would like to answer a research question using a microbial genome but dont know how ...
The DOE Joint Genome Institute (JGI), collaborating with CRDs Biological Data Management and Technology Center (BDMTC), announced last month an upgrade of the metagenome data management and analysis system, IMG/M, on the anniversary of its launch.. Developed by BDMTCs data management and software engineers and scientists of JGIs Genome Biology and Microbial Ecology Programs, IMG/M is a valuable asset for a growing community of biologists. Metagenomics refers to the genomic study of batches of microbes in their natural environments instead of those cultivated individually in lab cultures. IMG/M provides tools for analyzing the capability of microbial communities based on their metagenome sequence-in the context of reference isolate genomes-using a variety of public functional and pathway resources.. Since the release of its initial experimental version in 2006, IMG/M has been used by JGI scientists and their collaborators for analyzing several environmental microbial communities, and has been ...
TY - JOUR. T1 - Human contamination in bacterial genomes has created thousands of spurious proteins. AU - Breitwieser, Florian P.. AU - Pertea, Mihaela. AU - Zimin, Aleksey V.. AU - Salzberg, Steven L.. PY - 2019. Y1 - 2019. N2 - Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have ...
Background: The genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life. Results: Here we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13 of 15, 19 of 23, and 3 of 6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes. ...
I just found this patch of yours that was never screened while cleaning up the rebase state in one of my clones. I have amended the patch to avoid warnings and to avoid running the test when the patch type does not allow coalescing. I think this should go into 2.16 as it clarifies what works with the new rebase implementation. It is of course also valuable to avoid regressions. 1 patch for repository http://darcs.net/screened: patch ba4ca2fb7b6969a24356d36bc4551b43cf7b7e95 Author: Ganesh Sittampalam ,[email protected], Date: Thu May 14 21:29:32 CEST 2020 * test for whether rebase suspend/unsuspend introduces ...
This article explores the beginning of the terrain beyond filing a mechanics lien-the terrain covered by two little Latin words: lis pendens.
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Among the tRNA population of the archaeal parasite Nanoarchaeum equitans are five species assembled from separate 5 and 3 tRNA halves and four species derived from tRNA precursors containing introns. In both groups an intervening sequence element must be removed during tRNA maturation. A bulge-hel …
Strains C23T and HBSQ001 were isolated from solar salterns and are novel square-shaped, aerobic, extremely halophilic members of the domain Archaea and family Halobacteriaceae. Cells stained Gram-negative and grew optimally in media containing 18 % salts at around neutral pH. Mg2+ is not required. The DNA G+C content of both isolates was 46.9 mol% and DNA-DNA cross-hybridization showed a relatedness of 80 %. Their 16S rRNA gene sequences showed only 2 nucleotide differences (99.9 % identity) and phylogenetic tree reconstructions with other recognized members of the Halobacteriaceae indicated that they formed a distinct clade, with the closest relative being Halogeometricum borinquense PR 3T (91.2 % sequence identity). The major polar glycolipid of both isolates was the sulfated diglycosyl diether lipid S-DGD-1. Electron cryomicrosopy of whole cells revealed similar internal structures, such as gas vesicles and polyhydroxyalkanoate granules, but the cell wall of isolate HBSQ001 displayed a more complex S
This list of sequenced eubacterial genomes contains all the eubacteria known to have publicly available complete genome sequences. Most of these sequences have been placed in the International Nucleotide Sequence Database Collaboration, a public database which can be seKarched on the web. A few of the listed genomes may not be in the INSDC database, but in other public databases[verification needed]. Genomes listed as Unpublished are in a database, but not in the peer-reviewed scientific literature. For the genomes of archaea see list of sequenced archaeal genomes. Genome project Human microbiome project List of sequenced eukaryotic genomes List of sequenced archaeal genomes List of sequenced plastomes Entrez Genome Database Search. National Center for Biotechnology Information. Search for details on specific genomes by organism name and strain. Schell MA, et al. (2002). The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. ...
Planchestainer, Matteo and Segaud, Nathalie and Shanmugam, Muralidharan and McMaster, Jonathan and Paradisi, Francesca and Albrecht, Martin (2018) Carbene in cupredoxin protein scaffolds: replacement of a histidine ligand in the active site substantially alters copper redox properties. Angewandte Chemie International Edition, 57 (33). pp. 10677-10682. ISSN 1521-3773 Carucci, Cristina and Bruen, Larah and Gascón, Victoria and Paradisi, Francesca and Magner, Edmond (2018) Significant enhancement of structural stability of the hyperhalophilic ADH from Haloferax volcanii via entrapment on metal organic framework support. Langmuir . ISSN 0743-7463 Contente, Martina L. and Paradisi, Francesca (2018) Self-sustaining closed-loop multienzyme mediated conversion of amines into alcohols in continuous reactions. Nature Catalysis . ISSN 2520-1158 Cassidy, Jennifer and Paradisi, Francesca (2018) Haloquadratum walsbyi yields a versatile, NAD+/NADP+ dual affinity, thermostable, alcohol dehydrogenase (HwADH). ...
RNA degradation can be an essential aspect in the regulation of gene appearance. the examined mRNAs displaying half-lives between 8 and 12 min. The entire mean half-life was 10 min, which is certainly considerably longer compared to the ones within the various other prokaryotes investigated so far. As seen in and NRC-1 previously, is among simply two archaea sequenced to time that are lacking the primary subunits from the archaeal exosome. This complicated orthologous towards the RNA degrading exosome of eukarya is situated in all the archaeal genomes sequenced so far. Fast decay of mRNA allows quick version of microorganisms to adjustments in the surroundings by altering the appearance of chosen genes. The half-lives of specific transcripts as well as transcript sections in a organism show significant variations adding to differential gene appearance. The stabilities of many bacterial transcripts vary in response to exterior factors (analyzed in guide 46); the stabilities of eukaryotic ...
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From: Elijah Newren via GitGitGadget ,[email protected], To: [email protected] Cc: [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], Junio C Hamano ,[email protected],, Elijah Newren ,[email protected], Subject: [PATCH v2 12/15] rebase tests: mark tests specific to the am-backend with --am Date: Mon, 23 Dec 2019 18:49:56 +0000 Message-ID: ,c905d[email protected]gmail.com, (raw) In-Reply-To: ,[email protected], From: Elijah Newren ,[email protected], We have many rebase tests in the testsuite, and often the same test is repeated multiple times just testing different backends. For those tests that were specifically trying to test the am backend, add the --am flag. Signed-off-by: Elijah Newren ,[email protected], --- t/t3400-rebase.sh , 10 +++++----- t/t3401-rebase-and-am-rename.sh , 4 ++-- ...
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Arheju šūnu izmēri ir līdzīgi lielākajai prokariotu daļai - vidējais diametrs ap 1 μm. Vissīkākie starp arhejiem ir sugas Nanoarchaeum equitans pārstāvji - 0,4 μm. Šūnu forma ir visdažādākā. Sastopamas ir sfēriskas, iegarenas, spirāliskas, trīsstūra un taisnstūra formas. Daudziem arhejiem ir viciņas, kuru sastāvā, atšķirībā no baktērijām, ietilpst vairāku veidu flagellīni. Arheji nespēj sintezēt sarežģītus hidrolītiskus fermentus, tāpēc tie lielākoties spēj pārstrādāt tikai vienkāršākās organiskās vielas. Tomēr tie spēj eksistēt daudz plašākā ārējās vides diapazonā un ir mazāk no tās atkarīgi.. Bez 16S rRNS arhejiem ir arī citas unikālas īpatnības:. ...
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Some Archaea thrive in extreme places such as in thermal pools, hot vents at the bottom of the sea, extremely salty water, and even in underground oil reserves. This book examines the diverse Archaea kingdom and the division of these organisms by their unusual biology into three main groups. It also explains why little in general is known about them, and why further classification of Archaea is so difficult.
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Review the elements of reading passages to prepare for the PSAT exam. Video lessons and quizzes incorporate all of the elements of the reading...
I am finding that PSAT is 6 MINUTES behind the predictions of the previously provided original Launch TLE : ULTRASat3 1 99993U 15140.67013889 .00040043 00000-0 10235-2 0 00009 2 99993 055.0004 339.9238 0251027 182.3314 074.3075 15.12517086000014 So until I get new ones. Just point at AOS and wait 6 miuntes. Also, I had said not to TX PSK31 on the 10m u plink until you heard the downlink. Well, that was dumb advise, because the transponder does not come up unless it hears PSK31! So the new rule is, Listen first. If not heard, TX anyway. If not heard then, Fix your problem, and try again? We dont know how the power budget will work out. So all we can do is watch. Bob, WB4APR ...
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Made with love for the nicest guy in the world.. A selfless & caring man who is there for everyone when needed.. Now we are there for you.. #neverbeenaverage. ♥. ...
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Brueckner J, Martin WF (April 2020). "Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes". Genome Biology and ... From a consortium of bacterial and archaeal DNA originated the nuclear genome of eukaryotic cells. Spirochetes gave rise to the ... Biology portal Eukaryote hybrid genome Evolution of sexual reproduction List of sequenced eukaryotic genomes Parakaryon ... The known eukaryote genome sizes vary from 8.2 megabases (Mb) in Babesia bovis to 112,000-220,050 Mb in the dinoflagellate ...
In addition, the genome contains 68 RNA genes and 252 scaffolds. The genome includes genes for restriction endonuclease ... Podstawka, Adam (2017). "Strain-linked information about bacterial and archaeal biodiversity". 10.13145/bacdive3869.20171208. ... The contigs gathered from Illumina were then delivered to the DOE Joint Genome Institute (JGI), where the whole genome sequence ... The Deinococcus marmoris genome was found to contain 4,800,021 base pairs and a G+C content of 64.4 percent. Of the total ...
Genome Biol. Evol. 7 (1): 191-204. doi:10.1093/gbe/evu274. PMC 4316627. PMID 25527841. Eugene V. Koonin (2015). "Archaeal ... Proteoarchaeota are a proposed archaeal kingdom thought to be closely related to the Eukaryotes. The phylogenetic relationship ...
There is limited knowledge about the archaeal genome sequences. Therefore, there is also limited knowledge about the ... "Drosophila mitochondrial topoisomerase III alpha affects the aging process via maintenance of mitochondrial function and genome ...
Some DnaG-like (bacteria-like; InterPro: IPR020607) primases have been found in archaeal genomes. Eukaryote and archaeal ... PolpTN2 is an Archaeal primase found in the TN2 plasmid. A fusion of domains homologous to PriS and PriL, it exhibits both ... PriS, the archaeal primase small subunit, has a role in translesion synthesis (TLS) and can bypass common DNA lesions. Most ... Archaeal and eukaryote primases are heterodimeric proteins with one large regulatory and one small catalytic subunit. The RNA ...
... one archaeal genome may encode two different archaeosortase systems. Invariant residues shared by all archaeosortases and ... In the archaeal model species Haloferax volcanii, archaeosortase A belongs to a fairly large collection of identified membrane- ... A genome that encodes one archaeosortase may encode over fifty target proteins. The best characterized archaeosortase target is ... Giménez MI, Cerletti M, De Castro RE (2015). "Archaeal membrane-associated proteases: insights on Haloferax volcanii and other ...
2004). "Environmental Genome Shotgun Sequencing of the Sargasso Sea". Science. 304 (5667): 66-74. Bibcode:2004Sci...304...66V. ... Wu, Martin; A.J. Scott (2012). "Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2". Bioinformatics. 28 (7 ... Wu, Martin; J.A. Eisen (2008). "A simple, fast, and accurate method of phylogenomic inference". Genome Biol. 9 (10): R151. doi: ... AMPHORA2 uses 31 bacterial and 104 archaeal phylogenetic marker genes for inferring phylogenetic information from metagenomic ...
Not only eukaryotic viruses integrate into the genomes of their hosts; many bacterial and archaeal viruses also employ this ... All families of bacterial viruses with circular (single-stranded or double-stranded) DNA genomes or replicating their genomes ... A provirus does not directly make new DNA copies of itself while integrated into a host genome in this way. Instead, it is ... A provirus is a virus genome that is integrated into the DNA of a host cell. In the case of bacterial viruses (bacteriophages ...
of gene pair conservation across nine bacterial and archaeal genomes. The method is most effective in prokaryotes with operons ... The adjacency of these two genes was shown to be conserved across nine different bacterial and archaeal genomes. Classification ... The Joint Genome Institute provides an Integrated Microbial Genomes and Microbiomes database (JGI IMG) that has a phylogenetic ... For instance, two or more separate proteins in a genome may be identified as fused into one single protein in another genome. ...
... www.nature.com/ismej/journal/vaop/ncurrent/full/ismej20168a.htm KEGG GENOME: Candidatus Nitrososphaera Gargensis. KEGG GENOME: ... "Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota." Nature Reviews Microbiology6.3 (2008): 245 ... Nitrososphaera gargensis' genome is 2.83 Mb in size with a GC content of 48%, which is much larger than most other ammonia- ... 2014). "Genome Sequence of Candidatus Nitrososphaera evergladensis from Group I.1b Enriched from Everglades Soil Reveals Novel ...
"Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proceedings of the National ... "Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a ... "Genome Biol. Evol. 7 (1): 191-204. PMC 4316627. PMID 25527841. doi:10.1093/gbe/evu274. ... "Genome Biol. 3 (2): REVIEWS0003. PMC 139013. PMID 11864374. doi:10.1186/gb-2002-3-2-reviews0003. ...
The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. U.S. ... The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. U.S. ... Archaeal "Dark Matter" and the Origin of Eukaryotes. S. 474-481. Genome Biology and Evolution [online]. 12. únor 2014. Svazek 6 ... Integrative modeling of gene and genome evolution roots the archaeal tree of life. S. E4602-E4611. Proceedings of the National ...
Li, Sen; Yang, Jie (21 August 2014). "System analysis of synonymous codon usage biases in archaeal virus genomes". Journal of ...
"Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging". Nature Communications. 8 (1): 1436. doi: ... It does not integrate into the host genome. The genome contains 14 open reading frames, none of which share similarity with ... Virions are highly thermostable and remain infectious after incubation at 100 °C for 3 h The genome is a circular double- ... "Diversity of viruses of the hyperthermophilic archaeal genus Aeropyrum, and isolation of the Aeropyrum pernix bacilliform virus ...
Genome Research. 12:1159-1167. Gill, E., and F.S.L. Brinkman (2011). The proportional lack of archaeal pathogens: do phages ... The Bovine Genome Sequencing and Analysis Consortium, C.G. Elsik, R.L. Tellam, K.C. Worley (2009). The Genome Sequence of ... She was involved in the Pseudomonas Genome Project and is the coordinator of the Pseudomonas genome database, a database of ... Pseudomonas aeruginosa Genome Database and PseudoCAP: Facilitating community-based, continually updated, genome annotation. ...
DNA genomes or replicate their genomes through rolling circle replication (e.g., Caudovirales) have temperate members. Zygotic ... "Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere". Microbiol Mol Biol Rev. 75 (4): 610- ... Pro means ''before'', so, prophage means the stage of a virus in the form of genome inserted into host DNA before being ... A prophage is a bacteriophage (often shortened to "phage") genome inserted and integrated into the circular bacterial DNA ...
The smallest viral genomes - the ssDNA circoviruses, family Circoviridae - code for only two proteins and have a genome size of ... Archaeal viruses. Some viruses replicate within archaea: these are double-stranded DNA viruses with unusual and sometimes ... The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses and certain DNA viruses, the genome is ... Segmented genomes confer evolutionary advantages; different strains of a virus with a segmented genome can shuffle and combine ...
"Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics". Science. 350 (6259): 434-8. ...
Several Vulcanisaeta genomes have been sequenced, see List of sequenced archaeal genomes. The G + C content of its DNA, which ... Mavromatis, Konstantinos (2010). "Complete genome sequence of Vulcanisaeta distributa type strain (IC-017(T))". Standards in ... Vulcanisaeta grows in the absence of vitamin mixture or archaeal cell-extract solution in the medium. Strains of Vulcanisaeta ...
Hassani II, Robert C, Michelle C, Raoult D, Hacène H, Desnues C (October 2013). "Non-contiguous finished genome sequence and ... an archaeal ectosymbiont of the hypersaline ciliate Platynematum salinarum". Systematic and Applied Microbiology. 37 (4): 244- ... Ikram HI, Catherine R, Caroline M, Didier R, Hocine H, Christelle D (June 2014). "Non-contiguous finished genome sequence and ... Ugalde JA, Narasingarao P, Kuo S, Podell S, Allen EE (December 2013). "Draft Genome Sequence of "Candidatus Halobonum ...
She is the maintainer of a database of archaeal proteins and their relations. McKay, Kathryn (January 8, 2018), "Focus on NLM ... Interest in the system heightened after other researchers subsequently used it to perform genome editing. Makarova's ongoing ...
"Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proc Natl Acad Sci U S A. 109 ... The GC-content of the genome is 46.7%. The genome is predicted to have 57 open reading frames (ORFs) larger than 40 codons, ... However, some other archaeal viruses also have coil-shaped virions like ACV, which may indicate such morphology is an ancient ... The viral genome is positive-sense, single-stranded DNA ((+)ssDNA) and encodes for significantly more genes than other known ...
... discovery of the ARMAN group of archaea Browse any completed archaeal genome at UCSC Comparative Analysis of Archaeal Genomes ( ... The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it ... Comparative analysis of archaeal genomes has also identified several molecular conserved signature indels and signature ... October 2003). "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". ...
"Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes". Frontiers in Microbiology. 9. doi: ...
April 2002). "The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens". ... The complete genome of Methanopyrus kandleri was sequenced by researchers at Fidelity Systems. It was determined to be a GC- ... rich genome containing 1,694,969 nucleotides of which about 62.1% is Guanine or Cytosine.Overall, the genome of M. kandleri is ... considered 'minimalist' because so few genes have been transferred from other bacteria into its own genome. This could be due ...
Guo FB, Ou HY, Zhang CT (2003). "ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes". ... Zhang R, Zhang CT (2005). "Identification of replication origins in archaeal genomes based on the Z-curve method". Archaea. 1 ( ... The Z curve (or Z-curve) method is a bioinformatics algorithm for genome analysis. The Z-curve is a three-dimensional curve ... The Z-curve method has been used in many different areas of genome research, such as replication origin identification,, ab ...
June 2017). "Integrative modeling of gene and genome evolution roots the archaeal tree of life". Proceedings of the National ... "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proceedings of the ... "Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from ... Genomes Online Database Comolli LR, Baker BJ, Downing KH, Siegerist CE, Banfield JF (February 2009). "Three-dimensional ...
"Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proc Natl Acad Sci USA 109: ... "Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a ... Prangishvili D, Bamford DH, Forterre P, Iranzo J., Koonon EV, and Krupovic M (2017) "The enigmatic archaeal virosphere". Nature ... Peng, Xu; Garrett, Roger A.; She, QunXin (2012). "Archaeal viruses-novel, diverse and enigmatic". Science China Life Sciences. ...
"The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proc. Natl. Acad. Sci. ... The Arabidopsis Genome Initiative (2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana". Nature ... 2006). "The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)". Science 313 (5793): 1596-604. doi:10.1126/science. ... 2002). "A draft sequence of the rice genome (Oryza sativa L. ssp. indica)". Science 296 (5565): 79-92. doi:10.1126/science. ...
The genome of M. acetivorans is one of the largest archaeal genomes ever sequenced. Furthermore, one strain of M. acetivorans, ... 2002). "The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity". Genome Research. 12 (4): 532-42 ... Reductase and Ferredoxin from Methanosarcina acetivorans Are Required for the Synthesis of Fully Reduced Archaeal Membrane ...
... a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes. . In: ... Fusariviridae, auf: NCBI Genomes *↑ D. F. Quito-Avila, P. M. Brannen, W. O. Cline, P. F. Harmon, R. R. Martin: Genetic ... Marion Heller-Dohmen et al.: The nucleotide sequence and genome organization of Plasmopara halstedii virus, in: Virol J. 2011; ... Xin-Cheng Qin et al.: A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors, in: ...
List of sequenced eukaryotic genomes. *List of sequenced archaeal genomes. *RefSeq - the Reference Sequence Database ... Bulk submissions of Expressed Sequence Tag (EST), Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput ... Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group ...
"Genome Res. 19 (1): 92-105. doi:10.1101/gr.082701.108. PMC 2612969 . PMID 18955434.. CS1 maint: Multiple names: authors list ( ... RAD51 family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51.[5][6] The protein is highly conserved ... "RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange". Genes & Development. 12 (9): 1248-1253. ...
The tiny 490,885 base-pair genome of Nanoarchaeum equitans is one-tenth of this size and the smallest archaeal genome known; it ... On average, archaeal DNA sequences (whole genome) show higher levels of complexity than those of Bacteria.[33] ... Comparative analysis of archaeal genomes has also identified several molecular signatures in the form of conserved signature ... Koonin, E.V.; Mushegian, A.R.; Galperin, M.Y.; Walker, D.R. (1997). "Comparison of archaeal and bacterial genomes: computer ...
"Genome Research. 11 (5): 677-84. doi:10.1101/gr.gr-1640r. PMC 311086. PMID 11337467.. ... which is now known to be the sequence that interacts with the homologue of the archaeal TATA-binding protein (TBP). Also, even ... In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" ... Most research on the TATA box has been conducted on yeast, human, and Drosophila genomes, however, similar elements have been ...
H3K56Acx is required for genome stability.[88][89] H3K56 is acetylated by the p300/Rtt109 complex,[90][91][92] but is rapidly ... Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack ... Archaeal histones may well resemble the evolutionary precursors to eukaryotic histones.[12] Histone proteins are among the most ... This enables the compaction necessary to fit the large genomes of eukaryotes inside cell nuclei: the compacted molecule is ...
"Browse any completed archaeal genome at UCSC," apud archaea.ucsc.edu. *"Comparative Analysis of Archaeal Genomes," apud img.jgi ... "Integrative modeling of gene and genome evolution roots the archaeal tree of life". Proceedings of the National Academy of ... Lipps, G. (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends. Caister Academic Press. ISBN 978-1-904455- ... gov (United States Department of Energy, Integrated Microbial Genomes System) ...
1997). ""Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and ... "Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group ... Lipps, G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends (en inglés). Caister Academic Press. ISBN ... "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proc. Natl. Acad. Sci. U. ...
Analysis of the genome of one korarchaeote that was enriched from a mixed culture revealed a number of both Crenarchaeota- and ... 23, www.pnas.org/cgi/doi/10.1073/pnas.0801980105 Guy L, Ettema TJ (2011). "The archaeal 'TACK' superphylum and the origin of ... James G. Elkins et al., A korarchaeal genome reveals insights into the evolution of the Archaea, Harvard University, PNAS, June ... Barns, SM; Fundyga RE; Jeffries MW; Pace NR (1994). "Remarkable archaeal diversity detected in a Yellowstone National Park hot ...
2500 prokaryotic genomes showed that many of them miss one or more aaRS genes whereas many genomes have 1 or more paralogs.[11] ... AARS human gene details in the UCSC Genome Browser.. This article incorporates text from the public domain Pfam and InterPro: ... GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. ... AARS human gene location in the UCSC Genome Browser.. * ... Protein biosynthesis: translation (bacterial, archaeal, ...
Within the eukaryotic genome are regions of DNA known as silencers. These DNA sequences bind to repressors to partially or ... Archaeal transcription factor B. Elongation. *bacterial RNA polymerase: rpoB. *eukaryotic RNA polymerase: RNA polymerase II ...
"Distribution and diversity of ribosome binding sites in prokaryotic genomes". BMC Genomics. 16 (1). doi:10.1186/s12864-015- ... Protein biosynthesis: translation (bacterial, archaeal, eukaryotic). Proteins. Initiation factor. Bacterial. *PIF-1 ... Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes". ...
Bonisch, H.; Schmidt, C. L.; Schafer, G.; Ladenstein, R. (June 2002). "The structure of the soluble domain of an archaeal ... have an acidified cytoplasm which forces nearly all proteins in the genome to evolve acid stability.[7] For this reason, ...
"Genome Res. 14 (10B): 2121-7. doi:10.1101/gr.2596504. PMC 528928. PMID 15489334.. ...
Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. „Appl. Environ. ... Müller V. An exceptional variability in the motor of archaeal A1A0 ATPases: from multimeric to monomeric rotors comprising 6-13 ...
There are only 5 ABCG genes in the human genome, but there are 15 in the Drosophelia genome and 10 in yeast. The ABCG2 gene was ... ISBN 981-4280-06-2. Classification of ABC transporters in TCDB ABCdb Archaeal and Bacterial ABC Systems database, ABCdb ATP- ... The genome of the model plant Arabidopsis thaliana is capable of encoding 120 ABC proteins compared to 50-70 ABC proteins that ... There are 48 known ABC transporters present in humans, which are classified into seven families by the Human Genome ...
Margulis, Lynn, and Dorion Sagan (2002). Acquiring Genomes: A Theory of the Origins of Species, Perseus Books Group, ISBN 0-465 ... "Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life". Proceedings of the National ... Margulis, Lynn (2009). "Genome acquisition in horizontal gene transfer: symbiogenesis and macromolecular sequence analysis". In ... Gogarten, Maria Boekels; Gogarten, Johann Peter; Olendzenski, Lorraine C. Horizontal Gene Transfer:Genomes in Flux. 532. Humana ...
Guy, L; Ettema, TJ (১৯ ডিসেম্বর ২০১১)। "The archaeal 'TACK' superphylum and the origin of eukaryotes."। Trends Microbiol.। 19 ( ... Ciaramella M, Napoli A, Rossi M; Napoli; Rossi (ফেব্রুয়ারি ২০০৫)। "Another extreme genome: how to live at pH 0"। Trends ... Archaeal Richmond Mine acidophilic nanoorganisms]] (আরমান)[১৮] অন্যান্য ক্ষুদ্রতম জীব। [১৯] ... "A korarchaeal genome reveals insights into the evolution of the Archaea"। Proceedings of the National Academy of Sciences of ...
Typically, the genome is replicated by use of concatemers, in which overlapping segments of DNA are made, and then put together ... Bacteriophages occur in over 195 bacterial or archaeal genera. They arose repeatedly in different hosts and there are at least ... Viral capsid proteins come together to form a precursor prohead, into which the genome enters. Once this has occurred, the ... However, some tailed bacteriophage genomes can vary quite significantly in nucleotide sequence, even among the same genus. Due ...
... which is part of every bacterial and archaeal genome and is highly conserved, bacteria can be taxonomically classified by ... National Human Genome Research Institute *^ a b Stanley, J. (2002). Essentials of Immunology & Serology by Jacqueline Stanley. ... DNA sequencing technologies such as next-generation sequencing have made it possible to study amplicons in genome biology and ... and reinserted elsewhere in the genome, and to a fragment of extrachromasomal DNA known as a double minute, each of which can ...
List of sequenced archaeal genomes. *List of Archaea genera. *Species problem. *Evolutionary grade ... LPSN, list of accepted bacterial and archaeal names. *Cyanobacteria, a phylum of common bacteria but poorly classified at ... in archaeal terms, and organisms that live in cooler environments appeared only later.[50] Since the Archaea and Bacteria are ... of their genome. Being so diverse it should be given a higher taxonomic ranking. However, due to the medical conditions ...
The archaeal host transferred much of its functional genome to the virus during the evolution of cytoplasm, but retained the ... is the size of the genome in bits.[51]. Libertine bubble theoryEdit. The evolution of sex can alternatively be described as a ... For the nematode worm Caenorhabditis elegans, the mutation rate per effective genome per sexual generation is 0.036.[46] ... Genetic noise can occur as either physical damage to the genome (e.g. chemically altered bases of DNA or breaks in the ...
... s have some of the largest genomes among all organisms.[73] The largest plant genome (in terms of gene number) is that of ... Michael, Todd P.; Jackson, Scott (1 July 2013). "The First 50 Plant Genomes". The Plant Genome. 6 (2): 0. doi:10.3835/ ... Arabidopsis Genome Initiative (14 December 2000). "Analysis of the genome sequence of the flowering plant Arabidopsis thaliana ... "The Norway spruce genome sequence and conifer genome evolution". Nature. 497 (7451): 579-584. Bibcode:2013Natur.497..579N. doi: ...
Their genome is usually a circular bacterial chromosome - a single loop of DNA, although they can also harbor small pieces of ... Karner, M.B.; DeLong, E.F.; Karl, D.M. (2001). "Archaeal dominance in the mesopelagic zone of the Pacific Ocean". Nature. 409 ( ... They evolved from symbiotic bacteria and retain a remnant genome.[59] Like bacteria, plant cells have cell walls, and contain ... The nucleus is an organelle that houses the DNA that makes up a cell's genome. DNA (Deoxyribonucleic acid) itself is arranged ...
"Genome Biology and Evolution. 4 (1): 52-58. doi:10.1093/gbe/evr127. PMC 3268669. PMID 22117085.. ... The mitochondrial genome in the medusozoan cnidarians, unlike those in other animals, is linear with fragmented genes.[62] The ... "First Complete Mitochondrial Genome Sequence from a Box Jellyfish Reveals a Highly Fragmented Linear Architecture and Insights ...
Archaeal variationsEdit. Archaea have variants of the Entner-Doudoroff Pathway. These variants are called the ... diatom model species presents functional phosphogluconate dehydratase and dehoxyphosphogluconate aldolase genes in its genome [ ...
In the bacteria, oxidative phosphorylation in Escherichia coli is understood in most detail, while archaeal systems are at ... The genes that encode the individual proteins are contained in both the cell nucleus and the mitochondrial genome, as is the ... "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255". Appl. Environ. ...
Organisms vary in the number of tRNA genes in their genome. For example, the nematode worm C. elegans, a commonly used model ... or archaeal counterpart. This initial tRNA binding site is called the A/T site. In the A/T site, the A-site half resides in the ... In the human genome, which, according to January 2013 estimates, has about 20,848 protein coding genes [24] in total, there are ... 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860-921. doi:10.1038/35057062. PMID 11237011. ...
... totalling 150 Archaeal genomes. Genome project Human microbiome project Lists of sequenced genomes Bult CJ, White O, Olsen GJ, ... This list of sequenced archaeal genomes contains all the archaea known to have publicly available complete genome sequences ... Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM, Banfield JF (February 2007). "Genome dynamics in a natural archaeal ... October 2003). "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". ...
Comparative analysis of the M. kandleri genome and other sequenced archaeal and bacterial genomes led to three principal ... suggesting that there are fewer traces of horizontal gene exchange with bacteria in this genome than in other archaeal genomes ... All archaeal genomes sequenced so far encode a substantial number of predicted DNA-binding proteins of the helix-turn-helix and ... The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Alexei I. Slesarev, ...
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens.. Slesarev AI1, ... The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens ... The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens ... The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens ...
Preserving genome integrity over many generations is a basic requirement of biological success, and involves co-operation among ... Conversely, genome alterations, which represent the first step of evolutionary adaptation and speciation, reflect phenomena ... It also provides a route to improved genetic methods for archaea and technological applications based on archaeal proteins.This ... Analyzing the processes which shape the genomes of archaea therefore promises to yield new insights into early cellular ...
Read more about the manipulation of the SSV1 genome and how it may lead to discovery of a minimal SSV genome for future studies ... Researchers have found its genome is surprisingly tolerant of mutation, including loss of one of its structural capsid genes, ... SSV1 is an archaeal virus found in the hot, acidic waters where its Sulfolobus bacterial hosts reside. ... The SSV1 genome tolerates the DNA insertions necessary to generate shuttle vectors, allowing manipulation of its genome via ...
Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost. United States: N. p., 2019. Web. doi: ... Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost. United States. doi:10.1128/mra.00516-19 ... Wed . "Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost". United States. doi:10.1128/mra. ... title = {Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost},. author = {Xue, Yaxin and ...
... genome signatures). The variations in bacterial and archaeal genome DNA sequences are not only explained by neutral mutations. ... However, some bacteria, for example Actinobacteria, have maintained a high GC content genome. In addition, genomes with similar ... have short and low GC content genomes. In bacterial genomes, mutations from GC to adenosine-thymine (AT) are more common than ... Genome size and GC content are weakly correlated in bacteria and archaea. The obligate host-associated bacteria (with the ...
Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life.. Prangishvili D1, Garrett RA, ... Here we describe a re-analysis of the proteins encoded by archaeal viruses, with an emphasis on comparative genomics of the ... In accord with this distinction, the sequenced genomes of euryarchaeal viruses encode many proteins homologous to bacteriophage ... In contrast, initial analysis of the crenarchaeal viral genomes revealed no relationships with bacteriophages and, generally, ...
However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature ... Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. ... Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging Denis Ptchelkine 1, 2 Ashley Gillum 3 ... However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature ...
In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses ... Integrative modeling of gene and genome evolution roots the archaeal tree of life. ... A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing ... Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based ...
Although bacterial and archaeal genomes lacking ATP synthase genes have been recovered from a contaminated aquifer (7, 24), the ... Two reconstructed archaeal genomes reveal that methane metabolism is more diverse than anticipated. [Also see Perspective by ... Two reconstructed archaeal genomes reveal that methane metabolism is more diverse than anticipated. [Also see Perspective by ... 1 Phylogenetic trees showing the placement of the BA1, BA2, and E09 genomes in the archaeal phylum Bathyarchaeota.. (A) Maximum ...
From Genome to Watershed Scales. Microbial Functions at Soil-Aquatic Interfaces. DNA Methylation Role in Basal Fungi. Fungal ... DAS Tool for Genome Reconstruction from Metagenomes. Through the JGIs Emerging Technologies Opportunity Program (ETOP), ... Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization ... Why sequence ammonia-oxidizing archaeal enrichment culture?. Ammonia-oxidizing bacteria are key players in the nitrogen cycle ...
... FEMS Microbiol Lett. ... To identify and reconstruct functional ABC transporters encoded by archaeal and bacterial genomes, we have developed a ... However, in order to face the rapid increase in the number of published genomes, we also include analyses of genomes issuing ...
... but also facilitate comparative studies of prokaryotic genomes. This paper describes a new prokaryotic genefinding algorithm ... of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. ... Furthermore, MED 2.0 adapts to a broad range of archaeal genome as well as to bacterial genomes. For archaeal genomes with more ... The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific ...
The genome of the archaeal virus SIRV1 has features in common with genomes of eukaryal viruses. Virology 281:6-9. ... Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus ... Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. Virus Res. 117:52-67. ... Genome Replication and Regulation of Viral Gene Expression. A Dimeric Rep Protein Initiates Replication of a Linear Archaeal ...
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Published in:. Nat Biotechnol ( ... 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life ... This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is ... Most of the genomes were uncovered using a "mini-metagenomics" approach that reduced the complexity of the soil microbial ...
... and ArsR families were universally and abundantly identified in all the archaeal genomes. We found that archaeal TFs are ... In this work, 3,918 TFs were identified and exhaustively analyzed in 52 archaeal genomes. TFs represented less than 5% of the ... Identification and Genomic Analysis of Transcription Factors in Archaeal Genomes Exemplifies Their Functional Architecture and ... Identification and Genomic Analysis of Transcription Factors in Archaeal Genomes Exemplifies Their Functional Architecture and ...
... we are concerned with here are mainly used to examine similarities between archaeal and bacterial DNA from different genomes. ... The dinucleotide ZOM method produced high correlation values when used to compare real genomes to an artificially constructed ... random genome with similar %GC, and should therefore be used with care. The tetranucleotide ZOM measure was a good measure to ... The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed ...
Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures ... Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures. Journal ... gene containing a 12-bp archaeal intron, and a 1,008-bp repeat-rich region near the center of the genome. ... The double-stranded DNA genome contains 31,787 bp and carries eight open reading frames homologous to those of other ...
The consensus genome sequence of a new member of the fa ... Genome sequence of a novel archaeal fusellovirus assembled from ... Genome sequence of a novel archaeal fusellovirus assembled from the metagenome of a mexican hot spring.. Authors * Servín- ... Genome Announcements 2169-8287 Publisher. American Society for Microbiology Publication Date. Jan 01, 2013 Volume. 1 Issue. 2 ... The complete circular genome was recovered from a metagenomic study of a Mexican hot spring. SMF1 exhibits an exceptional ...
Genome annotation databases. Ensembl bacterial and archaeal genome annotation project. More...EnsemblBacteriai. AAY80327; ... Genome annotation databases. Ensembl bacterial and archaeal genome annotation project. More...EnsemblBacteriai. AAY80327; ... They may also represent different stages in a genome project and include components such as contigs, scaffolds or Whole Genome ... Conserved Archaeal proteinImported. ,p>Information which has been imported from another database using automatic procedures.,/p ...
Genome annotation databases. Ensembl bacterial and archaeal genome annotation project. More...EnsemblBacteriai. CAF30231; ... Conserved hypothetical archaeal proteinImported. ,p>Information which has been imported from another database using automatic ... tr,Q6LZF4,Q6LZF4_METMP Conserved hypothetical archaeal protein OS=Methanococcus maripaludis (strain S2 / LL) OX=267377 GN= ... of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.,p>,a href=/help/ ...
Cell cycle transcription factor e2f-dp family domain assignments in all archaeal genomes. Domain assignment details for each ... all archaeal genomes. No domain assignments for these genomes.. Add assignments from groups of genomes. View all assignments ... Home > Genomes > Cell cycle transcription factor e2f-dp domains in all archaeal genomes ... Jump to [ Top of page · Assignment details · Add assignments from groups of genomes · Add assignments from individual genomes ] ...
... complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and partially sequenced mammalian genomes (human, ... The test was performed on clusters of orthologous protein sequences from complete bacterial genomes (Chlamydia trachomatis, C. ... From: Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and ...
Lang, J. M., Darling, A. E., & Eisen, J. A. (2013). Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: ... Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices. PLoS One. 2013 Apr 25;8(4). ... Lang, JM, Darling, AE & Eisen, JA 2013, Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and ... Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes : Supertrees and Supermatrices. In: PLoS One. 2013 ; Vol. 8, ...
Curiously, the genes encoding dUTPase and Dfp are located next to each other in the E. coli genome, although there has been no ... P45 Enhances Other Archaeal DNA Polymerases.. Because dU-DNA inhibition appears to be a property of all archaeal family B DNA ... Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Holly H. Hogrefe, ... Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation ...
BPTI-like superfamily domain assignments in all bacterial and archaeal genomes. Domain assignment details for each protein ... all bacterial and archaeal genomes. Assignment details. (show help) Click on a sequence ID to see the domain architecture and ... Jump to [ Top of page · Assignment details · Add assignments from groups of genomes · Add assignments from individual genomes ] ... Add assignments from groups of genomes. View all assignments containing a BPTI-like domain in each group of genomes. ...
... this is potentially due to structural differences between bacterial and archaeal signals, and does not discount a quorum ... this is potentially due to structural differences between bacterial and archaeal signals, and does not discount a quorum ... Published research has shown that archaeal genomes contain toxin-antitoxin loci (Gerdes et al., 2005; Pandey and Gerdes, 2005 ... Archaeal Persisters: Persister Cell Formation as a Stress Response in Haloferax volcanii. Julianne Megaw and Brendan F. Gilmore ...
Genome, Archaeal* * Genome, Bacterial * In Situ Hybridization, Fluorescence * Recombination, Genetic* * Thermoplasmales / ... Genetic exchange across a species boundary in the archaeal genus ferroplasma Genetics. 2007 Sep;177(1):407-16. doi: 10.1534/ ... comprehensive investigation of variation in individuals from two coexisting natural archaeal populations. Individuals are ...
Bacterial Genome Replication and Expression. 14. Regulation of Bacterial Cellular Processes 15. Eukaryotic and Archaeal Genome ... 4. Archaeal Cell Structure 5. Eukaryotic Cell Structure 6. Viruses and Other Acellular Infectious Agents. Part Two Microbial ...
  • This list of sequenced archaeal genomes contains all the archaea known to have publicly available complete genome sequences that have been assembled, annotated and deposited in public databases. (wikipedia.org)
  • Currently in this list there are 39 genomes belonging to Crenarchaeota species, 105 belonging to the Euryarchaeota, 1 genome belonging to Korarchaeota and to the Nanoarchaeota, 3 belonging to the Thaumarchaeota and 1 genome belonging to an unclassified Archaea, totalling 150 Archaeal genomes. (wikipedia.org)
  • The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C". Archaea. (wikipedia.org)
  • The number of COGs that include a given archaeal species and two or more bacteria, but no other archaea, is shown in brackets. (nih.gov)
  • Genome trees of archaea. (nih.gov)
  • Analyzing the processes which shape the genomes of archaea therefore promises to yield new insights into early cellular evolution and a clearer understanding of how modern archaea diversify. (frontiersin.org)
  • It also provides a route to improved genetic methods for archaea and technological applications based on archaeal proteins. (frontiersin.org)
  • This Research Topic focuses on molecular processes in archaea that determine or influence the content or integrity of their genomes. (frontiersin.org)
  • Genome size and GC content are weakly correlated in bacteria and archaea. (frontiersin.org)
  • The two reconstructed genomes are members of the recently described Bathyarchaeota and not the phylum to which all previously known methane-metabolizing archaea belonged. (sciencemag.org)
  • Methanogenic archaea are estimated to produce one billion tons of methane per year, with an equal amount estimated to be oxidized by archaeal methanotrophs ( 1 ). (sciencemag.org)
  • Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. (biomedcentral.com)
  • We found that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could supply the probable deficit of TFs in archaea, by possibly forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery. (iupui.edu)
  • Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). (beds.ac.uk)
  • Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. (beds.ac.uk)
  • Our lab recently determined the structure of histone-based archaeal chromatin that showed striking similarities to eukaryotic nucleosomes, but crystal lattice packing and biochemical experiments suggested that archaea may form repeated stacking interactions, potentially forming long "slinky-like" extended chromatin arrangements. (aps.org)
  • Hildenbrand C, Stock T, Lange C, Rother M, Soppa J. Genome copy numbers and gene conversion in methanogenic archaea. (harvard.edu)
  • including some of the researchers from the earlier work-use VirSorter to predict viral DNA from publicly available bacteria and archaea genome data. (elifesciences.org)
  • Interestingly, while numbers of Bacteria were consistently higher than those of Archaea , the ratio of archaeal 16S rRNA genes to the total of both Bacteria and Archaea 16S rRNA genes increased with soil depth from 12 to 38% ( 39 ). (asm.org)
  • The use of environmental genomics to understand uncultured archaeal diversity has recently shed light on many new potential lineages of Archaea and continues to expand and revise our understanding of Archaea in natural environments. (els.net)
  • In diverse bacteria, as well as archaea and eukaryotes, a drastic reduction in overall genome size is associated with obligate dependence on a host (e.g., see references 1 , 10 , 17 , and 34 ). (asm.org)
  • single genome within the Archaea domain. (kenyon.edu)
  • In archaea, no homologs of FliM have been identified, and the interaction of CheY-P with different partners in bacteria and archaea has been considered to be a factor that separates the archaeal system of motility from the bacterial system of motility. (iucr.org)
  • The Dodonova group aims to understand the mechanisms and evolutionary principles of genome packaging and chromatin 3D organisation by studying archaea using a combination of biochemistry, biophysics, and high-resolution structural biology in near-native contexts. (embl.org)
  • The genomes of all eukaryotes and most archaea are organised into chromatin, a complex of DNA and histone proteins. (embl.org)
  • Deciphering the principles of chromatin architecture in archaea will provide a broader understanding of how chromatin has evolved to package genomes and to enable gene expression regulation across the eukaryotic and archaeal domains. (embl.org)
  • Explore the mechanisms of genome packaging regulation in several groups of archaea. (embl.org)
  • Exterkate: 'Other archaea have similar genes, which are probably also suited to producing different cardiolipins, indicating that the variety in archaeal cardiolipins could be synthesized by the same enzyme. (sciencecodex.com)
  • Here, 56 prokaryotic metagenome-assembled genome (MAG) sequences from 13 phyla are reported. (osti.gov)
  • article{osti_1572795, title = {Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost}, author = {Xue, Yaxin and Jonassen, Inge and Øvreås, Lise and Taş, Neslihan}, abstractNote = {ABSTRACT Permafrost contains one of the least known soil microbiomes, where microbial populations reside in an ice-locked environment. (osti.gov)
  • The variations in bacterial and archaeal genome DNA sequences are not only explained by neutral mutations. (frontiersin.org)
  • Therefore, virus resistance systems have resulted in changes in bacterial and archaeal genome DNA sequences during evolution. (frontiersin.org)
  • I welcome investigators to contribute any types of the tier 1 articles focusing on the evolution and function of bacterial (or archaeal) genome sequences to this Research Topic. (frontiersin.org)
  • For microbial organisms, genome sequences are now commonly used as a basis for determining phylogenetic relationships. (biomedcentral.com)
  • Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure. (cam.ac.uk)
  • The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. (elsevier.com)
  • Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes (ICNP) while taking into account proposals to formally recognise the rank of phylum and to use genome sequences as type material. (rxivist.org)
  • Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. (beds.ac.uk)
  • Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. (biomedsearch.com)
  • Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. (biomedsearch.com)
  • Earlier in 2015, researchers developed a new computational tool called VirSorter that can predict virus genome sequences within the DNA extracted from microbes. (elifesciences.org)
  • VirSorter identifies viral genome sequences based on the presence of 'hallmark' genes that encode for components found in many virus particles, together with a reference database of genomes from many viruses. (elifesciences.org)
  • These data increase the number of viral genome sequences that are publically available by a factor of ten and identify the first viruses associated with 13 new types of bacteria, which include species that are abundant in particular environments. (elifesciences.org)
  • In particular, the Crenarchaeota 16S rRNA sequences are largely unique to each horizon, sharing a distribution and diversity similar to those of the putative ( amoA -based) ammonia-oxidizing archaeal community. (asm.org)
  • Similarly, declines in archaeal 16S rRNA genes ( 39 ) and pronounced archaeal community shifts, including a decrease in the proportion of euryarchaeal to crenarchaeal ribosomal DNA sequences, have been observed along depth gradients within forest soils ( 61 ). (asm.org)
  • Despite this massive gene loss, the three completed genome sequences for B. aphidicola of different aphid species show that each retains the enzyme-encoding genes for the biosynthesis of all or most essential amino acids. (asm.org)
  • the sequenced genome of ''M. stadtmanae'''s is found to also lack "37 protein-coding sequences present in all other methanogens, which are involved in synthesis of a compound required for catalyzing the first step of methanogenesis from CO2 and H2. (kenyon.edu)
  • TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. (umd.edu)
  • We have characterized new Artemis/Artemis-like sequences from the genomes of fungi and non-mammalian metazoan species using an in-depth phylogenetic analysis coupled to hydrophobic cluster analysis and three-dimensional modeling of selected sequences. (iscb.org)
  • Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. (biomedcentral.com)
  • While this is a tremendous benefit for biology, this deluge of genome sequences presents new challenges for the management, distribution and analysis of data. (biomedcentral.com)
  • Genome sequences form the basis for our significantly improved understanding of the diversity of proteins. (biomedcentral.com)
  • 1992. Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the Archaeal domain. (tolweb.org)
  • However, genome comparisons indicate that, in both trees constructed using concatenated alignments of ribosomal proteins and trees based on gene content, M. kandleri consistently groups with other archaeal methanogens. (pnas.org)
  • The gene repertoires of M. kandleri and other archaeal methanogens. (nih.gov)
  • JVirology: Extreme Mutation Tolerance: Nearly Half of the Archaeal Fusellovirus Sulfolobus Spindle-Shaped Virus 1 Genes are Not Required for Virus Function, Including the Minor Capsid Protein Gene vp3 . (asm.org)
  • By comparing these gene lists, the researchers determined the core genome to be less tolerant of mutagenesis than the overall genome. (asm.org)
  • Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. (wur.nl)
  • This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. (wur.nl)
  • In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer. (wur.nl)
  • The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. (biomedcentral.com)
  • In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation. (biomedcentral.com)
  • Evolution of a Fungal Gene Expression Regulator The abundance of fungal genomes underscores the need for a more comprehensive exploration of genomic DNA modifications (epigenome). (doe.gov)
  • The double-stranded DNA genome contains 31,787 bp and carries eight open reading frames homologous to those of other lipothrixviruses, a single tRNA(Lys) gene containing a 12-bp archaeal intron, and a 1,008-bp repeat-rich region near the center of the genome. (uni-regensburg.de)
  • The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. (beds.ac.uk)
  • The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. (beds.ac.uk)
  • We indicate that the placement of N. equitans in archaeal phylogenies on the basis of ribosomal protein concatenation may be strongly biased by the coupled effect of its above-average evolutionary rate and lateral gene transfers. (biomedcentral.com)
  • Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. (springer.com)
  • Results of 16S and 18S ribosomal RNA (rRNA) gene-targeted pyrosequencing using primers sets specific to each domain have revealed its bacterial, archaeal, and fungal diversities. (springer.com)
  • All sequenced archaebacterial genomes exhibit only one gene homologous to the NAC subunits. (rcsb.org)
  • These mutants contained a transposable element in the lacS gene with features typical of bacterial and archaeal ISs, including terminal inverted repeats, a putative transposase gene, and short direct flanking repeats. (asm.org)
  • Reconstructions of the gene set of the shared ancestor of the γ- Proteobacteria provide strong evidence that B. aphidicola genomes are derived from larger genomes through loss of most genes ( 12 , 19 ). (asm.org)
  • Contemporary genomes are, and extinct genomes were, complex mixtures of genetic mergers [ 12 , 13 ], with the horizontal gene flows being as normal as vertical gene flows. (royalsocietypublishing.org)
  • Genomes in flux: the evolution of archaeal and proteobacterial gene content. (semanticscholar.org)
  • It presented the smallest genome size of its genus and a lower number of genes because of the loss of many gene families compared with the other genomes. (deepdyve.com)
  • 1998. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. (tolweb.org)
  • GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. (semanticscholar.org)
  • By searching the genomes of archaeal species, Exterkate found several gene candidates for cardiolipin synthase. (sciencecodex.com)
  • Our results show that although the DNA-binding domains of archaeal TFs are similar to bacteria, there is an underrepresentation of ligand-binding domains in smaller TFs, which suggests that protein-protein interactions may act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs' functionality. (iupui.edu)
  • We also show that the Hi-C signal can secondarily be used to create scaffolded genome assemblies of individual eukaryotic species present within the microbial community, with higher levels of contiguity than some of the species' published reference genomes. (g3journal.org)
  • Eukaryotic organisms package genomes that are significantly larger and more complex than genomes that are typically found in prokaryotes. (aps.org)
  • We reconstructed the evolution of stop codons in 40 groups of closely related prokaryotic and eukaryotic genomes. (nature.com)
  • To these ends, we calculated the frequencies of stop codon switches in sets of closely related genomes including 36 bacterial, one archaeal, and 3 eukaryotic ones, with varying GC content, and identified stop codon swaps that appear to be affected by purifying selection, whereas others are neutral, or possibly, could be subject to positive selection. (nature.com)
  • Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. (mdpi.com)
  • Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. (ebi.ac.uk)
  • During evolution, eukaryotic cells have developed a complex network of proteins that, by sensing all types of DNA-damage and inducing the appropriate response, maintain the genome s integrity. (iscb.org)
  • The guanine-cytosine (GC) content of bacterial genomes is ranges between 13.5% (Candidatus Zinderia insecticola) and 74.9% (Anaeromyxobacter dehalogenans). (frontiersin.org)
  • In bacterial genomes, mutations from GC to adenosine-thymine (AT) are more common than mutations from AT to GC. (frontiersin.org)
  • To identify and reconstruct functional ABC transporters encoded by archaeal and bacterial genomes, we have developed a bioinformatic strategy. (nih.gov)
  • Waiting to Respire UC Berkeley and JGI researchers joined forces and data sets to describe bacterial genomes for related ("sibling") lineages that diverged from the bacterial tree before Cyanobacteria and its contemporaries. (doe.gov)
  • Reduced bacterial genomes are particularly lacking in genes regulating transcription. (asm.org)
  • The genome comparison reported here reveals clustering of M. kandleri with other methanogens in phylogenetic trees based on concatenated alignments of ribosomal proteins, which is mimicked by congruence of the sets of predicted genes, suggesting monophyly of this group. (pnas.org)
  • In accord with this distinction, the sequenced genomes of euryarchaeal viruses encode many proteins homologous to bacteriophage capsid proteins. (nih.gov)
  • In contrast, initial analysis of the crenarchaeal viral genomes revealed no relationships with bacteriophages and, generally, very few proteins with detectable homologs. (nih.gov)
  • Here we describe a re-analysis of the proteins encoded by archaeal viruses, with an emphasis on comparative genomics of the unique viruses of Crenarchaeota. (nih.gov)
  • Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. (asm.org)
  • In RCR, Rep proteins also catalyze closure or ligation of the newly synthesized genomes once replication is complete. (asm.org)
  • New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. (beds.ac.uk)
  • We tested the placement of N. equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes. (biomedcentral.com)
  • For example, the E. coli genome encodes 233 experimentally verified regulatory proteins, including those targeting individual pathways and those acting as global regulatory proteins ( 27 ), but B. aphidicola contains only about five such genes, as inferred from homology. (asm.org)
  • The Che proteins, encoded by genes that cluster in genomes, constitute the chemotaxis signal transduction system. (iucr.org)
  • Conversely, genome alterations, which represent the first step of evolutionary adaptation and speciation, reflect phenomena ranging from spontaneous chemical alteration to sophisticated genetic transactions. (frontiersin.org)
  • Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life. (nih.gov)
  • Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. (elsevier.com)
  • Here we propose a standardized archaeal taxonomy, as part of the Genome Taxonomy Database (GTDB), derived from a 122 concatenated protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. (rxivist.org)
  • An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. (beds.ac.uk)
  • The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. (beds.ac.uk)
  • Such a classification is indispensable both for the functional annotation of sequenced genomes and for any genome-wide evolutionary reconstruction. (beds.ac.uk)
  • All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. (mdpi.com)
  • One of the best-studied cases of genome reduction is that of the intracellular bacterial symbiont Buchnera aphidicola , which shows a long evolutionary history of strict maternal transmission in its aphid hosts (Insecta: Homoptera: Aphidoidea) ( 18 ). (asm.org)
  • Two previously overlooked archaeal strains fill an evolutionary gap for microbes. (the-scientist.com)
  • The simple comparison of nucleotide content (AT/GC content) between species is probably the most used and one of the easiest methods for whole genome comparisons. (biomedcentral.com)
  • The extreme environments favored by many archaeal species and limited knowledge about their biochemistry and biology exacerbate this problem. (asm.org)
  • Cultivable archaeal species are assigned to two phyla - the Crenarchaeota and the Euryarchaeota - by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. (biomedcentral.com)
  • In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme thermophile Pyrococcus furiosus and the extreme halophile Haloferax volcanii . (springer.com)
  • Here, we demonstrate how this signal can be exploited to reconstruct the individual genomes of microbial species present within a mixed sample. (g3journal.org)
  • We apply this approach to two synthetic metagenome samples, successfully clustering the genome content of fungal, bacterial, and archaeal species with more than 99% agreement with published reference genomes. (g3journal.org)
  • Related to the challenge of determining which contigs belong to the same species are the problems of how to further define and assemble the one or multiple chromosomes that comprise each species' genome, and how to define and assign plasmid content to one or multiple species. (g3journal.org)
  • Investigate native 3D organisation of chromatin in model archaeal species by cryo-ET. (embl.org)
  • To survive in extremely salty environments, this archaeon-as with other halophilic Archaeal species-utilizes compatible solutes (in particular potassium chloride) to reduce osmotic stress. (wikipedia.org)
  • The Crenarchaeota/Euryarchaeota divide indicated by SSU rRNA phylogenies is strongly supported by comparative genomics, as a number of genes present in euryarchaeal genomes are missing altogether in crenarchaeal ones and vice versa. (biomedcentral.com)
  • Two features in particular stand out: the turrets, which are proposed to function in host recognition and DNA translocation, and two electron-dense layers sandwiched between the protein capsid and the packaged genome that may be composed of lipids ( 30 ) (Fig. 1 ). (asm.org)
  • Members of this protein family are the archaeal form ofribosomal protein uL6 (previously L9 in yeast and human). (jcvi.org)
  • Gopalan, V. Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P. Biomolecules 2016 , 6 , 22. (mdpi.com)
  • Samanta MP, Lai SM, Daniels CJ, Gopalan V. Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P. Biomolecules . (mdpi.com)
  • Genomes of B. aphidicola are only 500 to 640 kb in length and contain 450 to 580 protein-coding genes, essentially all of which have orthologs in related bacteria, including Escherichia coli ( 12 , 28 - 30 , 33 ). (asm.org)
  • The Genome Properties database, available at http://www.jcvi.org/genome-properties , specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. (umd.edu)
  • The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. (biomedcentral.com)
  • While these databases have been and remain useful resources for biological sequence analysis, they are generally not designed to be able to rapidly discover and accommodate new protein families that may be revealed through the sequencing of new genomes. (biomedcentral.com)
  • A new report from the Journal of Virology refutes that idea and demonstrates that an archaeal virus, Sulfolobus spindle-shaped virus 1 (SSV1), can withstand mutations in 17 of its 35 genes while remaining replication competent. (asm.org)
  • Characterizing the six unannotated core ORFs is a potential starting place to understand the replication cycle of this archaeal parasite. (asm.org)
  • Replication of the poxvirus genome, which occurs in cytoplasmic DNA replication factories ( 29 ), results in the generation of head-to-head concatemers that are resolved by a Holliday junction-resolving enzyme ( 7 , 12 ). (asm.org)
  • The Rudiviridae also generate head-to-head intermediates, ruling out a rolling-circle mechanism of replication ( 24 ), and encode a resolving enzyme that is assumed to be required for the deconcatamerization of the replicated rudiviral genome ( 2 ). (asm.org)
  • In most bacteria, the distribution of guanine compared to cytosine on the same strand (GC-skew) varies along the chromosome [ 8 , 9 ], with G's generally biased towards the replication leading strand for nearly all genomes studied so far. (biomedcentral.com)
  • Worning and coworkers [ 8 ] found that scoring strand bias frequencies of progressively larger oligonucleotides, from dinucleotides up to heptanucleotides, and their reverse complements, the chromosomal location of the origin and terminus of DNA replication could be predicted for nearly all sequenced prokaryotic genomes. (biomedcentral.com)
  • MCM complexes are recruited to replication origins for genome duplication. (rcsb.org)
  • However, limited information on the diversity and replication of archaeal viruses, in general, has hampered further analysis. (asm.org)
  • Chromatin allows for efficient packaging of the genome and adds multiple layers of regulation of DNA repair, replication, and transcription. (embl.org)
  • Scientists expand the microbial tree of life by publishing more than 1,000 novel reference genomes. (the-scientist.com)
  • We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). (sciencemag.org)
  • All previously described archaeal methane-metabolizing microorganisms belong to the phylum Euryarchaeota ( 2 ) and share a core set of bidirectional enzymes responsible for their respective metabolisms ( 3 ). (sciencemag.org)
  • This restricted phylogenetic distribution has led to the hypothesis that archaeal methane metabolism originated within the Euryarchaeota ( 4 ), although an origin outside this phylum has also been proposed ( 5 ). (sciencemag.org)
  • In total, 16 archaeal phyla are described, including reclassification of three major monophyletic units from the Euryarchaeota and one phylum resulting from uniting the TACK superphylum into a single phylum. (rxivist.org)
  • Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? (biomedcentral.com)
  • The recently described hyperthermophile Nanoarchaeum equitans , harboring the smallest cellular genome ever sequenced (480 kb), has been suggested as the representative of a new phylum - the Nanoarchaeota - that would have diverged before the Crenarchaeota/Euryarchaeota split. (biomedcentral.com)
  • We suggest that N. equitans may more probably be the representative of a fast-evolving euryarchaeal lineage (possibly related to Thermococcales) than the representative of a novel and early diverging archaeal phylum. (biomedcentral.com)
  • Genomes of the uncultivated members of the proposed 'Bathyarchaeota' phylum suggest that these organisms may be key members in global carbon cycling and have been implicated in acetogenesis. (els.net)
  • Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. (elsevier.com)
  • In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. (elifesciences.org)
  • SSV1 is a fusellovirus with a 15.5-kilobase, double-stranded DNA genome containing 35 open reading frames (ORFs). (asm.org)
  • The virion contains a discontinuous, circular, double-stranded DNA genome of 16 992 bp, in which both nicks and single-stranded regions are present preceded by a 'GCCCA' motif. (ovid.com)
  • I hypothesize that origin of plasmids and viruses is a part of genome DNA (See image). (frontiersin.org)
  • Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. (archives-ouvertes.fr)
  • The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. (asm.org)
  • Archaeal viruses display tremendous diversity of both morphology and genome content. (asm.org)
  • The genome arrangement, including the presence of inverted terminal repeats (ITRs), is reminiscent of those of the large cytoplasmic DNA viruses, such as the Poxviridae ( 3 , 10 ). (asm.org)
  • Proviral regions have been identified in the genomes of many haloarchaea, but only a few archaeal halophilic temperate viruses have been studied. (ovid.com)
  • Many viruses integrate their genome into the DNA of their host cell, and there are computational tools available that exploit this ability to identify viruses and link them to their host. (elifesciences.org)
  • However, other viruses can live and multiply inside cells without integrating their genome into the host's DNA. (elifesciences.org)
  • These new viral genomes will serve as a useful resource for researchers as they explore the communities of viruses and microbes in natural environments, the human body and in industrial processes. (elifesciences.org)
  • many bacterial and archaeal viruses also employ this strategy of propagation. (wikipedia.org)
  • All families of bacterial viruses with circular (single-stranded or double-stranded) DNA genomes or replicating their genomes through a circular intermediate (e.g., tailed dsDNA viruses) have temperate members. (wikipedia.org)
  • Seven viral families from the Crenarchaeota have been described, all with linear or circular double-stranded DNA (dsDNA) genomes but with few genes in common ( 28 ). (asm.org)
  • The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. (beds.ac.uk)
  • Perhaps the most distinctive feature of M. kandleri is its apparent position in the archaeal phylogeny. (pnas.org)
  • To better understand the function of other SSV1 genes, 78 mutant genomes were constructed and tested for their ability to infect Sulfolobus cells. (asm.org)
  • This could help better define the minimal SSV1 genome, which would improve the molecular tools scientists have to study both the bacteriophage itself and the Sulfolobus bacteria that they infect. (asm.org)
  • Sulfolobus turreted icosahedral virus (STIV), isolated from a hot spring in Yellowstone National Park, was the first icosahedral virus with an archaeal host to be described. (asm.org)
  • The virus was subsequently shown to infect virus-free isolates of Sulfolobus solfataricus strain P2, for which the complete genome has been sequenced. (asm.org)
  • Genome Biology. (wikipedia.org)
  • Genomes are central to the biology of unicellular organisms, embodying both the history and the functional potential of each microbial lineage. (frontiersin.org)
  • New Software Tools Streamline DNA Sequence Design-and-Build Process Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. (doe.gov)
  • A provirus is a virus genome that is integrated into the DNA of a host cell. (wikipedia.org)
  • DAS Tool for Genome Reconstruction from Metagenomes Through the JGI's Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. (doe.gov)
  • JGI-EMSL FICUS Call Ongoing Letters of Intent (LOI) are due March 20, 2019, for collaborative research applications with the Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL). (doe.gov)
  • This suggests that members of these two archaeal subdomains may employ critically different molecular strategies for key cellular processes. (biomedcentral.com)
  • Understand principles of archaeal chromatin architecture at the molecular level by using cryo-EM and functional assays on reconstituted chromatin. (embl.org)
  • Among 25 putative SNJ2 open reading frames (ORFs), five of them form a cluster of conserved ORFs homologous to archaeal pleolipoviruses isolated from hypersaline environments. (ovid.com)
  • The viral genome contains a cluster of five ORFs homologous to archaeal pleolipoviruses isolated from hypersaline environments. (ovid.com)
  • Mechanisms of DNA Recombination and Genome Rearrangements: Methods to Study Homologous Recombination, Volume 600 , the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. (elsevier.com)
  • The genome encodes DNA repair enzymes homologous to those in both bacteria and eukaryotes. (wikipedia.org)
  • A diagram showing the evolution/genealogy of archaeal models since the reconstruction of M. jannaschii in 2004. (hindawi.com)
  • Such a dramatic split is intriguing as it may be more profound than that separating the different bacterial phyla and leaves open different scenarios for the origin of these important differences during early archaeal evolution. (biomedcentral.com)
  • In PNAS this week: precision medicine strategy to screen for disease risk, genome evolution in Haemophilus influenzae , and more. (genomeweb.com)
  • As a consequence, the divergence between pairs of genomes in the population steadily increases in the course of their evolution. (genetics.org)
  • These findings indicate that archaeal methanogens are monophyletic. (pnas.org)
  • Several analyses, based on phylogenetic trees for 16S rRNA and the presence/absence of an 11-aa insertion in EF-1α, placed M. kandleri close to the root of the Euryarchaeota and did not suggest any specific affinity with other archaeal methanogens ( 13 - 15 ). (pnas.org)
  • In contrast, analysis of the methyl coenzyme M reductase operon of M. kandleri identified a group of genes unique to archaeal methanogens ( 15 ). (pnas.org)
  • Comparative genome analysis of M. kandleri , Methanococcus jannaschii , and Methanothermobacter thermoautotrophicum resulted in the delineation of a distinct set of genes characteristic of archaeal methanogens. (pnas.org)
  • B ) A Venn diagram of the shared and unique portions of the proteomes of archaeal methanogens. (nih.gov)
  • used metagenomics to assemble two nearly complete archaeal genomes from deep groundwater methanogens (see the Perspective by Lloyd). (sciencemag.org)
  • To enable robust reconstruction of individual genomes from within a complex microbial community, additional information beyond standard shotgun sequencing libraries is required. (g3journal.org)
  • However, based on a more complete archaeal genomic tree, they were assigned to a new superphylum named DPANN. (wikipedia.org)
  • A novel filamentous virus, AFV2, from the hyperthermophilic archaeal genus Acidianus shows structural similarity to lipothrixviruses but differs from them in its unusual terminal and core structures. (uni-regensburg.de)
  • We determined and annotated the complete 2.2-megabase genome sequence of Pyrobaculum aerophilum, a facultatively aerobic nitrate-reducing hyperthermophilic (T-opt = 100 degrees C) crenarchaeon. (caltech.edu)
  • Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes. (semanticscholar.org)
  • Why sequence ammonia-oxidizing archaeal enrichment culture? (doe.gov)
  • The genomes of three ARMAN groups were sequenced at the DOE Joint Genome Institute during a 2006 Community Sequencing Program. (wikipedia.org)
  • The archaeal domain consists of numerous metabolically diverse phyla which are ubiquitously distributed among both extreme and mesic environments. (els.net)
  • Many proposed new archaeal phyla have been discovered with the use of environmental genomic techniques and remain uncultured. (els.net)
  • This is due, in part, to the relatively recent delineation of the archaeal domain of life but, more significantly, to the challenges of isolating and culturing the host organisms ( 42 ). (asm.org)
  • Metagenomic analyses would benefit greatly from a more generalizable methodology that can identify the sequence content belonging to each taxon without any a priori knowledge of the genomes of these organisms, especially the genomes of low-abundance taxa. (g3journal.org)
  • The composition and diversity of microbial communities and specific functional groups involved in key pathways in the geochemical cycling of nitrogen, Fe, and sulfur were characterized using a coupled approach involving cultivation-independent analysis of both 16S rRNA (bacterial and archaeal) and functional genes ( amoA and dsrAB ) as well as cultivation-based analysis of Fe(III)-reducing organisms. (asm.org)
  • Members include SIRV1 and SIRV2 ( 24 ), ARV1 ( 36 ), and SRV1 ( 37 ), all of which have covalently closed linear dsDNA genomes of 30 to 40 kb encoding up to 50 open reading frames (ORFs). (asm.org)
  • A BLASTP-based survey of the phylogenetic pattern of all open reading frames (ORFs) in the genome of N. equitans revealed a surprisingly high fraction of close hits with Euryarchaeota, notably Thermococcales. (biomedcentral.com)
  • In addition, genomes with similar GC contents have similar oligonucleotide frequencies (genome signatures). (frontiersin.org)
  • Single-cell genome analyses reveal the amount of mutations a human brain cell will collect from its fetal beginnings until death. (the-scientist.com)
  • Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. (elifesciences.org)
  • In large-scale genome sequencing of bacterial strains, we see thousands of recombination events [ 15 ], and indeed, on occasion, explaining phenotypes requires methods that explicitly need to account for and remove vertical transmission signals [ 16 ]. (royalsocietypublishing.org)
  • However, the details of how the competition between clonality and recombination shapes genome diversity remains poorly understood. (genetics.org)
  • In contrast, in the metastable regime, characterized by a high recombination frequency combined with low barriers to recombination, genomes continuously recombine with the rest of the population. (genetics.org)
  • the pair of genomes is likely to become sexually isolated from each other in this region within the time that separates two successive recombination events. (genetics.org)
  • Also, many of the fragments of viral genomes that have been identified have not yet been linked to their host microbes. (elifesciences.org)
  • The study identifies over 12,000 viral genomes and links them to their microbial hosts. (elifesciences.org)
  • s findings demonstrate the value of searching publicly available microbial genome data for fragments of viral genomes. (elifesciences.org)
  • While not restricted only to extreme habitats, there is a significant amount of archaeal diversity in thermal and acidic habitats, where they are often dominant members of microbial communities there. (els.net)
  • We utilize these data to explore how inherent dynamics of archaeal slinky chromatin may regulate transcription. (aps.org)
  • We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. (biomedcentral.com)
  • However, in order to face the rapid increase in the number of published genomes, we also include analyses of genomes issuing directly from the automated strategy. (nih.gov)
  • eLife 2017) to characterise chromatin in near-native conditions inside archaeal cells. (embl.org)
  • These genomes contain divergent homologs of the genes necessary for methane metabolism, including those that encode the methyl-coenzyme M reductase (MCR) complex. (sciencemag.org)
  • Mobile genetic elements may have played a role in the plasmid and virus genesis, which is related to genome reduction. (frontiersin.org)
  • We used the Clusters of Orthologous Groups database and information from published genomes to search for other universally conserved genes that have the same phylogenetic pattern as ribosomal RNA, and therefore constitute the ancestral genetic core of cells. (semanticscholar.org)
  • It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. (biomedcentral.com)
  • Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. (biomedcentral.com)
  • Advantages with these statistical methods include measurements of phylogenetic relationship with relatively small pieces of DNA sampled from almost anywhere within genomes, detection of foreign/conserved DNA, and homology searches. (biomedcentral.com)
  • Methanococcus jannaschii was the first archaeon whose genome was sequenced, in 1996. (wikipedia.org)
  • Multiple factors shape the diversification of the core genome. (genetics.org)
  • Whole genome computational analysis confirmed experiments showing that P. aerophilum (and perhaps all crenarchaea) lack 5' untranslated regions in their mRNAs and thus appear not to use a ribosome-binding site (Shine-Dalgarno)-based mechanism for translation initiation at the 5' end of transcripts. (caltech.edu)
  • From single-cell analysis to whole-genome sequencing, this year's best new products shine on many levels. (the-scientist.com)
  • The epub computational methods for understanding bacterial and archaeal genomes series on advances in bioinformatics of gem-quality was been such in its Malay today for three locations, but here cut the organization. (ramblermania.net)
  • A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq. (genomeweb.com)
  • Metagenomic data from an acidophilic microbial community enabled a genomewide, comprehensive investigation of variation in individuals from two coexisting natural archaeal populations. (nih.gov)
  • Hidden Giants in Forest Soils In Nature Communications, giant virus genomes have been discovered for the first time in a forest soil ecosystem by JGI and University of Massachusetts-Amherst researchers. (doe.gov)
  • Interestingly, comparisons of the genomes of pathogenic and nonpathogenic strains of bacteria have shown that many suspected PAIs reside in both and that PAIs themselves are insufficient for pathogenicity. (answersingenesis.org)