Proteins found in any species of archaeon.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
Deoxyribonucleic acid that makes up the genetic material of archaea.
The functional genetic units of ARCHAEA.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Viruses whose hosts are in the domain ARCHAEA.
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)
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.
Ribonucleic acid that makes up the genetic material of viruses.
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE).
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 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)
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
A genus of anaerobic coccoid METHANOCOCCACEAE whose organisms are motile by means of polar tufts of flagella. These methanogens are found in salt marshes, marine and estuarine sediments, and the intestinal tract of animals.
A species of thermoacidophilic ARCHAEA in the family Sulfolobaceae, found in volcanic areas where the temperature is about 80 degrees C and SULFUR is present.
A species of halophilic archaea found in the Dead Sea.
A species of strictly anaerobic, hyperthermophilic archaea which lives in geothermally-heated marine sediments. It exhibits heterotropic growth by fermentation or sulfur respiration.
The large subunit of the archaeal 70s ribosome. It is composed of the 23S RIBOSOMAL RNA, the 5S RIBOSOMAL RNA, and about 40 different RIBOSOMAL PROTEINS.
Viruses whose genetic material is RNA.
A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.
The relationships of groups of organisms as reflected by their genetic makeup.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
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.
A species of gram-negative hyperthermophilic ARCHAEA found in deep ocean hydrothermal vents. It is an obligate anaerobe and obligate chemoorganotroph.
RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.
RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
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.
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 processes of RNA tertiary structure formation.
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.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
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.
The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.
Anaerobic hyperthermophilic species of ARCHAEA, isolated from hydrothermal fluid samples. It is obligately heterotrophic with coccoid cells that require TRYPTOPHAN for growth.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
A family of proteins that promote unwinding of RNA during splicing and translation.
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
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 genus of facultatively anaerobic coccoid ARCHAEA, in the family SULFOLOBACEAE. Cells are highly irregular in shape and thermoacidophilic. Lithotrophic growth occurs aerobically via sulfur oxidation in some species. Distribution includes solfataric springs and fields, mudholes, and geothermically heated acidic marine environments.
The simplest saturated hydrocarbon. It is a colorless, flammable gas, slightly soluble in water. It is one of the chief constituents of natural gas and is formed in the decomposition of organic matter. (Grant & Hackh's Chemical Dictionary, 5th ed)
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Short chains of RNA (100-300 nucleotides long) that are abundant in the nucleus and usually complexed with proteins in snRNPs (RIBONUCLEOPROTEINS, SMALL NUCLEAR). Many function in the processing of messenger RNA precursors. Others, the snoRNAs (RNA, SMALL NUCLEOLAR), are involved with the processing of ribosomal RNA precursors.
A phylum of ARCHAEA comprising at least seven classes: Methanobacteria, Methanococci, Halobacteria (extreme halophiles), Archaeoglobi (sulfate-reducing species), Methanopyri, and the thermophiles: Thermoplasmata, and Thermococci.
A kingdom of hyperthermophilic ARCHAEA found in diverse environments.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
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 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 multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
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.
Nucleic acid structures found on the 5' end of eukaryotic cellular and viral messenger RNA and some heterogeneous nuclear RNAs. These structures, which are positively charged, protect the above specified RNAs at their termini against attack by phosphatases and other nucleases and promote mRNA function at the level of initiation of translation. Analogs of the RNA caps (RNA CAP ANALOGS), which lack the positive charge, inhibit the initiation of protein synthesis.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and 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.
An enzyme that catalyzes the conversion of linear RNA to a circular form by the transfer of the 5'-phosphate to the 3'-hydroxyl terminus. It also catalyzes the covalent joining of two polyribonucleotides in phosphodiester linkage. EC 6.5.1.3.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
A family of THERMOPROTEALES consisting of variable length rigid rods without septa. They grow either chemolithoautotrophically or by sulfur respiration. The four genera are: PYROBACULUM; THERMOPROTEUS; Caldivirga; and Thermocladium. (From Bergey's Manual of Systematic Bacteriology, 2d ed)
A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)
A genus of anaerobic, rod-shaped METHANOBACTERIACEAE. Its organisms are nonmotile and use ammonia as the sole source of nitrogen. These methanogens are found in aquatic sediments, soil, sewage, and the gastrointestinal tract of animals.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
An order of anaerobic methanogens in the kingdom EURYARCHAEOTA. There are two families: METHANOSARCINACEAE and Methanosaetaceae.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
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.
RNA present in neoplastic tissue.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The small subunit of archaeal RIBOSOMES. It is composed of the 16S RIBOSOMAL RNA and about 28 different RIBOSOMAL PROTEINS.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
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.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
A family of archaea, in the order DESULFUROCOCCALES, consisting of anaerobic cocci which utilize peptides, proteins or carbohydrates facultatively by sulfur respiration or fermentation. There are eight genera: AEROPYRUM, Desulfurococcus, Ignicoccus, Staphylothermus, Stetteria, Sulfophoboccus, Thermodiscus, and Thermosphaera. (From Bergey's Manual of Systematic Bacteriology, 2d ed)
The 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.
A large family of RNA helicases that share a common protein motif with the single letter amino acid sequence D-E-A-D (Asp-Glu-Ala-Asp). In addition to RNA helicase activity, members of the DEAD-box family participate in other aspects of RNA metabolism and regulation of RNA function.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
A process facilitated by specialized bacteria involving the oxidation of ammonium to nitrite and nitrate.
A family of anaerobic METHANOCOCCALES whose organisms are motile by means of flagella. These methanogens use carbon dioxide as an electron acceptor.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
An order of CRENARCHAEOTA consisting of aerobic or facultatively aerobic, chemolithotrophic cocci which are extreme thermoacidophiles. They lack peptidoglycan in their cell walls.
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.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. The enzyme functions in the nucleolar structure and transcribes DNA into RNA. It has different requirements for cations and salts than RNA polymerase II and III and is not inhibited by alpha-amanitin. EC 2.7.7.6.
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.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
The variety of all native living organisms and their various forms and interrelationships.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
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.
A species of halophilic archaea found in salt lakes. Some strains form a PURPLE MEMBRANE under anaerobic conditions.
A reaction that severs one of the sugar-phosphate linkages of the phosphodiester backbone of RNA. It is catalyzed enzymatically, chemically, or by radiation. Cleavage may be exonucleolytic, or endonucleolytic.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
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).
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.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
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 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.
The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.
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 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.
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.
A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.
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.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Proteins found in any species of bacterium.
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.
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.
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Group II chaperonins found in species of ARCHAEA.
A group of different species of microorganisms that act together as a community.
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
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.
The small RNAs which provide spliced leader sequences, SL1, SL2, SL3, SL4 and SL5 (short sequences which are joined to the 5' ends of pre-mRNAs by TRANS-SPLICING). They are found primarily in primitive eukaryotes (protozoans and nematodes).
Small, linear single-stranded RNA molecules functionally acting as molecular parasites of certain RNA plant viruses. Satellite RNAs exhibit four characteristic traits: (1) they require helper viruses to replicate; (2) they are unnecessary for the replication of helper viruses; (3) they are encapsidated in the coat protein of the helper virus; (4) they have no extensive sequence homology to the helper virus. Thus they differ from SATELLITE VIRUSES which encode their own coat protein, and from the genomic RNA; (=RNA, VIRAL); of satellite viruses. (From Maramorosch, Viroids and Satellites, 1991, p143)
The genetic complement of a BACTERIA as represented in its DNA.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
Proteins prepared by recombinant DNA technology.
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.
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.
The rate dynamics in chemical or physical systems.
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)
A family of extremely halophilic archaea found in environments with high salt concentrations, such as salt lakes, evaporated brines, or salted fish. Halobacteriaceae are either obligate aerobes or facultative anaerobes and are divided into at least twenty-six genera including: HALOARCULA; HALOBACTERIUM; HALOCOCCUS; HALOFERAX; HALORUBRUM; NATRONOBACTERIUM; and NATRONOCOCCUS.
The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.
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 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 transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.
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.
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
A functional system which includes the organisms of a natural community together with their environment. (McGraw Hill Dictionary of Scientific and Technical Terms, 4th ed)
A colorless alkaline gas. It is formed in the body during decomposition of organic materials during a large number of metabolically important reactions. Note that the aqueous form of ammonia is referred to as AMMONIUM HYDROXIDE.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
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.
An order of extremely thermophilic, sulfate-reducing archaea, in the kingdom EURYARCHAEOTA. The single family Archaeoglobaceae contains one genus ARCHAEOGLOBUS.
A genus of obligately anaerobic ARCHAEA, in the family THERMOPROTEACEAE. They are found in acidic hot springs and water holes.
An RNA POLYMERASE II specific transcription factor. It plays a role in assembly of the pol II transcriptional preinitiation complex and has been implicated as a target of gene-specific transcriptional activators.
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.
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.
Established cell cultures that have the potential to propagate indefinitely.
The spectrum of different living organisms inhabiting a particular region, habitat, or biotope.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.
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.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Enzymes that catalyze the S-adenosyl-L-methionine-dependent methylation of ribonucleotide bases within a transfer RNA molecule. EC 2.1.1.
A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
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.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
The functional hereditary units of BACTERIA.
Nuclear nonribosomal RNA larger than about 1000 nucleotides, the mass of which is rapidly synthesized and degraded within the cell nucleus. Some heterogeneous nuclear RNA may be a precursor to mRNA. However, the great bulk of total hnRNA hybridizes with nuclear DNA rather than with mRNA.
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)
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.
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.
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.
A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.
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.
Presence of warmth or heat or a temperature notably higher than an accustomed norm.
Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).
The steps that generate the 3' ends of mature RNA molecules. For most mRNAs (RNA, MESSENGER), 3' end processing referred to as POLYADENYLATION includes the addition of POLY A.
The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.
Intermediates in protein biosynthesis. The compounds are formed from amino acids, ATP and transfer RNA, a reaction catalyzed by aminoacyl tRNA synthetase. They are key compounds in the genetic translation process.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
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 conversion of uncharged TRANSFER RNA to AMINO ACYL TRNA.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
Short RNA, about 200 base pairs in length or shorter, that does not code for protein.
The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.
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.
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
A family of enzymes that catalyze the exonucleolytic cleavage of RNA. It includes EC 3.1.13.-, EC 3.1.14.-, EC 3.1.15.-, and EC 3.1.16.-. EC 3.1.-
Enzymes that recognize CRUCIFORM DNA structures and introduce paired incisions that help to resolve the structure into two DNA helices.
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
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.
A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.

Purification and characterization of an extremely thermostable cyclomaltodextrin glucanotransferase from a newly isolated hyperthermophilic archaeon, a Thermococcus sp. (1/469)

The extremely thermophilic anaerobic archaeon strain B1001 was isolated from a hot-spring environment in Japan. The cells were irregular cocci, 0.5 to 1.0 micrometers in diameter. The new isolate grew at temperatures between 60 and 95 degrees C (optimum, 85 degrees C), from pH 5.0 to 9.0 (optimum, pH 7.0), and from 1.0 to 6.0% NaCl (optimum, 2.0%). The G+C content of the genomic DNA was 43.0 mol%. The 16S rRNA gene sequencing of strain B1001 indicated that it belongs to the genus Thermococcus. During growth on starch, the strain produced a thermostable cyclomaltodextrin glucanotransferase (CGTase). The enzyme was purified 1,750-fold, and the molecular mass was determined to be 83 kDa by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. Incubation at 120 degrees C with SDS and 2-mercaptoethanol was required for complete unfolding. The optimum temperatures for starch-degrading activity and cyclodextrin synthesis activity were 110 and 90 to 100 degrees C, respectively. The optimum pH for enzyme activity was pH 5.0 to 5.5. At pH 5.0, the half-life of the enzyme was 40 min at 110 degrees C. The enzyme formed mainly alpha-cyclodextrin with small amounts of beta- and gamma-cyclodextrins from starch. This is the first report on the presence of the extremely thermostable CGTase from hyperthermophilic archaea.  (+info)

Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1. (2/469)

The complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1, which optimally grows at 95 degrees C, has been determined by the whole genome shotgun method with some modifications. The entire length of the genome was 1,669,695 bp. The authenticity of the entire sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2,694 open reading frames (ORFs) were assigned. By similarity search against public databases, 633 (23.5%) of the ORFs were related to genes with putative function and 523 (19.4%) to the sequences registered but with unknown function. All the genes in the TCA cycle except for that of alpha-ketoglutarate dehydrogenase were included, and instead of the alpha-ketoglutarate dehydrogenase gene, the genes coding for the two subunits of 2-oxoacid:ferredoxin oxidoreductase were identified. The remaining 1,538 ORFs (57.1%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs suggested that a considerable member of ORFs were generated by sequence duplication. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 47 tRNA genes including 14 genes with intron structures. All the assigned ORFs and RNA coding regions occupied 89.12% of the whole genome. The data presented in this paper are available on the internet homepage (http://www.mild.nite.go.jp).  (+info)

Coordinate transcriptional control in the hyperthermophilic archaeon Sulfolobus solfataricus. (3/469)

The existence of a global gene regulatory system in the hyperthermophilic archaeon Sulfolobus solfataricus is described. The system is responsive to carbon source quality and acts at the level of transcription to coordinate synthesis of three physically unlinked glycosyl hydrolases implicated in carbohydrate utilization. The specific activities of three enzymes, an alpha-glucosidase (malA), a beta-glycosidase (lacS), and an alpha-amylase, were reduced 4-, 20-, and 10-fold, respectively, in response to the addition of supplementary carbon sources to a minimal sucrose medium. Western blot analysis using anti-alpha-glucosidase and anti-beta-glycosidase antibodies indicated that reduced enzyme activities resulted exclusively from decreased enzyme levels. Northern blot analysis of malA and lacS mRNAs revealed that changes in enzyme abundance arose primarily from reductions in transcript concentrations. Culture conditions precipitating rapid changes in lacS gene expression were established to determine the response time of the regulatory system in vivo. Full induction occurred within a single generation whereas full repression occurred more slowly, requiring nearly 38 generations. Since lacS mRNA abundance changed much more rapidly in response to a nutrient down shift than to a nutrient up shift, transcript synthesis rather than degradation likely plays a role in the regulatory response.  (+info)

RNase P RNAs from some Archaea are catalytically active. (4/469)

The RNA subunits of RNase Ps of Archaea and eukaryotes have been thought to depend fundamentally on protein for activity, unlike those of Bacteria that are capable of efficient catalysis in the absence of protein. Although the eukaryotic RNase P RNAs are quite different than those of Bacteria in both sequence and structure, the archaeal RNAs generally contain the sequences and structures of the bacterial, phylogenetically conserved catalytic core. A spectrum of archaeal RNase P RNAs were therefore tested for activity in a wide range of conditions. Many remain inactive in ionically extreme conditions, but catalytic activity could be detected from those of the methanobacteria, thermococci, and halobacteria. Chimeric holoenzymes, reconstituted from the Methanobacterium RNase P RNA and the Bacillus subtilis RNase P protein subunits, were functional at low ionic strength. The properties of the archaeal RNase P RNAs (high ionic-strength requirement, low affinity for substrate, and catalytic reconstitution by bacterial RNase P protein) are similar to synthetic RNase P RNAs that contain all of the catalytic core of the bacterial RNA but lack phylogenetically variable, stabilizing elements.  (+info)

Archaeal aminoacyl-tRNA synthesis: diversity replaces dogma. (5/469)

Accurate aminoacyl-tRNA synthesis is essential for faithful translation of the genetic code and consequently has been intensively studied for over three decades. Until recently, the study of aminoacyl-tRNA synthesis in archaea had received little attention. However, as in so many areas of molecular biology, the advent of archaeal genome sequencing has now drawn researchers to this field. Investigations with archaea have already led to the discovery of novel pathways and enzymes for the synthesis of numerous aminoacyl-tRNAs. The most surprising of these findings has been a transamidation pathway for the synthesis of asparaginyl-tRNA and a novel lysyl-tRNA synthetase. In addition, seryl- and phenylalanyl-tRNA synthetases that are only marginally related to known examples outside the archaea have been characterized, and the mechanism of cysteinyl-tRNA formation in Methanococcus jannaschii and Methanobacterium thermoautotrophicum is still unknown. These results have revealed completely unexpected levels of complexity and diversity, questioning the notion that aminoacyl-tRNA synthesis is one of the most conserved functions in gene expression. It has now become clear that the distribution of the various mechanisms of aminoacyl-tRNA synthesis in extant organisms has been determined by numerous gene transfer events, indicating that, while the process of protein biosynthesis is orthologous, its constituents are not.  (+info)

Genetic diversity of archaea in deep-sea hydrothermal vent environments. (6/469)

Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.  (+info)

Cell-free transcription at 95 degrees: thermostability of transcriptional components and DNA topology requirements of Pyrococcus transcription. (7/469)

Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100 degrees. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100 degrees. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg(2+) ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95 degrees was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70 degrees and 90 degrees. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.  (+info)

Control of ribosomal protein L1 synthesis in mesophilic and thermophilic archaea. (8/469)

The mechanisms for the control of ribosomal protein synthesis have been characterized in detail in Eukarya and in Bacteria. In Archaea, only the regulation of the MvaL1 operon (encoding ribosomal proteins MvaL1, MvaL10, and MvaL12) of the mesophilic Methanococcus vannielii has been extensively investigated. As in Bacteria, regulation takes place at the level of translation. The regulator protein MvaL1 binds preferentially to its binding site on the 23S rRNA, and, when in excess, binds to the regulatory target site on its mRNA and thus inhibits translation of all three cistrons of the operon. The regulatory binding site on the mRNA, a structural mimic of the respective binding site on the 23S rRNA, is located within the structural gene about 30 nucleotides downstream of the ATG start codon. MvaL1 blocks a step before or at the formation of the first peptide bond of MvaL1. Here we demonstrate that a similar regulatory mechanism exists in the thermophilic M. thermolithotrophicus and M. jannaschii. The L1 gene is cotranscribed together with the L10 and L11 gene, in all genera of the Euryarchaeota branch of the Archaea studied so far. A potential regulatory L1 binding site located within the structural gene, as in Methanococcus, was found in Methanobacterium thermoautotrophicum and in Pyrococcus horikoshii. In contrast, in Archaeoglobus fulgidus a typical L1 binding site is located in the untranslated leader of the L1 gene as described for the halophilic Archaea. In Sulfolobus, a member of the Crenarchaeota, the L1 gene is part of a long transcript (encoding SecE, NusG, L11, L1, L10, L12). A previously suggested regulatory L1 target site located within the L11 structural gene could not be confirmed as an L1 binding site.  (+info)

RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative
The KIF1 subfamily members are monomeric and contain a number of amino acid inserts in surface loops. A particularly striking insertion of several lysine/arginine residues occurs in L12 and is called the K-loop. Two recent studies have employed both kinetic and single-molecule methods to investigate KIF1 motor properties and have produced very different conclusions about how these motors generate motility. Here we show that a hitherto unstudied member of this group, KIF1D, is not chemically processive and drives fast motility despite demonstrating a slow ATPase. The K-loop of KIF1D was analysed by deletion and insertion mutagenesis coupled with characterization by steady state and transient kinetics. Together, the results indicate that the K-loop not only increases the affinity of the motor for the MT, but crucially also inhibits its subsequent isomerization from weak to strong binding, with coupled ADP release. By stabilizing the weak binding, the K-loop establishes a pool of motors primed to ...
() Scientists know that physical and biochemical signals can guide cells to make, for example, muscle, blood vessels or bone. But the exact recipes to produce the desired tissues have proved elusive.
eds for Everyday American download canon eos digital rebel xti methods and expectation syntax in the camera and Enchantress of new elements. Course Information: 2 general books. 160; 250; and apt download canon eos digital rebel or Irreducible; or hide of the use.
Plasmid PPP2R2D B8.5 gRNA from Dr. Iain Cheesemans lab contains the insert PPP2R2D (Guide Designation B8.5) and is published in Dev Cell. 2017 Feb 27;40(4):405-420.e2. doi: 10.1016/j.devcel.2017.01.012. Epub 2017 Feb 16. This plasmid is available through Addgene.
This visual uses Regional Price Parities (RPPs) to show which states are the most expensive (and cheapest) for buying everyday goods and services.
...Scientists know that physical and biochemical signals can guide cells ...Now researchers at Case Western Reserve University have taken a step ...Ultimately one of their goals is to engineer systems to manipulate st... If we can control the spatial presentation of signals we may be able...,Signal,gradients,in,3-D,guide,stem,cell,behavior,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
Scientists know that physical and biochemical signals can guide cells to make, for example, muscle, blood vessels or bone. But the exact recipes to produce the desired tissues have proved elusive. Now, researchers at Case Western Reserve University have taken a step toward identifying that mix by developing an easy and versatile way of forming physical and biochemical gradients in three dimensions.
Symbiotic Genomics- Emerging Viruses, Superbugs and Prions, 978-613-9-45078-7, Lamarckian hereditability of acquired characteristics proposed natural cooperation as opposed to natural selection. The endosymbiotic archaea secrete RNA viroids. The archaeal RNA viroids are converted to DNA viroids by endogenous HERV reverse transcriptase and integrated into the genome by HERV integrase. Archaeal endosymbiosis can occur consequent to global warming, stress, dietary fibre deficiency and exposure to low level EMF which leads to increased colonic archaeal growth and endosymbiosis. The archaea will secrete RNA viroids which can get converted to DNA viroids and get integrated into the genome functioning as jumping genes modulating gene expression. The RNA viroids and their DNA templates getting integrated into the genome consequent to environmental stress leads to genomic flexibility and dynamicity which can be inherited. Exposure to environmental stress can alter the genome changing body function in response to
Fingerprint Dive into the research topics of Electrophysiological characterization of the archaeal transporter NCX_Mj using solid supported membrane technology. Together they form a unique fingerprint. ...
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 …
Haloarcula marismortui ATCC ® 43049D-5™ Designation: Genomic DNA from Haloarcula marismortui strain DSM 3752 TypeStrain=True Application:
Fibrillarin (recently identified as the methyltransferase; Omer et al., 2002) becomes cross‐linked to the D, D′ and (both substituted positions of the) C′ boxes, but does not appear to contact either 4SU position within the C box. In box C/D snoRNAs, the guide sequence is positioned 5′ of the D or D′ box, with the nucleotide to be modified located exactly 5 bp upstream of the conserved sequence. Fibrillarin cross‐linking to boxes D and D′ is consistent with its role as the 2′‐O‐methytransferase. Surprisingly, none of the mutations within the C′ or D′ boxes perturbed the observed cross‐linking interaction with fibrillarin.. The asymmetry of the box C/D particle is evident from the distinct cross‐linking patterns of Nop56 and Nop58, homologous proteins that exhibit 37% sequence identity in human (Lyman et al., 1999). Cross‐linked Nop58 was observed only with 4SU in the second position of the C box, while Nop56 appears to contact both U positions in the consensus C′ ...
An outstanding share! I have just forwarded this onto a colleague who was doing a little research on this. And he actually ordered me dinner simply because I found it for him… lol. So allow me to reword this…. Thanks for the meal!! But yeah, thanx for spending some time to talk about this topic here on your web site.. ...
Archaeal enzymes have great potential for industrial use; however, expressing them in their natural hosts has proven challenging. Growth conditions for many archaea are beyond typical fermentation capabilities, and to compound the problem, archaea generally achieve much lower biomass yields than Esc …
By employing next generation DNA sequencing of genomes isolated from single cells, great strides are being made in the monumental task of systematically bringing to light and filling in uncharted branches in the bacterial and archaeal tree of life.
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 ...
Archaea are best known in their capacities as extremophiles, i.e. micro-organisms able to thrive in some of the most drastic environments on Earth. The protein-based surface layer that envelopes many archaeal strains must thus correctly assemble and maintain its structural integrity in the face of the physical challenges associated with, for instance, life in high salinity, at elevated temperatures or in acidic surroundings. Study of archaeal surface-layer (glyco)proteins has thus offered insight into the strategies employed by these proteins to survive direct contact with extreme environments, yet has also served to elucidate other aspects of archaeal protein biosynthesis, including glycosylation, lipid modification and protein export. In this mini-review, recent advances in the study of archaeal surface-layer (glyco)proteins are discussed.
View Notes - chapter+19 from BIOL 2051 at LSU. Chapter 19 Archaeal Diversity Archaeal Traits and Diversity Widest temperature range 2C121C Widest range of environments pH 0, high pressure,
2-Carboxyphenyl phosphate methyl ester | C8H9O6P | CID 577581 - structure, chemical names, physical and chemical properties, classification, patents, literature, biological activities, safety/hazards/toxicity information, supplier lists, and more.
130 APPENDIX D GUIDE FOR PBL IN CLASS IMPLEMENTATION Before beginning the experiment, there was a need for explanation about the teaching method since none of the students has had information about it. The role of the student, the role of the teacher, the reasoning behind this method is explained in the clas s. Sample of in class problem cases: Introduce the problem: You are a design build company and one day a client walks in and tells you that he wants a house built similar to the ones in the pictures. This picture is the only information you have about th e house. Now look at the picture and write down the known information about the project (1mins). Dont give them so much time since there isnt that much information given. Now write down your goals. What do you want to accomplish with this project? ( Again I dont think they need that much time for this part. After each group discussion ask one of them from their group to come to the board and write down what they found What they need to know ...
WoRMS (2011). Thaumarchaeota. Accessed through: World Register of Marine Species at http://marinespecies.org/aphia.php?p=taxdetails&id=559429 on 2017-12- ...
General Information: Temp: Mesophile. Haloterrigena turkmenica, formerly Halococcus turkmenicus, is a halophilic archaeon isolated from soil. ...
Provide tutorials and other workshop materials for 3D RNA Modeling and Simulation Tools: NAST/C2A, RNABuilder, and OpenMM Zephyr.
Hosted by the USGS Core Science Analytics and Synthesis. Page designed through the cooperative efforts of interagency ITIS Teams. Point of Contact: [email protected]
These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure or prevent any disease.. ©2019 - 2021 Designs for Health, Inc. All rights reserved. ...
bierparadijs vende allasta al prezzo di 5,40 € fino al lunedì 25 novembre 2019 19:08:00 CET un oggetto nella categoria Birra di Delcampe
A novel halophilic archaeon, strain KeC-11T, was isolated from a seawater aquarium at the Ocean Research Institute, University of Tokyo, Japan. The strain was aerobic, Gram-negative and chemo-organotrophic, growing optimally at 37 °C, at pH 7.0-8.0 and in 2.7 M (16 %) NaCl. The strain required at least 10 mM magnesium ions for growth. Cells of strain KeC-11T were non-motile and generally irregular coccoids or discoids. The DNA G+C content of the isolate was 67.7 mol%. Phylogenetic tree reconstructions indicated that it was distantly related to the other recognized members of the family Halobacteriaceae, with the closest relative being Natronomonas pharaonis GabaraT (91 % sequence similarity). The strain contained C20C20 and C20C25 diether derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, a glycolipid chromatographically identical to the glycosyl-mannosyl-glucosyl diether (TGD-2) and at least one unidentified glycolipid. Phenotypic characterization and phylogenetic data
CRISPR-Cas systems are adaptive immune systems in bacteria and archaea, consisting of a clustered regularly interspaced short palindromic repeats (CRISPR) array and CRISPR associated (Cas) proteins. In this work, the type I-E CRISPR-Cas system of Escherichia coli was studied.. CRISPR-Cas immunity is divided into three stages. In the first stage, adaptation, Cas1 and Cas2 store memory of invaders in the CRISPR array as short intervening sequences, called spacers. During the expression stage, the array is transcribed, and subsequently processed into small CRISPR RNAs (crRNA), each consisting of one spacer and one repeat. The crRNAs are bound by the Cascade multi-protein complex. During the interference step, Cascade searches for DNA molecules complementary to the crRNA spacer. When a match is found, the target DNA is degraded by the recruited Cas3 nuclease.. Host factors required for integration of new spacers into the CRISPR array were first investigated. Deleting recD, involved in DNA repair, ...
FIG. 5. Strains deficient in 20S proteasomal α1 are sensitive to heat stress, whereas strains deficient in PanA are superthermotolerant. Parent (H26) and proteasomal mutant strains were grown to log phase at 42°C in GMM-Ala. Cells were diluted to an OD600 of 0.04 units and the effects of heat on cell viability were measured by a shift to 65°C (see Materials and Methods for details). Aliquots of cells were removed at 0-, 2-, 4-, 6-, and 8-h intervals. Cells were diluted, plated on GMM-Ala, and incubated at 42°C for 5 days. Experiments were performed in triplicate and the mean ± SD was calculated. ...
CRISPR-Cas systems are common in prokaryotes and can provide small RNA-based adaptive immunity against mobile genetic elements. A CRISPR-Cas system consists of DNA loci with Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR ass
CiteSeerX - Scientific documents that cite the following paper: Effect of temperature on carbon and electron flow and on the archaeal community in methanogenic rice field soil
Domain Archaea is currently represented by one phylum (Euryarchaeota) and two superphyla (TACK and DPANN). However, gene surveys indicate the existence of a vast diversity of uncultivated archaea for which metabolic information is lacking. We sequenced DNA from complex sediment- and groundwater-associated microbial communities sampled prior to and during an acetate biostimulation field experiment to investigate the diversity and physiology of uncultivated subsurface archaea. We sampled 15 genomes that improve resolution of a new phylum within the TACK superphylum and 119 DPANN genomes that highlight a major subdivision within the archaeal domain that separates DPANN from TACK/Euryarchaeota lineages. Within the DPANN superphylum, which lacks any isolated representatives, we defined two new phyla using sequences from 100 newly sampled genomes. The first new phylum, for which we propose the name Woesearchaeota, was defined using 54 new sequences. We reconstructed a complete (finished) genome for an ...
Natura - nature Mundus - physical world;material world Naturalia Biota 3.1 Domain Archaea C.R. Woese et al., 1990 H,N,P,R,B,L; Ref:G.M. Garrity et al., 2007:6 (implicit position); Count:[*]4p;9c;15o;25f;97g;326s 1.1 Phylum Crenarchaeota G.M. Garrity & J.G. Holt, 2001 H,N,P,R,B,L; Ref:G.M. Garrity et al., 2007:6; Count:[*]1c;4o;6f;26g;54s 1.2 Phylum Thaumarchaeota H,N,P,R,B,L; Ref:J.P. Euz by, 1997-present:15 Jun 2009 (validity questionable); Count:[*]1o;1f;1g;1s 2 Phylum Euryarchaeota G.M. Garrity & J.G. Holt, 2001 H,N,P,R,B,L; Ref:G.M. Garrity et al., 2007:10; Count:[*]8c;10o;18f;69g;270s 3 Phylum Nanoarchaeota Huber et al., 2002 H,N,P,R,B,L; Ref:H. Huber et al., 2002 (new taxon); Count:[*]1g;1s ...
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:. ...
Their phytanyl tails are primarily hooked to their glycerols using ether, not ester, linkages (see 2, above), which resist destruction better than esters. And their glycerols have opposite handedness to the glycerols in our membrane lipids (note mirror orientation in the bacterial and archaeal lipids in figure).. Molecular handedness -- chirality in chemistry-speak -- is not a thing changed easily by evolution. For instance, the vast majority of protein building blocks called amino acids used by life on Earth are exclusively left-handed. Why? No one really knows, although some have guesses. Once lefty amino acids took over, though, there was no going back biochemically -- the enzymes were set up a certain way and that was that. Thus, that archaeal and bacterial enzymes use glycerols with opposite handedness implies that bacteria and archaea parted ways long, long ago.. Some archaeal lipids have a property that is rarely or never seen in bacteria or eukaryotes. Bacteria and eukaryotes have ...
Relative abundance of archaeal OTUs defined using the 16S rRNA gene hyper-variable region V3V4. The bar chart shows the diversity of Archaea at the lowest relia
Prosser , J I & Nicol , G W 2012 , Archaeal and bacterial ammonia-oxidisers in soil : the quest for niche specialisation and differentiation Trends in Microbiology , vol 20 , no. 11 , pp. 523-531 . DOI: 10.1016/j.tim.2012.08. ...
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) protein 9 system provides a robust and multiplexable genome editing tool, enabling researchers to precisely manipulate specific genomic elements, and facilitating the elucidation of target gene function in...
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) protein 9 system provides a robust and multiplexable genome editing tool, enabling researchers to precisely manipulate specific genomic elements, and facilitating the elucidation of target gene function in...
Nunoura, T.; Takaki, Y.; Kakuta, J.; Nishi, S.; Sugahara, J.; Kazama, H.; Chee, G.J.; Hattori, M.; Kanai, A.; Aatomi, H.; Takai, K. and akami, H. 2011: Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res., 39, 3204-3223. doi: doi: 10.1093/nar/gkq1228 ...
The latter term is the odds ratio of the population (literally, the ratio of the odds of disease in those with the risk factor, a/b, to the odds of disease in those without the risk factor, c/d). a/c in the population equals a/c in the sample is the cases are representative of all cases in the population (i.e., have the same prevalence of the risk factor). Similarly, b/d equals b/d if the controls are representative. Therefore, the population parameters in this last term can be replaced by the sample parameters, and we are left with the fact that the odds ratio observed in the sample, ad/bc, is a close approximation of the relative risk in the population [a/(a + b)]/[c/(c + d)], provided that the disease is rare. Why cant calculate risk in a case-control study? For most people, the risk of some particular outcome, being akin to probability, makes more sense and is easier to interpret than the odds for that same outcome. To calculate the risk, you need to know two things: the total ...
The Office of the Chief Actuary has released a new fact sheet on Registered Pension Plans (RPPs) and Retirement Savings Coverage. ...
CRISPR (pronounced Crisper) is more than just a better way to prepare your bacon. In the genetics world, CRISPR stands for Clustered regularly interspaced short palindromic repeats. CRISPRs are found in prokaryotes as … Continue reading. ...
CRISPR (pronounced Crisper) is more than just a better way to prepare your bacon. In the genetics world, CRISPR stands for Clustered regularly interspaced short palindromic repeats. CRISPRs are found in prokaryotes as… Continue reading. ...
Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser. ...
Hosted by the USGS Core Science Analytics and Synthesis. Page designed through the cooperative efforts of interagency ITIS Teams. Point of Contact: [email protected]
1. Compute the mean, median, and mode for each of the following distributions. A B C D 3 2 1 2 3 2 3 3 4 2 3 4 6 5 3 4 7 5 5 4 8 7 5 5 10 7 8 7 8 8 8 10 8 8 11 9 11 2. I grew up in a very tiny town in the Midwestern United.
Persister cells are phenotypic variants within a microbial population, which are dormant and transiently tolerant to stress. Persistence has been studied extensively in bacteria, and in eukaryotes to a limited extent, however, it has never been observed in archaea. Using the model haloarchaeon, Haloferax volcanii DS2, we demonstrated persister cell formation in this domain, with time-kill curves exhibiting a characteristic biphasic pattern following starvation or exposure to lethal concentrations of various biocidal compounds. Repeated challenges of surviving cells showed that, as with bacteria, persister formation in H. volcanii was not heritable. Additionally, as previously shown with bacteria, persister formation in H. volcanii was suppressed by exogenous indole. The addition of spent culture media to assays conducted on planktonic cells showed that H. volcanii-conditioned media stimulated persistence, whereas conditioned media of other haloarchaea or halophilic bacteria did not, suggesting the
Reproduction among Haloferax volcanii occurs when two cells fuse, establish cytoplasmic bridges, and exchange genetic information, forming two daughter cells. While this practice may sound similar to the mating habits of eukaryotes, Haloferax volcanii appears to be indiscriminatory when it comes to choosing prospective reproductive partner cells. They appear to be capable of fusing with the cells of any species within the Haloferax genus; their methods of specificity are virtually unknown. Haloferax volcanii processes carbohydrates for energy. Their cell wall S-layer, like all halobacteria, is made up of a glycoprotein. And in keeping with their halophilic categorization, Haloferax volcanii cells contain proteins to allow them to maintain balance between the cell material and the hypersaline environment. ...
Most mammalian snoRNAs are encoded within the introns of pre-mRNA genes. The majority of snoRNAs are released from the pre-mRNA via a splicing-dependent pathway, while some are processed via endonucleolytic cleavage of the pre-mRNA. The remaining mammalian snoRNAs, such as U3, U8 and U13, are expressed from independent genes and contain an m3G cap structure (9, 30, 43, 52). The biogenesis of box C/D snoRNAs takes place in the nucleoplasm, where the nascent transcribed RNAs are processed, assembled into RNPs, and transported to the nucleolus. The box C/D motif has been shown to be essential for each of these steps in snoRNP biogenesis. This RNA element is a protein binding site that has been proposed to participate in both the biogenesis and function of snoRNAs via the selective recruitment of specific box C/D binding factors (9, 41, 52).. Four common core proteins are associated with the mature snoRNP, namely, fibrillarin (Nop1p in yeast), NOP56, NOP58, and the 15.5K protein (Snu13p in yeast) ...
Evans, TW, Könneke, M, Lipp, JS, Adhikari, RR, Taubner, H, Elvert, M and Hinrichs, KU (2018) Lipid biosynthesis of Nitrosopumilus maritimus dissected by lipid specific radioisotope probing (lipid-RIP) under contrasting ammonium supply. Geochimica et Cosmochimica Acta, 242. 51-63. doi:10.1016/j.gca.2018.09.001 ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Archaea are divided into two main groups based on rRNA trees, the Euryarchaeota and Crenarchaeota. Two other groups have been tentatively created for certain environmental samples and the peculiar species Nanoarchaeum equitans, discovered in 2002 by Karl Stetter, but their affinities are uncertain. Woese argued that the bacteria, archaea, and eukaryotes each represent a primary line of descent that diverged early on from an ancestral progenote with poorly developed genetic machinery. This hypothesis is reflected in the name Archaea, from the Greek archae or ancient. Later he treated these groups formally as domains, each comprising several kingdoms. This division has become very popular, although the idea of the progenote itself is not generally supported. Some biologists, however, have argued that the archaebacteria and eukaryotes arose from specialized eubacteria. The relationship between Archaea and Eukarya remains an important problem. Aside from the similarities noted above, many genetic ...
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been used as a complementary typing tool in diagnostic, epidemiologic, and evolutionary analyses of prokaryotic strains. The discovery that CRISPR spacers are often identical to sequence fragments of mobile genetic elements was a major breakthrough that eventually led to the elucidation of CRISPR-Cas as an adaptive immunity system. Key elements of this unique prokaryotic defense system are small CRISPR RNAs that guide nucleases to complementary target nucleic acids of invading viruses and plasmids, generally followed by the degradation of the invader. In addition, several recent studies have pointed at direct links of CRISPR-Cas to regulation of a range of stress-related phenomena. An interesting example ...
Looking for Halococcus? Find out information about Halococcus. A genus of bacteria in the family Halobacteriaceae; nonmotile cocci which occur in pairs, tetrads, or clusters of tetrads Explanation of Halococcus
Endosymbiotic Actinidic Archaeal Digoxin Inhibited Sodium Potassium ATPase Mediated ATP Synthesis and Archaeal Ectoatpases Produce Neuro-Immuno- Metabolic-Endocrine/Cell Cycle Regulation
Archaea are nowadays known as the third domain of life. Before 1970 archaea were thought to belong to the domain bacteria, since archaeal cells have similar sizes as bacterial cells and like bacteria possess neither a nucleus nor cell organelles. In the 1970s Carl Woese sequenced ribosomal RNAs of prokaryotic organisms and discovered two different types of rRNA sequences. Because of this discovery Woese proposed that the prokaryotic domain has to be subdivided into two separate domains, namely Bacteria and Archaea. Since then more and more data accumulated which show that Archaea indeed belong to a separate domain. Initially people thought that archaea are freaks living only at sites with extreme living conditions like f.i. hot geysers in Yellowstone National Park and Black Smokers at the bottom of the ocean. But nowadays it is known that archaea also constitute a big part of the biomass in normal environments. Asgard archaea: Close relatives to the first eukaryotic cell? ...
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 ...
CRISPR-Cas RNA-guided nucleases are derived from an adaptive immune system that evolved in bacteria to defend against invading plasmids and viruses. Decades of work investigating CRISPR systems in various microbial species has elucidated a mechanism by which short sequences of invading nucleic acids are incorporated into CRISPR loci. They are then transcribed and processed into CRISPR RNAs (crRNAs) which, together with a trans-activating crRNAs (tracrRNAs), complex with CRISPR-associated (Cas) proteins to dictate specificity of DNA cleavage by Cas nucleases through Watson-Crick base pairing between nucleic acids. Building off of two studies showing that the three components required for the type II CRISPR nuclease system are the Cas9 protein, the mature crRNA and the tracrRNA, Doudna, Charpentier and colleagues showed through in vitro DNA cleavage experiments that this system could be reduced to two components by fusion of the crRNA and tracrRNA into a single guide RNA (gRNA). Furthermore, they ...
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.. -end && ...
50S ribosomal protein L18; This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance (160 aa ...
Exosome complex component Csl4; Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Increases the RNA binding and the efficiency of RNA degradation. Helpful for the interaction of the exosome with A-poor RNAs (183 aa ...
Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C/D sRNAs.
Our division studies the Biology of Archaea as well as bacterial symbioses with a focus on ecological, physiological and evolutionary aspects to shed light on the diversity and fundamental distinctions between these two prokaryotic groups. In particular we are interested in: - The ecological distribution of archaea from terrestrial, aquatic and hot environments - The phylogeny of archaea - The metabolism and genomes of ammonia oxidizing thaumarchaeota - virus-defense (CRISPR-) systems of hyperthermophilic archaea - physiology and biotechnological application of methanogenic archaea - bacterium-nematode symbioses ...
Our division studies the Biology of Archaea as well as bacterial symbioses with a focus on ecological, physiological and evolutionary aspects to shed light on the diversity and fundamental distinctions between these two prokaryotic groups. In particular we are interested in: - The ecological distribution of archaea from terrestrial, aquatic and hot environments - The phylogeny of archaea - The metabolism and genomes of ammonia oxidizing thaumarchaeota - virus-defense (CRISPR-) systems of hyperthermophilic archaea - physiology and biotechnological application of methanogenic archaea - bacterium-nematode symbioses ...
Cas9/Csn1 | CRISPR-associated endonuclease, anti-Cas9/Csn1, anti-Cas9, anti-Csn1 | CRISPR-associated endonuclease antibody, AS16 3690
CRISPR or clustered, regularly interspaced, short palindromic repeat sequences are commonly found in bacteria and function as part of their innate immune system to counter foreign nucleic acids such as viruses and plasmids. CRISPR DNA sequences are translated into CRISPR RNAs (crRNAs) which complex with Cas or (CRISPR-associated) proteins to bring about cleavage of invading DNA. These systems…
Cardolipins are a separate class of phospholipids present in the cell membranes of organisms from all domains of life. In studying the enzyme that is responsible for producing cardiolipins in archaea biochemists discovered a single archaeal enzyme can produce a range of natural and non-natural cardiolipins, as well as other phospholipids.
Last Updated: 2021-06-19T15:10:03, r1624115403 public-dev Switch to Stable. Copyright © University of Maryland.. HaloWeb is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.. Please direct your content comments to Dr. Shiladitya DasSarma and technical comments to the Webmaster Satyajit DasSarma.. ...
Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
View Notes - Chap 27 Prokaryotes-st from BIL 160 at University of Miami. Prokaryotes-Chap 27 The three major clades, often referred to as the three domains: Archaea, Bacteria, and Eukaryota. -largest
Provide tutorials and other workshop materials for 3D RNA Modeling and Simulation Tools: NAST/C2A, RNABuilder, and OpenMM Zephyr.
Typical growth inhibition of S. solfataricus on plates due to infectious virus. Lawns of S. solfataricus strain GΘ were prepared as in Stedman et al. (2003). T
Human ferritins have been extensively studied to be used as nanocarriers for diverse applications and could represent a convenient alternative for targeted delivery of anticancer drugs and imaging agents. However, the most relevant limitation to their applications is the need for highly acidic experimental c
Our website has detected that you are using an outdated insecure browser that will prevent you from using the site. We suggest you upgrade to a modern browser. ...
I m looking for any info avaliable concerning maintenance of S. solfataricus. Please e-mail : dhatzini at orfeas.chemeng.ntua.gr ...
Genetic information processingProtein fateProtein and peptide secretion and traffickingprotein translocase SEC61 complex gamma subunit, archaeal and eukaryotic (TIGR00327; HMM-score: 8.1) ...
http://ecx.images-amazon.com/images/I/51JgzulwPHL._SL160_PIsitb-sticker-arrow-dp,TopRight,12,-18_SH30_OU01_.jpg|/div|Archaea Dain White (Author) http://g-ecx.images-amazon.com/images/G/01/detail/stars-4-0._V192261413_.gif(30) Download: $0.00 (Visit the Top Free in Action & Adventure
Mae testun y dudalen ar gael dan drwydded Creative Commons Attribution-ShareAlike; gall fod telerau ychwanegol perthnasol. Gweler Telerau Defnyddior Drwydded am fanylion pellach ...
Belzebuth is a Belgian Strong Pale Ale style beer brewed by Brasserie Grain d Orge (Brasserie Jeanne dArc SA) in Ronchin Lille, France. 3.42 average with 468 ratings, reviews and opinions.
Belzebuth is a Belgian Strong Pale Ale style beer brewed by Brasserie Grain d Orge (Brasserie Jeanne dArc SA) in Ronchin Lille, France. 3.42 average with 468 ratings, reviews and opinions.
"Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation". Nucleic Acids Research. 36 (4): 1187-99 ... Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, Hohn MJ, Cardoso AM, Whitman WB, Söll D (December 2006). "RNA-dependent ...
It catalyses the biosynthesis of DNA from RNA. This structure contains a three-stranded beta-sheet to the solvent, which lies ... Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K (July 2000). "Crystal structure of an archaeal intein-encoded homing ...
Gurha P, Gupta R (December 2008). "Archaeal Pus10 proteins can produce both pseudouridine 54 and 55 in tRNA". RNA. 14 (12): ... RNA. 1 (1): 102-12. PMC 1369054. PMID 7489483. Becker HF, Motorin Y, Planta RJ, Grosjean H (November 1997). "The yeast gene ... 2521-7. doi:10.1261/rna.1276508. PMC 2590954. PMID 18952823. TRNA+pseudouridine55+synthase at the US National Library of ... "Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA- ...
Charpentier E, Richter H, van der Oost J, White MF (2015). "Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR- ... Le Rhun A, Charpentier E (2012). "Small RNAs in streptococci". RNA Biol. 9 (4): 414-426. doi:10.4161/rna.20104. PMID 22546939. ... 2011). "CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III". Nature. 471 (7340): 602-607. Bibcode: ... In molecular biology, trans-activating crispr RNA (tracrRNA) is a small trans-encoded RNA. It was first discovered in the human ...
"Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity". FEMS Microbiology Reviews. 39 (3): ... Cas13 is an RNA-guided RNA endonuclease, which means that it does not cleave DNA, but only single-stranded RNA. Cas13 is guided ... "RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex". Cell. 139 (5): 945-956. doi:10.1016/j.cell.2009.07.040. PMC ... coli cut the CRISPR RNA precursor within the repeats into mature spacer-containing RNA molecules called CRISPR RNA (crRNA), ...
"Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs". RNA. 18 (3): 412-20. doi: ... RNA. 18 (3): 421-33. doi:10.1261/rna.030841.111. PMC 3285931. PMID 22274953. TRNA+(pseudouridine54-N1)-methyltransferase at the ... Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crécy-Lagard V (March 2012). "The archaeal ... Chen HY, Yuan YA (December 2010). "Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA ...
Bacterial, archaeal and plant plastid 11 See translation table 1. Alternative yeast nuclear 12 CTG CUG Ser (S) Leu (L) ... In RNA, it is replaced with uracil (U).[16] This is the only difference between the standard RNA codon table and the standard ... Standard RNA codon table[edit]. Amino-acid biochemical properties Nonpolar Polar Basic Acidic ↓ Termination: stop codon * ... RNA codon involved Translation with this code Standard translation Notes Standard 1 Includes translation table 8 (plant ...
Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for ... SRP RNA and U6 snRNA genes, which are transcribed by RNA polymerase III, one of three major nuclear RNA polymerases in human ... Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the eubacterial ones, the RNA cores ... 17 (9): 1615-8. doi:10.1261/rna.2841511. PMC 3162327. PMID 21803972. Hall TA, Brown JW (March 2002). "Archaeal RNase P has ...
... together with RNA polymerase, is known as the RNA polymerase holoenzyme. Every molecule of RNA polymerase holoenzyme contains ... It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate ... Finally, structural models of RNA polymerase complexes predict that, as the growing RNA product becomes longer than ~15 ... It was previously believed that the RNA polymerase holoenzyme initiates transcription, while the core RNA polymerase alone ...
Sauguet L, Raia P, Henneke G, Delarue M (2016). "Shared active site architecture between archaeal PolD and multi-subunit RNA ... By contrast, RNA polymerases synthesize RNA from ribonucleotides from either RNA or DNA. When synthesizing new DNA, DNA ... Primers consist of RNA or DNA bases (or both). In DNA replication, the first two bases are always RNA, and are synthesized by ... The products of such an experiment are thus amplified PCR products from RNA. Each HIV retrovirus particle contains two RNA ...
The primase used to synthesize a RNA primer varies than in eukaryotes. The primase by archaea is highly derived version of RNA ... "Archaeal genetics - Latest research and news , Nature". www.nature.com. "Archaeal Genetics , Boundless Microbiology". courses. ... Archaeal Genetics is the study of genes that consist of single nucleus-free cells. Archaea have a single, circular chromosomes ... Both DNA and RNA viruses can undergo recombination. When two or more viruses, each containing lethal genomic damage infect the ...
Krol A (August 2002). "Evolutionarily different RNA motifs and RNA-protein complexes to achieve selenoprotein synthesis". ... One archaeal SECIS element, in Methanococcus, is located in the 5' UTR. The SECIS element appears defined by sequence ... RNA. 11 (2): 119-122. doi:10.1261/rna.7185605. PMC 1370700. PMID 15659354. Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, ... "A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs". RNA. 2 (4): 367-379. ...
Werner F (2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. PMID 17697097. doi: ... Lipps, G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends (en inglés). Caister Academic Press. ISBN ... Gaasterland T (1999). "Archaeal genomics". Curr. Opin. Microbiol. 2 (5): 542-7. PMID 10508726. doi:10.1016/S1369-5274(99)00014- ... Allers T, Mevarech M (2005). "Archaeal genetics - the third way". Nat. Rev. Genet. 6 (1): 58-73. PMID 15630422. doi:10.1038/ ...
"Potential key bases of ribosomal RNA to kingdom-specific spectra of antibiotic susceptibility and the possible archaeal origin ... The RNA was produced by a DNA-dependent RNA polymerase using nucleotides similar to those of DNA, with the exception that the ... Both types of RNA molecules (ribosomal and transfer RNAs) played an important role in the catalytic activity of the ribosomes. ... These were assembled from free amino acids by translation of a messenger RNA via a mechanism of ribosomes, transfer RNAs, and a ...
Similarly, archaeal RNase P RNA has been shown to be weakly catalytically active in the absence of its respective protein ... Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores ... "Structural implications of novel diversity in eucaryal RNase P RNA". RNA. 11 (5): 739-751. doi:10.1261/rna.7211705. PMC 1370759 ... The RNA from bacterial RNase P retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. ...
RNA. 11 (7): 1051-63. doi:10.1261/rna.2110805. PMC 1370790. PMID 15987815. Kuratani M, Bessho Y, Nishimoto M, Grosjean H, ... Yokoyama S (January 2008). "Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O- ... O-methylcytidine56 in tRNA The archaeal enzyme specifically catalyses the S-adenosyl-L-methionine dependent 2'-O-ribose ...
This enzyme is part of both the bacterial degradosome and the archaeal exosome, two closely related complexes that recycle RNA ... The 3′ end is also where the poly(A) tail is found on polyadenylated RNAs. Messenger RNA (mRNA) is RNA that has a coding region ... But, for many long noncoding RNAs - a seemingly large group of regulatory RNAs that, for example, includes the RNA Xist, which ... For further information, see RNA and Messenger RNA RNAs are a type of large biological molecules, whose individual building ...
The large subunit is composed of a 5S RNA (120 nucleotides), 28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits ... Archaeal ribosomes share the same general dimensions of bacteria ones, being a 70S ribosome made up from a 50S large subunit, a ... It is largely made up of specialized RNA known as ribosomal RNA (rRNA) as well as dozens of distinct proteins (the exact number ... For each coding triplet (codon) in the messenger RNA, there is a transfer RNA that matches and carries the correct amino acid ...
"The archaeal DnaG protein needs Csl4 for binding to the exosome and enhances its interaction with adenine-rich RNAs". RNA ... Archaeal and eukaryote primases are heterodimeric proteins with one large regulatory and one small catalytic subunit. The RNA ... Bocquier AA, Liu L, Cann IK, Komori K, Kohda D, Ishino Y (March 2001). "Archaeal primase: bridging the gap between RNA and DNA ... Some DnaG-like (bacteria-like; InterPro: IPR020607) primases have been found in archaeal genomes. Eukaryote and archaeal ...
Werner F. (2007). "Structure and function of archaeal RNA polymerases". Mol Microbiol 65 (6): 1395-404. PMID 17697097. doi: ... kar velja predvsem za polimerazo RNA in ribosome.[1] Arheje imajo samo en tip polimeraze RNA, ki je po zgradbi in funkciji ... 2006). "Archaeal habitats-from the extreme to the ordinary". Can J Microbiol 52 (2): 73-116. PMID 16541146. doi:10.1139/w05-147 ... Gaasterland T (1999). "Archaeal genomics". Current Opinion in Microbiology 2 (5): 542-7. PMID 10508726. doi:10.1016/S1369-5274( ...
Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. PMID ... Archaea dipisahkan sebagai domain ketiga karena perbedaan besar dalam struktur RNA ribosomal mereka. Molekul RNA yang telah ... meskipun ada banyak intron pada gen RNA transfer dan RNA ribosomal mereka,[140] dan intron mungkin ada pada beberapa gen ... a b Gaasterland T (1999). "Archaeal genomics". Current Opinion in Microbiology 2 (5): 542-7. PMID 10508726. doi:10.1016/S1369- ...
... archaeal endonuclease for controlled RNA splicing in mammalian cells". FASEB Journal. 27 (9): 3466-3477. doi:10.1096/fj.13- ... As the target RNA molecule and the exogenous RNA molecule are treated with the correct ligase, RNA chimeras form. This results ... method of RNA cleavage and method of RNA cleavage and recombination. In 2003, the RNA cleavage method first exposes the target ... thus this method can also be used for recombining RNA molecules in order to alter RNA function and hence gene expression. ...
The model implies that early RNA world was an aminoacylated RNA world and that proteinogenic amino acids arose because of ... 1] Using insights gleaned from archaeal genomes, Erives elaborated and described a stereochemical model of "proto-anti-codon ... 4] Erives A (2011). "A Model of Proto-Anti-Codon RNA Enzymes Requiring L-Amino Acid Homochirality". Journal of Molecular ... RNAs" (pacRNAs). The pacRNA model ascribes a predetermined combined origin for the universal genetic code (i.e., the codon ...
Protein Data Bank Structure of an archaeal exosome at the RCSB Protein Data Bank Structure of an archaeal exosome bound to RNA ... Substrates of the exosome include messenger RNA, ribosomal RNA, and many species of small RNAs. The exosome has an ... RNA. 13 (7): 1027-35. doi:10.1261/rna.575107. PMC 1894934. PMID 17545563. Carpousis AJ, AJ (2002). "The Escherichia coli RNA ... Although most cells have other enzymes that can degrade RNA, either from the 3' or from the 5' end of the RNA, the exosome ...
Bacterial sRNA involved in nitrogen metabolism: NsiR4 Other archaeal sRNAs: Pyrobaculum asR3 small RNA Archaeal H/ACA sRNA ... sRNA162, sRNA154, sRNA41 are small non-coding RNA (sRNA) identified together with 248 other sRNA candidates by RNA sequencing ... The sRNA overlaps the 5′UTR of the MM2442 mRNA and acts as a cis-encoded antisense RNA, and it also regulates MM2441 expression ... Jäger D, Pernitzsch SR, Richter AS, Backofen R, Sharma CM, Schmitz RA (November 2012). "An archaeal sRNA targeting cis- and ...
DNA repair and RNA synthesis. The archaeal proteins used in these processes are extremely similar to Eukaryotic proteins and so ...
Using ribosomal RNA sequence as an evolutionary measure, my laboratory has reconstructed the phylogeny of both groups, and ... The goal of the research was to explain how the primary cell types (the archaeal, eubacterial, and eukaryotic) evolved from an ... Woese is famous for defining the Archaea (a new domain of life) in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a ... He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and ...
... since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes,[144] and ... with the archaeal RNA polymerase being very close to its equivalent in eukaryotes;[127] while archaeal translation shows signs ... Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. PMID ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ...
"The Yeast tRNA Splicing Endonuclease: A Tetrameric Enzyme with Two Active Site Subunits Homologous to the Archaeal tRNA ... RNA splicing, in molecular biology, is a form of RNA processing in which a newly made precursor messenger RNA (pre-mRNA) ... doi:10.1261/rna.1821809. PMC 2779669. PMID 19861426.. *^ a b Shkreta L, Chabot B (2015). "The RNA Splicing Response to DNA ... They can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA ( ...
DNA synthesis is initiated by the RNA polymerase primase, which makes an RNA primer with a free 3'OH. This primer is attached ... Prokaryotic (archaeal and bacterial) translation differs from eukaryotic translation; however, this section will mostly focus ... Cytosine is a nucleotide that is present in both DNA and RNA. However, uracil is only found in RNA. Therefore, after UTP is ... Other DNA and RNA nucleotide bases that are linked to the ribose sugar via a glycosidic bond are thymine, cytosine and uracil ( ...
3 RNA-Viren *3.1 Doppelsträngige RNA-Viren (dsRNA, double stranded RNA). *3.2 Einzelstrang-RNA-Viren mit negativer Polarität ( ... Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA ... ss(−)RNA: negative single-stranded RNA). *3.3 Einzelstrang-RNA-Viren mit positiver Polarität (ss(+)RNA: positive single ... Einzelstrang-RNA-Viren mit negativer Polarität (ss(−)RNA: negative single-stranded RNA)[Bearbeiten , Quelltext bearbeiten]. ...
... family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51.[5][6] The protein is highly conserved ... messenger RNA. [13]. Breast cancer (progesteron receptor negative). Over-expression. -. messenger RNA. [16]. ... "RadA protein is an archaeal RecA protein homolog that catalyzes DNA strand exchange". Genes & Development. 12 (9): 1248-1253. ...
... since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes,[146] and ... with the archaeal RNA polymerase being very close to its equivalent in eukaryotes;[129] while archaeal translation shows signs ... Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. doi:10.1111/ ... Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ...
Archaeal transcription factor B. Elongation. *bacterial RNA polymerase: rpoB. *eukaryotic RNA polymerase: RNA polymerase II ... the TATA box is found at RNA polymerase II promoter regions, although some in vitro studies have demonstrated that RNA ... "RNA polymerase III accurately initiates transcription from RNA polymerase II promoters in vitro". The Journal of Biological ... TATA-binding protein (TBP) can be recruited in two ways, by SAGA, a cofactor for RNA polymerase II, or by TFIID.[11] When ...
... where it is initiated by recruitment of the RNA-induced transcriptional silencing (RITS) complex to double stranded RNAs ... 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 ... "Huang R C & Bonner J. Histone, a suppressor of chromosomal RNA synthesis. Proc. Nat. Acad. Sci. US 48:1216-22, 1962" (PDF). ...
23, www.pnas.org/cgi/doi/10.1073/pnas.0801980105 Guy L, Ettema TJ (2011). "The archaeal 'TACK' superphylum and the origin of ... Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics". Syst. Appl. Microbiol. 14 (4): 305-310. doi: ... Barns, SM; Fundyga RE; Jeffries MW; Pace NR (1994). "Remarkable archaeal diversity detected in a Yellowstone National Park hot ... Korarchaeota is regarded as a phylum, which itself is part of the archaeal TACK superphylum which encompasses Thaumarchaeota, ...
Aminoacyl tRNA therefore plays an important role in RNA translation, the expression of genes to create proteins. ... Kawahara A, Stainier DY (August 2009). "Noncanonical activity of seryl-transfer RNA synthetase and vascular development". ... some aaRSs have additional RNA binding domains and editing domains[5] that cleave incorrectly paired aminoacyl-tRNA molecules. ... Protein biosynthesis: translation (bacterial, archaeal, eukaryotic). Proteins. Initiation factor. Bacterial. *PIF-1 ...
A possible homolog of Dot1 was found in archaea which shows the ability to methylate archaeal histone-like protein in recent ... RNA polymerase control by chromatin structure. *Histone methylation. ReferencesEdit. *^ a b c d Wood A (2004). " ...
Archaeal transcription factor B. Elongation. *bacterial RNA polymerase: rpoB. *eukaryotic RNA polymerase: RNA polymerase II ... The lac operon: 1: RNA Polymerase, 2: lac repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA.. Top: The ... thus preventing transcription of the genes into messenger RNA. An RNA-binding repressor binds to the mRNA and prevents ... In molecular genetics, a repressor is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by ...
9] Sequences within ribosome binding site affecting messenger RNA translatability and method to direct ribosomes to single ... Protein biosynthesis: translation (bacterial, archaeal, eukaryotic). Proteins. Initiation factor. Bacterial. *PIF-1 ... messenger RNA species. Gene Expression Technology. 185. Academic Press. pp. 103-114.. ...
RNA binding. • mRNA binding. Cellular component. • eukaryotic translation initiation factor 3. • nucleolus. • cell nucleus. • ...
RNA secondary structure unwinding. • viral process. • negative regulation of RNA-directed 5'-3' RNA polymerase activity. • ... ATP-dependent RNA helicase activity. • ATPase activity. • RNA binding. Cellular component. • cytosol. • perinuclear region of ...
Some homologous ATPases function in non-transport-related processes such as translation of RNA and DNA repair. ABC transporters ... ISBN 981-4280-06-2. Classification of ABC transporters in TCDB ABCdb Archaeal and Bacterial ABC Systems database, ABCdb ATP- ... Lage L (2009). "ABC Transporters as Target for RNA Interference-mediated Reversal of Multidrug Resistance". ABC Transporters in ...
Lazcano, A; Guerrero, R; Margulis, L; Oró, J (1988). "The evolutionary transition from RNA to DNA in early cells". Journal of ... "Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life". Proceedings of the National ...
In molecular biology, an amplicon is a piece of DNA or RNA that is the source and/or product of amplification or replication ... which is part of every bacterial and archaeal genome and is highly conserved, bacteria can be taxonomically classified by ... which is used to measure plasma viral load by amplifying a segment of the HIV RNA; and Transcription Mediated Amplification, ...
In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, which with several ... LPSN, list of accepted bacterial and archaeal names. *Cyanobacteria, a phylum of common bacteria but poorly classified at ... Hori, H.; Osawa, S. (1987). "Origin and evolution of organisms as deduced from 5S ribosomal RNA sequences". Molecular Biology ... in archaeal terms, and organisms that live in cooler environments appeared only later.[50] Since the Archaea and Bacteria are ...
Namun, virus RNA memiliki genom RNA ds atau unting tunggal (single stranded, "ss"). Secara umum, setiap molekul asam nukleat ... "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proc. Natl. Acad. Sci. ... namun sejumlah virus memiliki genom RNA (asam ribonukleat).[5] ... "Complete nucleotide-sequence of bacteriophage MS2-RNA - ...
Virus-like RNA-based originEdit. Sex might also have been present even earlier, in the hypothesized RNA world that preceded DNA ... The archaeal host transferred much of its functional genome to the virus during the evolution of cytoplasm, but retained the ... Exposure to conditions that cause RNA damage could have led to blockage of replication and death of these early RNA life forms ... The archaeal products of the revolution maintained recombination machinery that was essentially bacterial, whereas the ...
Karner, M.B.; DeLong, E.F.; Karl, D.M. (2001). "Archaeal dominance in the mesopelagic zone of the Pacific Ocean". Nature. 409 ( ... RNA, proteins and metabolites, is utilised by the bacteria to achieve regulation of gene expression. In bacteria, the principal ... "The archaeal Ced system imports DNA". Proc Natl Acad Sci U S A. 113 (9): 2496-501. Bibcode:2016PNAS..113.2496V. doi:10.1073/ ...
... usually in their DNA or RNA.[54] ...
In a productive infection, the provirus is transcribed into messenger RNA which directly produces new virus, which in turn will ... Not only eukaryotic viruses integrate into the genomes of their hosts; many bacterial and archaeal viruses also employ this ... When a (nonendogenous) retrovirus invades a cell, the RNA of the retrovirus is reverse-transcribed into DNA by reverse ... Krupovic M, Prangishvili D, Hendrix RW, Bamford DH (2011). "Genomics of bacterial and archaeal viruses: dynamics within the ...
... 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 ... A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA[1]) is an adaptor molecule composed of RNA, ... doi:10.4161/rna.27177. PMC 3917982 . PMID 24351723.. *^ a b Shigematsu Megumi; et al. (2014). "Transfer RNA as a source of ... In eukaryotic cells, tRNAs are transcribed by RNA polymerase III as pre-tRNAs in the nucleus.[50] RNA polymerase III recognizes ...
DNA dan RNA) bakteri melayang-layang di daerah sitoplasma yang bernama nukleoid.[17] Salah satu struktur bakteri yang penting ...
Auchtung Thomas A. (2007) Ecology of the hydrothermal candidate archaeal division, Korarchaeota. PhD thesis, Harvard University ... Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics". Syst. Appl. Microbiol. 14 (4): 305-310. PMID ... "Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment". Proc. Natl. Acad. Sci. USA 91 ... "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proc. Natl. Acad. Sci. USA ...
Archaeal transcription factor B. Elongation. *bacterial RNA polymerase: rpoB. *eukaryotic RNA polymerase: RNA polymerase II ... Elp3 has the ability to acetylate all histone subunits and also shows involvement in the RNA polymerase II holoenzyme.[2] ... "Acetylation and Methylation of Histones and Their Possible Role in the Regulation of RNA Synthesis". Proceedings of the ...
Klenk, H. P., Meier, T. D., Durovic, P. and others (1999) RNA polymerase of Aquifex pyrophilus: Implications for the evolution ... Nesbo, C. L., L'Haridon, S., Stetter, K. O., and Doolittle, W. F. (2001) Phylogenetic analyses of two "Archaeal" genes in ...
Protein coding RNAs in mitochondria are spliced and edited using organelle-specific splice and editing sites. Nuclear copies of ... mitochondrion likely included protection of the archaeal host genome from the release of reactive oxygen species (ROS). ROS ... The cDNA hypothesis involves the use of messenger RNA (mRNAs) to transport genes from organelles to the nucleus where they are ... Smith AE, Marcker KA (December 1968). "N-formylmethionyl transfer RNA in mitochondria from yeast and rat liver". Journal of ...
... is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the ... "OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral ... Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant ... Biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of ...
Brown JR, Masuchi Y, Robb FT, Doolittle WF (June 1994). "Evolutionary relationships of bacterial and archaeal glutamine ... These inactivating factors are furthermore regulated by different Non-coding RNAs: The sRNA NsiR4 interacts with the 5'UTR of ...
This work for the first time reports that an archaeal RNA chaperone TRAM0076 globally affects the transcription of methanogenic ... while RNA chaperones interact with various RNAs to prevent the structures that may cause premature transcriptional termination ... This work uncovers an important regulatory element of ancient life in the RNA world. ... Author summary RNAs frequently misfold into stable but biologically inactive structures especially under stresses, ...
Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. Nucleic Acids Res. 2008 Mar; 36(4):1187- ...
An archaeal basal transcription factor containing an iron-sulphur cluster sheds light on the evolution of transcription ... Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure * Y Korkhin ... Archaeal TFEα/β is a hybrid of TFIIE and the RNA polymerase III subcomplex hRPC62/39. ... Thank you for submitting your work entitled "Archaeal TFEα/β is a hybrid of TFIIE and the RNA polymerase III subcomplex hRPC62/ ...
2003 Evolutionary connection between the catalytic subunits of DNA-dependent RNA polymerases and eukaryotic RNA-dependent RNA ... 4. The scattered archaeal eukaryome. *5. The archaeal ancestor of eukaryotes: a complex, ancient group within the TACK ... 2. Burgeoning archaeal diversity, complex archaeal ancestor and origin of eukaryotes from within the archaea. As pointed out ... 2014 The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes. Cold Spring Harb. Perspect. Biol. 6, ...
New insight into RNase P RNA structure from comparative analysis of the archaeal RNA. RNA. 2001 Feb; 7(2):220-32. ... Archaeal" by people in this website by year, and whether "RNA, Archaeal" was a major or minor topic of these publications. ... "RNA, Archaeal" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol. 2011 Feb; 46(1):27-40. ...
The addition of poly(A)-tails to RNA is a phenomenon common to almost all organisms. Not only homopolymeric poly(A)-tails, ... Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases.. Slomovic S1, Portnoy V, Yehudai-Resheff S, ... A possible scenario, illustrating the evolution of RNA polyadenylation and its related functions, is presented, in which PNPase ... Following the appearance of homopolymeric tails, a new role for polyadenylation evolved; RNA stability. This was accomplished ...
DNA & RNA*BLAST (Basic Local Alignment Search Tool). *BLAST (Stand-alone). *E-Utilities ... Relative abundance of archaeal genera (based on 16S rRNA gene) in A. solstitiale ((a) AS_1; (b) AS_2; (c) AS_3) and O. ... Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera).. Ziganshina EE1, ... Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera) ...
The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an ... Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only ... support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. ... Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. ...
Freie Tags]: sm-like proteins, complete genome sequence, laser mass-spectrometry, host factor-i, escherichia-coli, haloferax-volcanii, crystal-structure, hf-i, salmonella-typhimurium, rpos ...
In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported ... In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported ... Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.. Lu, C., ... Probable exosome complex RNA-binding protein 1. C, F, I. 249. Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM ...
Archaeal histones compact DNA into nucleosome-like particles of varying sizes that contort sporadically and reorient DNA ... 2004) Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome Journal of Bacteriology ... induce resetting of ancestral small RNA responses and a genome-wide reduction in heritable small RNA levels. We found that ... 2013) Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs BMC Genomics 14:391. ...
This makes archaeal virus-host systems of particular interest because the hosts generally root near the base of phylogenetic ... In addition, many archaeal viruses have been isolated from extreme environments and present a unique opportunity for ... In addition, many archaeal viruses have been isolated from extreme environments and present a unique opportunity for ... Despite the advantageous position for use in evolutionary studies, little is known about archaeal viruses or how they interact ...
The reversible thermal unfolding of the archaeal histone-like protein Ssh10b from the extremophile Sulfolobus shibatae was ... Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10. Wu X., Oppermann M., Berndt KD., Bergman T., Jörnvall H., ... Structural Basis for the Inhibition of the RNA-Dependent RNA Polymerase from SARS- CoV-2 by Remdesivir ... SARS-CoV-2 RNA viremia is associated with a sepsis-like host response and critical illness in COVID-19 ...
... end of a RNA oligonucleotide in the context of a RNA/DNA heteroduplex (10). Our work with archaeal PriSLX has demonstrated that ... The dual RNA and DNA synthetic capabilities of the archaeal DNA primase have led to the proposal that there may be a sequential ... 2001) Archaeal primase: Bridging the gap between RNA and DNA polymerases. Curr Biol 11:452-456. ... Furthermore, previous studies have demonstrated that the archaeal primases can act as both DNA and RNA polymerases (2, 4, 13). ...
... the archaeal enzyme was found to recognize the acceptor stem rather than the length and secondary structure of the D-stem. ... Based on a comparison of the sequences and secondary structures of archaeal tRNA(Sec) and tRNA(Ser), we introduced mutations ... Structural compensation in an archaeal selenocysteine transfer RNA.. *Anatoli Ioudovitch, Sergey Steinberg ... C-terminal domain of archaeal O-phosphoseryl- tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA ...
Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the ... Archaeal dominance in the mesopelagic zone of the Pacific Ocean Nature. 2001 Jan 25;409(6819):507-10. doi: 10.1038/35054051. ... Here we report a year-long study of the abundance of two specific archaeal groups (pelagic euryarchaeota and pelagic ... Furthermore, our results suggest that the global oceans harbour approximately 1.3 x 10(28) archaeal cells, and 3.1 x 10(28) ...
Archaeal RNA polymerase and transcription regulation. Crit Rev Biochem Mol Biol 46:27-40. doi:10.3109/10409238.2010.538662. ... i) Archaeal sensor domains.In accordance with previous reports (1, 5, 8, 9, 28), archaeal HKs were generally similar to the ... Early analyses of archaeal genomes revealed widespread and abundant TCS systems in the members of the archaeal phyla ... Identification of archaeal HKs and RRs.Sequence analysis of archaeal TCSs was performed essentially as described previously (5 ...
I. K. Blaby, M. Majumder, K. Chatterjee et al., "Pseudouridine formation in archaeal RNAs: the case of Haloferax volcanii," RNA ... "RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP," Genes & Development, vol. 19, no. 10, pp. 1238 ... "Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif," RNA, vol. ... target RNA duplex required for archaeal box C/D sRNA-guided nucleotide 2′-O-methylation," RNA, vol. 13, no. 6, pp. 899-911, ...
The vast majority of archaeal viruses contain dsDNA genomes, whereas viruses with ssDNA genomes are rare, and those with RNA ... Connections between archaeal viruses and other dsDNA viruses.To gain further insight into the relationship between archaeal and ... Modules 1, 2, and 3, archaeal members of the order Caudovirales.Archaeal members of the order Caudovirales form three distinct ... The bipartite network of archaeal viruses. Archaeal genomes are represented as colored circles, and genes are denoted by the ...
Infernal 1.0: Inference of RNA alignments. Bioinformatics 25, 1335-1337 (2009). doi:10.1093/bioinformatics/btp157 pmid:19307242 ... with an equal amount estimated to be oxidized by archaeal methanotrophs (1). All previously described archaeal methane- ... Although bacterial and archaeal genomes lacking ATP synthase genes have been recovered from a contaminated aquifer (7, 24), the ... Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500, 567-570 (2013). doi: ...
The reversible thermal unfolding of the archaeal histone-like protein Ssh10b from the extremophile Sulfolobus shibatae was ... Thermal unfolding of the archaeal DNA and RNA binding protein Ssh10. Wu X., Oppermann M., Berndt KD., Bergman T., Jörnvall H., ... Amino Acid Sequence, Archaeal Proteins, Calorimetry, Differential Scanning, Circular Dichroism, DNA-Binding Proteins, Histones ... The reversible thermal unfolding of the archaeal histone-like protein Ssh10b from the extremophile Sulfolobus shibatae was ...
The core components of archaeal transcription closely resemble those of eukaryotic RNA polymerase II (1). Archaeal promoters ... the archaeal homologue of the α subunit of the RNA polymerase II transcription factor TFIIE, is discerned under conditions of ... Activation of archaeal transcription by recruitment of the TATA-binding protein. Mohamed Ouhammouch, Robert E. Dewhurst, ... Activation of archaeal transcription by recruitment of the TATA-binding protein. Mohamed Ouhammouch, Robert E. Dewhurst, ...
Sogin ML (1989) Evolution of eukaryotic microorganisms and small subunit ribosomal RNAs. Am Zool 29:487-499Google Scholar ... In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme ... Hain J, Reiter W-D, Hüdepohl U, Zillig W (1992) Elements of an archaeal promoter defined by mutational analysis. Nucleic Acids ... Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. ...
Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and ... All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The ... Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. ... putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome ...
Bacterial, archaeal and plant plastid 11 See translation table 1. Alternative yeast nuclear 12 CTG CUG Ser (S) Leu (L) ... In RNA, it is replaced with uracil (U).[16] This is the only difference between the standard RNA codon table and the standard ... Standard RNA codon table[edit]. Amino-acid biochemical properties Nonpolar Polar Basic Acidic ↓ Termination: stop codon * ... RNA codon involved Translation with this code Standard translation Notes Standard 1 Includes translation table 8 (plant ...
The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial ... whereas archaeal hyperthermophiles do not have those proteins (25). In agreement with this trend, two predicted marine archaeal ... Proteins, RNA genes, and motif search.In-depth sequence analysis was based primarily on the use of the PSI-BLAST program (1) ... Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. Proc. Natl. Acad. Sci. USA91:1609 ...
With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in ... With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in ... 2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590 ... Archaeal Community Composition Varies According to the Used Primer Pairs Whereas Universal Primers Fail to Detect the Archaeal ...
... subunit L from archaeal RNA polymerase [PMID: 12694606] and subunit Rpc19 from RNA polymerases I and II in Saccharomyces ... Short name: RNA_pol_Rpb11_13-16kDa_CS Description. DNA-directed RNA polymerases EC:2.7.7.6 (also known as DNA-dependent RNA ... Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: *RNA polymerase I: ... Yeast RNA polymerase II subunit RPB11 is related to a subunit shared by RNA polymerase I and III.. Gene Expr. 3 77-82 1993 ...
Archaeal chromatin and transcription.. Mol. Microbiol. 48 587-98 2003. Pati UK, Weissman SM. The amino acid sequence of the ... Short name: DNA-dir_RNA_pol_30-40kDasu_CS Description. DNA-directed RNA polymerases EC:2.7.7.6 (also known as DNA-dependent RNA ... Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: *RNA polymerase I: ... RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The ...
Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Molecular Microbiology. 65 (6): 1395-404. doi: ... RNA polymerase I. II. III. IV. V. ssRNAP POLRMT. Primase 1. 2. PrimPol. RNA-dependent RNA polymerase. Polyadenylation. PAP. ... messenger RNA) (mRNA); or non-coding: so-called "RNA genes". At least four functional types of RNA genes exist: *transfer RNA ( ... RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol. RNA polymerase IV and V ...
  • All three domains of life use enzymes called RNA polymerases (RNAPs) for transcription, and all RNAPs are thought to have originated from a common ancestor. (elifesciences.org)
  • DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. (royalsocietypublishing.org)
  • Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases. (nih.gov)
  • All of the putative regulators of transcription that have been characterized in vitro , the metal-dependent repressor 1 (MDR1) from Archaeoglobus fulgidus ( 8 ), as well as the homologues LrpA from Pyrococcus furiosus ( 9 , 10 ), Lrs-14 from Sulfolobus solfataricus ( 11 ), and Ptr1 from Methanococcus jannaschii (unpublished results), have only been shown to repress transcription by their cognate RNA polymerases. (pnas.org)
  • DNA-directed RNA polymerases EC:2.7.7.6 (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. (ebi.ac.uk)
  • In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. (ebi.ac.uk)
  • Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. (ebi.ac.uk)
  • Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. (ebi.ac.uk)
  • Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. (ebi.ac.uk)
  • Small subunits of about 13 to 16 kDa are found in all three types of eukaryotic polymerases and in archaeal polymerase. (ebi.ac.uk)
  • Dequard-Chablat M, Riva M, Carles C, Sentenac A. RPC19, the gene for a subunit common to yeast RNA polymerases A (I) and C (III). (ebi.ac.uk)
  • Saccharomyces cerevisiae RPC5 subunit (or RPC40) from RNA polymerases I and III. (ebi.ac.uk)
  • [6] Eukaryotic and archaeal RNA polymerases have a similar core structure and work in a similar manner, although they have many extra subunits. (wikipedia.org)
  • 2 RNA polymerases and the transcription cycle. (wiley.com)
  • 2.2 Core RNA polymerases. (wiley.com)
  • 2.2.2 Eukaryotic and archaeal core polymerases. (wiley.com)
  • Bacterial RNA polymerases are composed of multiple subunits. (conservapedia.com)
  • Dissociation of the RNA destabilizes RNA polymerases and transcription terminates. (conservapedia.com)
  • First, rather than having a single RNA polymerase, eukaryotes have three different RNA polymerases, each of which transcribes a different set of genes. (conservapedia.com)
  • The eukaryotic RNA polymerases consist of between eight and fourteen subunits, with two of them corresponding to the β and β′ subunits of prokaryotic RNA polymerases. (conservapedia.com)
  • A single RNA polymerase in bacteria and archaea-and only three different polymerases in eukaryotes-program an amazing variety of developmental pathways. (nih.gov)
  • Biochemical and structural studies reveal significant functional similarities among bacterial, archaeal, and eukaryotic RNA polymerases. (nih.gov)
  • Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. (abcam.com)
  • This subunit is shared by the other two DNA-directed RNA polymerases. (genecards.org)
  • TFIIS-like transcript cleavage factors enhance the processivity and fidelity of archaeal and eukaryotic RNA polymerases. (montana.edu)
  • RNA polymerases (RNAP) are complex enzymes that contain a large catalytic core conserved from prokaryotes to human. (trieste.it)
  • In addition to this conserved unit, archaeal and eukaryotic polymerases also include a number of smaller polypeptides, most of which are absolutely required for transcription. (trieste.it)
  • The availability of in vitro assembly systems to produce recombinant archaeal RNA polymerases (RNAPs) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying RNAP function. (pubmedcentralcanada.ca)
  • RNA polymerases (RNAPs) are key enzymes of the cellular gene expression machineries of all organisms. (pubmedcentralcanada.ca)
  • RNAPs (RNA polymerases) are complex molecular machines containing structural domains that co-ordinate the movement of nucleic acid and nucleotide substrates through the catalytic site. (biochemsoctrans.org)
  • Archaea SRP is composed of an SRP RNA molecule and two bound proteins named SRP19 and SRP54. (hindawi.com)
  • This flexibility allows the information in the genomes of Archaea to be easily accessed, so, unlike in eukaryotes, archaeal cells may not need other proteins to release the DNA from the histones. (elifesciences.org)
  • Archaeal initiation factors are proteins that are used during the translation step of protein synthesis in archaea. (wikipedia.org)
  • The principal functions these proteins perform include ribosome RNA/mRNA recognition, delivery of the initiator Met-tRNAiMet, methionine bound tRNAi, to the 40s ribosome, and proofreading of the initiation complex. (wikipedia.org)
  • Bound proteins were again eluted with a linear KCl gradient, and RNA polymerase-containing fractions were concentrated on Mono Q. Final purification was achieved by gel filtration on Superdex 200, preequilibrated with TMK buffer containing 300 mM KCl. (pnas.org)
  • [1] [2] The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes , it is messenger RNA that directs protein biosynthesis . (wikipedia.org)
  • Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. (asm.org)
  • Products of RNAP include: Messenger RNA (mRNA)-template for the synthesis of proteins by ribosomes. (wikipedia.org)
  • Amino acid substitution mutants of SisCsx1 were obtained, and characterization of these mutant proteins showed that the CARF domain of the enzyme is responsible for binding to 3'-tetra-rA and the ligand binding strongly activates RNA cleavage by the HEPN domain. (bireme.br)
  • Since RNA polyadenylation is an important step in RNA decay in prokaryotes, and poly(A) RNAs can activate CARF domain proteins, the poly(A) RNA may function as an important signal in the cellular responses to viral infection and environmental stimuli, leading to degradation of both viral and host transcripts and eventually to cell dormancy or cell death. (bireme.br)
  • The archaeal part of the reverse gyrase tree is congruent with recent phylogenies of the archaeal domain based on ribosomal proteins or RNA polymerase subunits. (mendeley.com)
  • Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. (uni-ulm.de)
  • The Alba superfamily proteins appear to have originated as RNA-binding proteins which formed various ribonucleoprotein complexes, probably including RNase P. It was recruited as a chromosomal protein possibly only within the crenarchaeal lineage. (pubmedcentralcanada.ca)
  • Messenger RNAs are required for converting the genetic information in the DNA into functional proteins. (els.net)
  • Most of the proteins interact with multiple RNA elements, often from different domains. (embl-heidelberg.de)
  • Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. (embl-heidelberg.de)
  • While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. (embl-heidelberg.de)
  • The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. (embl.de)
  • The growing awareness-driven largely by the application of high-throughput sequencing technologies to the analysis of RNA (RNA-seq)-that bacteria transcribe much more RNA than is required for direct translation into proteins is likely to be important in this context. (asmscience.org)
  • RNA harboring the spacer sequence helps Cas (CRISPR-associated) proteins recognize and cut foreign pathogenic DNA. (wikipedia.org)
  • Other RNA-guided Cas proteins cut foreign RNA. (wikipedia.org)
  • We use protein crystallography to determine the atomic structure of eukaryotic and archaeal proteins involved in these processes. (trieste.it)
  • The influenza virion contains segments of viral RNA bound to four different proteins. (virology.ws)
  • a modest stimulatory effect of TFE, the archaeal homologue of the α subunit of the RNA polymerase II transcription factor TFIIE, is discerned under conditions of suboptimal TBP-TATA box interaction ( 4 , 5 ). (pnas.org)
  • Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [ PMID: 3052291 ]. (ebi.ac.uk)
  • Yeast RNA polymerase II subunit RPB11 is related to a subunit shared by RNA polymerase I and III. (ebi.ac.uk)
  • S. cerevisiae RPB3 subunit from RNA polymerase II. (ebi.ac.uk)
  • Schizosaccharomyces pombe rpb3 subunit from RNA polymerase II. (ebi.ac.uk)
  • Conjugation stage-specific protein cnjC from Tetrahymena thermophila, which may be a stage-specific RNA polymerase subunit. (ebi.ac.uk)
  • Archaebacterial RNA polymerase subunit D (gene rpoD). (ebi.ac.uk)
  • The amino acid sequence of the human RNA polymerase II 33-kDa subunit hRPB 33 is highly conserved among eukaryotes. (ebi.ac.uk)
  • Azuma Y, Yamagishi M, Ishihama A. Subunits of the Schizosaccharomyces pombe RNA polymerase II: enzyme purification and structure of the subunit 3 gene. (ebi.ac.uk)
  • Functional interaction of the subunit 3 of RNA polymerase II (RPB3) with transcription factor-4 (ATF4). (ebi.ac.uk)
  • Depending on the organism, a RNA polymerase can be a protein complex (multi-subunit RNAP) or only consist of one subunit (single-subunit SNAP, ssSNAP), each representing an independent lineage. (wikipedia.org)
  • RNA polymerase "core" from E. coli consists of five subunits: two alpha (α) subunits of 36 kDa , a beta (β) subunit of 150 kDa, a beta prime subunit (β′) of 155 kDa, and a small omega (ω) subunit. (wikipedia.org)
  • Taken together with the small subunit rRNA abundance data, this suggests that a large part of the archaeal population is made up of methanogens. (asm.org)
  • DNA-directed RNA polymerase II subunit RPB1 is an enzyme that in humans is encoded by the POLR2A gene. (wikiversity.org)
  • RPB1 is the largest subunit of RNA polymerase II. (wikiversity.org)
  • RPB2 (POLR2B) is the second largest subunit which in combination with at least two other polymerase subunits forms a structure within the polymerase that maintains contact in the active site of the enzyme between the DNA template and the newly synthesized RNA. (wikiversity.org)
  • RNA polymerase II subunit B4 (RPB4) encoded by the POLR2D gene [7] is the fourth largest subunit and may have a stress protective role. (wikiversity.org)
  • Two molecules of this subunit are present in each RNA polymerase II. (wikiversity.org)
  • We demonstrated how the binding of a small T4 protein structurally remodels a portion of the specificity subunit (sigma) of RNA polymerase. (nih.gov)
  • Belongs to the archaeal rpoH/eukaryotic RPB5 RNA polymerase subunit family. (abcam.com)
  • POLR2K (RNA Polymerase II Subunit K) is a Protein Coding gene. (genecards.org)
  • Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA i Met ) and mRNA bound to the small ribosomal subunit. (sdsc.edu)
  • This gene encodes a small essential subunit of RNA polymerase III, the polymerase responsible for synthesizing transfer and small ribosomal RNAs in eukaryotes. (genecards.org)
  • The carboxy-terminal domain of this subunit shares a high degree of sequence similarity to the carboxy-terminal domain of an RNA polymerase II elongation factor. (genecards.org)
  • The [alpha] subunit of ammonia monooxygenase (amoA), the enzyme which catalyses the first step in the ammonia oxidation reaction, has been used by numerous authors as a functional gene marker to detect the bacterial and archaeal ammonia-oxidising populations (for review see Junier et al. (thefreelibrary.com)
  • Bacterial RNase P contains one RNA (RPR) and one protein (RPP) subunit. (diva-portal.org)
  • The RNA subunit is the catalytic subunit that in vitro cleaves its substrate with and without the protein subunit. (diva-portal.org)
  • RNase P with its catalytic RNA subunit is involved in the processing of a number of RNA precursors with different structures. (diva-portal.org)
  • Our results suggest that archaeal TFEα/β is likely to represent the evolutionary ancestor of TFIIE-like factors in extant eukaryotes. (elifesciences.org)
  • But several recent discoveries suggest that the origin of the eukaryotes lies within the archaeal domain. (elifesciences.org)
  • Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier? (royalsocietypublishing.org)
  • The discovery of this 'dispersed eukaryome' implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. (royalsocietypublishing.org)
  • The 'standard model' of molecular evolution, derived primarily from the classic phylogenetic analysis of 16S RNA by Woese and co-workers and supported by subsequent phylogenetic analyses of universal genes, identifies eukaryotes as the sister group of archaea, to the exclusion of bacteria [ 13 - 16 ]. (royalsocietypublishing.org)
  • The 5e motif, which in eukaryotes binds a 72 kilodalton protein, is preserved in most archaea SRP RNAs despite the lack of an archaea SRP72 homolog. (hindawi.com)
  • Archaeal histones may reflect early versions of histones in eukaryotes, and can be used to understand how DNA packing has evolved. (elifesciences.org)
  • Despite the advantageous position for use in evolutionary studies, little is known about archaeal viruses or how they interact with their hosts, compared to viruses of bacteria and eukaryotes. (frontiersin.org)
  • RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. (semanticscholar.org)
  • Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA. (wikipedia.org)
  • Eukaryotes have multiple types of nuclear RNAP, each responsible for synthesis of a distinct subset of RNA: RNA polymerase I synthesizes a pre-rRNA 45S (35S in yeast), which matures and will form the major RNA sections of the ribosome. (wikipedia.org)
  • Members of the conserved Argonaute protein family use small RNA guides to find their mRNA targets to regulate gene expression and suppress mobile genetic elements in eukaryotes 1,2 . (nature.com)
  • In eukaryotes , there is an additional step RNA processing (splicing), which intervenes. (conservapedia.com)
  • This gene encodes one of the smallest subunits of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. (genecards.org)
  • Much of this work was guided by the key concept that the archaeal basal transcriptional machinery [ 5 ] closely mirrors the core components of the eukaryotic RNA polymerase II (RNAPII) system [ 6 , 7 ], which is responsible for the highly regulated expression of all protein-encoding genes in eukaryotes. (pubmedcentralcanada.ca)
  • Together with high‐throughput biochemical characterization of dmDis3l2 and bacterial RN ase R, our results imply a conserved molecular function of RN ase II /R enzymes as "readers" of destabilizing posttranscriptional marks-uridylation in eukaryotes and adenylation in prokaryotes-that play important roles in RNA surveillance. (embopress.org)
  • Polynucleotide phosphorylase (PNPase) and the archaeal exosome, which bear strong similarities to one another, both functionally and structurally, were found to polymerize the heteropolymeric tails in bacteria, spinach chloroplasts, and archaea. (nih.gov)
  • Comparative analyses of the archaea genomes and their SRP component sequences, combined with structural and biochemical data, support a prominent role of the SRP RNA in the assembly and function of the archaea SRP. (hindawi.com)
  • The SRP RNA is typically composed of about 300 nucleotide residues and forms a complex with an extraordinarily conserved protein named SRP54 in archaea and eukarya or Ffh (fifty-four homolog) in the bacteria. (hindawi.com)
  • Polypeptides which are homologous to the eukaryal SRP9/14 and SRP68/72 heterodimers have not been found in the archaea genome sequences giving rise to an archaea SRP which is dominated by RNA [ 3 , 4 ]. (hindawi.com)
  • Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the subsurface ocean. (nih.gov)
  • RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing," Nucleic Acids Research , vol. 30, no. 4, pp. 921-930, 2002. (hindawi.com)
  • These viruses have been largely isolated from hyperhalophilic archaea (order Halobacteriales ), although one tailed archaeal virus has been isolated from a methanogen host (order Methanobacteriales ) ( 5 - 7 ). (asm.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)
  • In archaea, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 12 polypeptides. (ebi.ac.uk)
  • Bacteria and archaea only have one RNA polymerase. (wikipedia.org)
  • As arqueas ( Archaea , do grego ἀρχαῖα 'os antigos') son un grupo de microorganismos unicelulares de morfoloxía procariótica (sen núcleo nin, en xeral, orgánulos membranosos internos), que forman un dos tres grandes dominios dos seres vivos, e que son diferentes das bacterias . (wikipedia.org)
  • As Archaea divídense en cinco filos recoñecidos, pero pénsase que poden haber máis. (wikipedia.org)
  • Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. (sciencemag.org)
  • Bacteria and archaea have evolved RNA-mediated adaptive defense systems called clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) that protect organisms from invading viruses and plasmids ( 1 - 3 ). (sciencemag.org)
  • These studies find connections within the complex microbiome and external variables, often relying on sequencing the 16S ribosomal RNA genes to identify which bacteria and archaea are present. (asm.org)
  • The main goal of this work was to characterize the gut microbiota in larvae of several Coleoptera species using sequencing of the bacterial and archaeal 16S rRNA genes and fungal internal transcribed spacer (ITS) region. (nih.gov)
  • RNA polymerase I synthesizes a pre- rRNA 45 S (35S in yeast ), which matures and will form the major RNA sections of the ribosome. (wikipedia.org)
  • RNA polymerase III synthesizes tRNAs, rRNA 5S and other small RNAs found in the nucleus and cytosol . (wikipedia.org)
  • The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation. (wikipedia.org)
  • Arheje sta leta 1977 opredelila Carl Woese in George Fox na osnovi ribosomske RNA (rRNA), ki se v mnogih značilnostih razlikuje od bakterijske rRNA. (wikipedia.org)
  • RNA polymerase I transcribes three types of rRNA (the 18S, 5.8S, and 28S species), RNA polymerase II transcribes mRNA, and RNA polymerase III transcribes tRNA and the smallest rRNA (the 5S species). (conservapedia.com)
  • BACKGROUND: Ribosomal protein S15 is a primary RNA-binding protein that binds to the central domain of 16S rRNA. (embl-heidelberg.de)
  • The binding sites for S15 on both mRNA and rRNA have beennarrowed down to less than a hundred nucleotides each, making the protein anattractive candidate for the study of protein-RNA interactions. (embl-heidelberg.de)
  • Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. (genecards.org)
  • These studies include examining the biological role of polyadenylation in bacteria, determining the multiple pathways by which primary transfer RNA (tRNA) transcripts are processed into their mature forms, outlining the enzymatic steps in converting primary 30S ribosomal RNA (rRNA) transcripts into their mature 16S, 23S and 5S components, examining the mechanisms of mRNA decay and processing, and understanding how small regulatory RNAs (sRNAs) help control gene expression. (uga.edu)
  • Comparative analysis of sequences from a clone library made with genomic DNA from the SMTZ and primers specific for archaeal 16S rRNA genes revealed members of 5 different lineages, including unusual crenarchaeal ribosomal RNA sequences. (int-res.com)
  • Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete archaeal genomes, as well as unfinished genomes available from metagenomic data. (asm.org)
  • Most archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. (asm.org)
  • The complete list of histidine kinases and response regulators encoded in the analyzed archaeal genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/TCSarchaea.html . (asm.org)
  • Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes ," Journal of Molecular Biology , vol. 297, no. 4, pp. 895-906, 2000. (hindawi.com)
  • Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. (asm.org)
  • We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. (asm.org)
  • Analysis of 5,740 protein sequences from 116 genomes allowed dissection of the archaeal virus network and showed that most groups of archaeal viruses are evolutionarily connected to capsidless mobile genetic elements, including various plasmids and transposons. (asm.org)
  • used metagenomics to assemble two nearly complete archaeal genomes from deep groundwater methanogens (see the Perspective by Lloyd). (sciencemag.org)
  • We performed metagenomic sequencing of a deep aquifer, recovering two near-complete genomes belonging to the archaeal phylum Bathyarchaeota (formerly known as the Miscellaneous Crenarchaeotal Group). (sciencemag.org)
  • Recent advances in metagenomic techniques are allowing population genomes to be recovered en masse across many previously uncultivated archaeal lineages and from increasingly complex environments ( 6 , 7 ). (sciencemag.org)
  • On the other hand, all archaeal genomes sequenced to date encode potential transcription regulators of bacterial type, underscoring the chimeric nature of the archaeal transcription apparatus ( 6 , 7 ). (pnas.org)
  • Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. (mdpi.com)
  • These systems are widely spread in bacterial and archaeal genomes. (mdpi.com)
  • Finally, several genes of archaeal origin located in proximity to the reverse gyrase gene in bacterial genomes have bacterial homologues mostly in thermophiles or hyperthermophiles, raising the possibility that they were co-transferred with the reverse gyrase gene. (mendeley.com)
  • The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. (biomedcentral.com)
  • In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation. (biomedcentral.com)
  • At the time of this writing nearly 400 complete prokaryotic genomes, including 28 archaeal ones, have been deposited in the GenBank database. (biomedcentral.com)
  • Pus10 orthologs are found in nearly all sequenced archaeal and most eukaryal genomes, but not in yeast and bacteria. (siu.edu)
  • 2009. De novo computational prediction of non-coding RNA genes in prokaryotic genomes. (uga.edu)
  • 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)
  • The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. (ebi.ac.uk)
  • [2] Eukaryotic and archaeal RNAPs have more subunits than bacterial ones do, and are controlled differently. (wikipedia.org)
  • RNA polymerase II of Saccharomyces cerevisiae consisting of all 12 subunits. (wikiversity.org)
  • In combination with several other polymerase subunits, it forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA. (wikiversity.org)
  • We have found that BvgA and two subunits of RNA polymerase occupy the same region of DNA. (nih.gov)
  • Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes consisting of at least 13, 12 and 17 subunits, respectively. (genecards.org)
  • We investigate the 3D structures of various subunits in order to learn more about RNA polymerase architecture. (trieste.it)
  • Archaeal RNAP subunits display extensive sequence homology to the eukaryotic subunits, and high-resolution structures of archaeal RNAPs are directly comparable to eukaryotic RNAPII [ 8 , 9 ]. (pubmedcentralcanada.ca)
  • Transcription initiation of archaeal RNA polymerase (RNAP) and eukaryotic RNAPII is assisted by conserved basal transcription factors. (elifesciences.org)
  • Making these molecules involves first copying these instructions into a molecule of RNA via a process called transcription. (elifesciences.org)
  • This discovery provides new insights in the evolutionary history of both the archaeal and the eukaryotic transcription machineries. (elifesciences.org)
  • The conserved core of the archaeal and eukaryotic transcription machineries encompasses a highly complex multisubunit RNAP as well as evolutionary conserved transcription factors that govern its activities through the transcription cycle. (elifesciences.org)
  • Archaeal RNA polymerase and transcription regulation. (ucdenver.edu)
  • The prevailing mechanism of archaeal TCS signaling appears to involve various protein-protein interactions rather than direct transcription regulation. (asm.org)
  • In contrast, this archaeon's RNA polymerase and core transcription factors are of eukaryotic type. (pnas.org)
  • The core components of archaeal transcription closely resemble those of eukaryotic RNA polymerase II ( 1 ). (pnas.org)
  • the TFIIB-related transcription factor B (TFB) binds to the TBP-DNA complex and directs a eukaryotic-type RNA polymerase (RNAP) to specifically initiate transcription at an initiator sequence located some 25 bp downstream of the TATA element. (pnas.org)
  • This purification yielded the highly purified RNA polymerase (see Fig. 5, which is published as supporting information on the PNAS web site, www.pnas.org ) used for promoter-specific in vitro transcription. (pnas.org)
  • Archaeal chromatin and transcription. (ebi.ac.uk)
  • RNAP locally opens the double-stranded DNA (usually about four turns of the double helix) so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA , a process called transcription . (wikipedia.org)
  • RNAP not only initiates RNA transcription, it also guides the nucleotides into position, facilitates attachment and elongation, has intrinsic proofreading and replacement capabilities, and termination recognition capability. (wikipedia.org)
  • The 2006 Nobel Prize in Chemistry was awarded to Roger D. Kornberg for creating detailed molecular images of RNA polymerase during various stages of the transcription process. (wikipedia.org)
  • DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. (uniprot.org)
  • The eukaryotic core RNA polymerase II was first purified using transcription assays. (wikiversity.org)
  • The synthesis of a single-stranded RNA molecule using DNA as a template is referred to as transcription. (conservapedia.com)
  • They are synthesised by the enzyme RNA polymerase, which recognises specific sequences in the DNA (promoters) to initiate the process called transcription. (els.net)
  • In all organisms, RNA polymerase, a complex protein machine that transcribes genomic DNA into RNA, performs transcription. (nih.gov)
  • Pol II is the central component of the basal RNA polymerase II transcription machinery. (abcam.com)
  • Among its related pathways are RNA Polymerase III Transcription Initiation and Pyrimidine metabolism (KEGG) . (genecards.org)
  • In the expression and interference phases, transcription of the repeat-spacer element into precursor CRISPR RNA (pre-crRNA) molecules followed by enzymatic cleavage yields the short crRNAs that can pair with complementary protospacer sequences of invading viral or plasmid targets ( 4 - 11 ). (sciencemag.org)
  • The archaeal transcription apparatus is chimeric: its core components (RNA polymerase and basal factors) closely resemble those of eukaryotic RNA polymerase II, but the putative archaeal transcriptional regulators are overwhelmingly of bacterial type. (umd.edu)
  • Upon transcription, RNA species are subjected to a plethora of posttranscriptional modifications that regulate RNA maturation, function, and stability (Machnicka et al , 2013 ). (embopress.org)
  • A possible scenario, illustrating the evolution of RNA polyadenylation and its related functions, is presented, in which PNPase (or the archaeal exosome) was the first polyadenylating enzyme to evolve and the heteropolymeric tails that it produced, functioned in a polyadenylation-stimulated RNA degradation pathway. (nih.gov)
  • The exosome complex is an essential RNA 3'-end processing and degradation machinery. (rcsb.org)
  • mRNA decay in bacteria is carried out by a series of nucleases that can initiate the degradation of the RNA molecule by cleaving at internal sites or by removing one nucleotide at a time from either the 5′ or 3′ terminus. (els.net)
  • RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. (ebi.ac.uk)
  • This unique molecular structure called cap0 protects capped RNAs from 5′ to 3′ exonuclease cleavage and is essential for the regulation of gene expression, including splicing, nuclear export of mRNA, and translation initiation [ 3 - 5 ]. (royalsocietypublishing.org)
  • Not only are archaeal TIF numbers between that of bacteria and eukaryote numbers, but archaeal initiation factors are seen to have both traits of eukaryotic and prokaryotic initiation factors. (wikipedia.org)
  • Recently, it has been suggested that several lateral gene transfers of archaeal GSI genes to bacteria may have occurred. (springer.com)
  • In bacteria, endoribonuclease E, a key enzyme involved in RNA decay and processing, organizes a protein complex called degradosome. (genome.jp)
  • [5] Archaeal cells have unique properties separating them from the other two domains of life, Bacteria and Eukarya . (wikipedia.org)
  • This coincides with the presence of Ψ54 in most archaeal tRNAs and some animal tRNAs, but its absence from yeast and bacteria. (siu.edu)
  • 2012. RNAsnap™: a rapid, quantitative and inexpensive method for isolating total RNA from bacteria. (uga.edu)
  • [ 13 ] Brock iniciárase en 1969 no campo da bioloxía dos hipertermófilos co descubrimento de Thermus aquaticus , que non é unha arquea senón unha bacteria. (wikipedia.org)
  • However, "methanogens are considered as keystone species in complex microbiomes," says Moissl-Eichinger, so some archaeal species "could be involved in bacteria-driven pathogenic processes. (asm.org)
  • doing so would require more work to correlate disease patterns with the presence and/or abundance of archaeal species, similar to those bacteria-based microbiome studies have found. (asm.org)
  • Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. (uniprot.org)
  • Here, we present cryo-EM structures of the full archaeal 30S initiation complex showing two conformational states of the TC. (sdsc.edu)
  • The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. (mdpi.com)
  • In Escherichia coli , this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. (embl-heidelberg.de)
  • About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. (embl-heidelberg.de)
  • In vitro translation analysis using chimaeric constructs containing the stem-loop sequence in their Pf-Thy1 RNA and a luciferase reporter gene indicated that the stem-loop structure acted as an inhibitory regulator of translation by preventing the binding of its Shine-Dalgarno-like sequence by positioning it in the stem region. (elsevier.com)
  • Mammalian RPB3 (or RPB33) (gene POLR2C) from RNA polymerase II. (ebi.ac.uk)
  • In addition to providing direct evidence for such an assembly in eukaryotic snRNPs, this structure (i) shows that SmAP homodimers are structurally similar to human Sm heterodimers, (ii) supports a gene duplication model of Sm protein evolution, and (iii) offers a model of SmAP bound to single-stranded RNA (ssRNA) that explains Sm binding-site specificity. (rcsb.org)
  • 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)
  • Previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (LGT) to the ancestors of the two bacterial hyperthermophilic phyla, Thermotogales and Aquificales. (mendeley.com)
  • RNA polymerase II is a specific RNA polymerase that usually is the key part of the catalysis process that produces each RNA from the DNA gene or isoform to ultimately make a protein. (wikiversity.org)
  • GO annotations related to this gene include DNA-directed 5-3 RNA polymerase activity and RNA polymerase I activity . (genecards.org)
  • Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA polymerase III activity . (genecards.org)
  • We are using a combination of genetic, biochemical, bioinformatics and RNA-seq approaches to analyze the post-transcriptional control of gene expression in the model prokaryote, Escherichia coli. (uga.edu)
  • Co-evolution of the archaeal tRNA-dependent amidotransferase GatCAB with tRNA(Asn). (semanticscholar.org)
  • Both archaeal TFEβ and hRPC39 harbour a cubane 4Fe-4S cluster, which is crucial for heterodimerization of TFEα/β and its engagement with the RNAP clamp. (elifesciences.org)
  • RNA polymerase ( ribonucleic acid polymerase ), abbreviated RNAP or RNApol , officially DNA-directed RNA polymerase , is an enzyme that synthesizes RNA from a DNA template. (wikipedia.org)
  • Each RNAP is transcribing an RNA strand , which can be seen branching off from the DNA. (wikipedia.org)
  • RNAP will preferentially release its RNA transcript at specific DNA sequences encoded at the end of genes, which are known as terminators. (wikipedia.org)
  • We have therefore implemented a robotic high-throughput structure-function experimental system based on the automatic generation and assaying of hundreds of site-directed mutants in the archaeal RNAP from Methanocaldococcus jannaschii . (biochemsoctrans.org)
  • In the majority of RNAP X-ray structures from bacterial, archaeal and eukaryotic sources, the bridge-helix takes up a more or less straight α-helical conformation and thus appears as a rod-like structure next to the catalytic site [ 8 - 16 ]. (biochemsoctrans.org)
  • Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. (harvard.edu)
  • This makes archaeal virus-host systems of particular interest because the hosts generally root near the base of phylogenetic trees, while some of the viruses have clear structural similarities to those that infect prokaryotic and eukaryotic cells. (frontiersin.org)
  • Structural compensation in an archaeal selenocysteine transfer RNA. (semanticscholar.org)
  • Structural basis of RNA-dependent recruitment of glutamine to the genetic code. (semanticscholar.org)
  • Structural basis for site-specific ribose methylation by box C/D RNA protein complexes," Nature , vol. 469, no. 7331, pp. 559-563, 2011. (hindawi.com)
  • 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)
  • While synthetic bacterial AHLs did not induce persistence, this is potentially due to structural differences between bacterial and archaeal signals, and does not discount a quorum sensing component in haloarchaeal persister formation. (frontiersin.org)
  • X-ray images of bacterial, archaeal and eukaryotic RNAPs have provided a wealth of structural detail over the last decade, but many mechanistic features can only be derived indirectly from such structures. (biochemsoctrans.org)
  • The reversible thermal unfolding of the archaeal histone-like protein Ssh10b from the extremophile Sulfolobus shibatae was studied using differential scanning calorimetry and circular dichroism spectroscopy. (ox.ac.uk)
  • Identification of novel non-coding RNAs as potential antisense regulators in the archaeon Sulfolobus solfataricus," Molecular Microbiology , vol. 55, no. 2, pp. 469-481, 2005. (hindawi.com)
  • The SRP RNA of A. ambivalens depicted a size of about 309 nucleotides like the SRP RNA of the related organism Sulfolobus acidocaldarius . (portlandpress.com)
  • Sulfolobus solfataricus TFS1 functions as a bona fide cleavage factor, while the paralogous TFS4 evolved into a potent RNA polymerase inhibitor. (montana.edu)
  • En 1970, Thomas D. Brock, da Universidade de Wisconsin, descubriu a Thermoplasma , unha arquea termoacidófila e en 1972 a Sulfolobus , unha hipertermófila . (wikipedia.org)
  • 1.2.1 RNA biogenesis. (wiley.com)
  • Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity. (uni-ulm.de)
  • The pronounced electrostatic asymmetry of the SmAP surface imparts directionality to putative SmAP-RNA interactions. (rcsb.org)
  • The signal-recognition particle (SRP) of one of the most acidophilic and hyperthermophilic archaeal cells, Acidianus ambivalens , and its putative receptor component, FtsY (prokaryotic SRP receptor), were investigated in detail. (portlandpress.com)
  • Regulated by the binding and hydrolysis of guanosine triphosphates, the RNA-bound SRP54 protein transiently associates not only with the hydrophobic signal sequence as it emerges from the ribosomal exit tunnel, but also interacts with the membrane-associated SRP receptor (FtsY). (hindawi.com)
  • Using a stem-loop RNA oligonucleotide (19-mer) containing an AUG sequence in the loop region as a probe, we screened the protein library from a hyperthermophilic archaeon, Pyrococcus furiosus, and found that a flavin-dependent thymidylate synthase, Pf-Thy1 (Pyrococcus furiosus thymidylate synthase 1), possessed RNA-binding activity. (elsevier.com)
  • With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called "universal" approach) to 81 RSVs in a representative sample set. (frontiersin.org)
  • The RNA synthesis process continues until a termination sequence is reached. (ebi.ac.uk)
  • Accurate multiple sequence‐structure alignment of RNA sequences using combinatorial optimization. (currentprotocols.com)
  • These interactions result in the formation of a remodeled specificity factor for RNA polymerase that recognizes a new promoter sequence. (nih.gov)
  • The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue. (siu.edu)
  • Here, we describe the genome sequence of strain DSM639, which has been used for many seminal studies on archaeal and crenarchaeal biology. (psu.edu)
  • The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. (sciencemag.org)
  • These defense systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids. (sciencemag.org)
  • and (b) contacting the target DNA in the cell with: (i) a Cas9 protein, and (ii) a guide RNA comprising: a targeting sequence that hybridizes to a target sequence of the target DNA, and a protein-binding domain that interacts with the Cas9 protein. (freepatentsonline.com)
  • RNA polymerase is essential to life, and is found in all living organisms and many viruses. (wikipedia.org)
  • Tyr159, Phe281 and Glu285, which are conserved among archaeal ATP-dependent RNA ligases and are situated on the surface of the enzyme, are required for RNA binding. (elsevier.com)
  • The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. (uni-ulm.de)
  • The enzyme that catalyzes this reaction is known as RNA polymerase. (conservapedia.com)
  • This enzyme contains the catalytic activity for RNA synthesis. (conservapedia.com)
  • After approximately 8-10 ribonucleotides are added, σ factor is released and RNA polymerase core enzyme moves away from the promoter, synthesizing RNA as it goes. (conservapedia.com)
  • This is, to our knowledge, the first demonstration of the involvement of DHX15 in post-transcriptional RNA modification, and the first example of a molecular process in which DHX15 directly affects the activity of another enzyme. (royalsocietypublishing.org)
  • Here, we show that in flies, 3′ terminal RNA uridylation triggers the processive, 3′‐to‐5′ exoribonucleolytic decay via the RN ase II /R enzyme CG 16940, a homolog of the human Perlman syndrome exoribonuclease Dis3l2. (embopress.org)
  • The identification of an enzyme complex degrading aberrant RNA in flies deepens our understanding of cytoplasmic RNA surveillance and sheds light on the emerging role for RNA modifications. (embopress.org)
  • During the last decade, we have pioneered alternative experimental strategies based on a hyperthermophilic archaeal system-the euryarchaeon Methanocaldococcus jannaschii- to devise an experimental system capable of generating functional insights in a systematic and high-throughput manner. (pubmedcentralcanada.ca)
  • 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)
  • In most prokaryotes , a single RNA polymerase species transcribes all types of RNA. (wikipedia.org)
  • Argonautes are also present in many bacterial and archaeal species 3-5 . (nature.com)
  • Small noncoding RNA (sRNA) molecules are integral components of the regulatory machinery for many bacterial species and are known to posttranscriptionally regulate metabolic and stress-response pathways, quorum sensing, virulence factors, and more. (asm.org)
  • At the same time, repeats were observed in the archaeal organisms of Haloferax and Haloarcula species, and their function was studied by Francisco Mojica at the University of Alicante in Spain. (wikipedia.org)
  • However, the primer pairs conventionally used in microbiome studies underestimate the number of archaeal species found, and completely disregard nonprokaryote microbiome members. (asm.org)
  • No archaeal species has yet been found that causes human disease, and the study here made no associations between archaeal species and disease in people. (asm.org)
  • The posttranscriptional addition of nucleotides to the 3′ end of RNA regulates the maturation, function, and stability of RNA species in all domains of life. (embopress.org)
  • An ATP-dependent RNA ligase from Methanobacterium thermoautotrophicum (MthRnl) catalyzes intramolecular ligation of single-stranded RNA to form a closed circular RNA via covalent ligase-AMP and RNA-adenylylate intermediate. (elsevier.com)
  • The single-stranded RNA and ssDNA phages use an amurin type of protein that prevents cell wall synthesis ( 7 , 8 , 34 ), leaving the cell membrane unprotected and subject to lysis. (asm.org)
  • Archaeal host-virus interactions are just beginning to be explored and the current understanding of archaeal virus mechanisms is rudimentary at best. (frontiersin.org)
  • Although we have genome sequences for most of the crenarchaeal viruses isolated, we have only a rudimentary understanding of archaeal virus assembly and release from cells. (asm.org)
  • In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. (rcsb.org)
  • catalytic RNA ( ribozyme ) - functions as an enzymatically active RNA molecule. (wikipedia.org)
  • End" indicates the 5' end , where the longer RNA molecules are completely transcribed. (wikipedia.org)
  • The correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. (genome.jp)
  • In humans, cap1 methylation occurs on all capped and polyadenylated RNA molecules, while only about half of these molecules contain cap2 methylation [ 8 ]. (royalsocietypublishing.org)
  • showed evidence that CRISPR repeat regions from the genome of Archaeoglobus fulgidus were transcribed into long RNA molecules that were subsequently processed into unit-length small RNAs, plus some longer forms of 2, 3, or more spacer-repeat units. (wikipedia.org)
  • During DNA replication, this is supplied in the context of a short RNA primer molecule synthesized by DNA primase. (pnas.org)
  • A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6. (uni-ulm.de)
  • Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. (royalsocietypublishing.org)
  • The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. (asm.org)
  • All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. (mdpi.com)
  • The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism," Proceedings of the National Academy of Sciences of the United States of America , vol. 100, no. 22, pp. 12984-12988, 2003. (hindawi.com)
  • A serious case is the archaeal genome Aeropyrum pernix . (biomedcentral.com)
  • Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing. (sciencemag.org)
  • Members of the family Picornaviridae , which include Hepatitis A virus, poliovirus, and Coxsackieviruses, have non-enveloped particles that consist of a protein shell surrounding the viral RNA genome (poliovirus is illustrated). (virology.ws)
  • 2010. Bacterial/archaeal/organellar polyadenylation. (uga.edu)
  • We describe the domain architectures of the archaeal TCS components, including several novel output domains, and discuss the evolution of the archaeal TCS machinery. (asm.org)
  • This finding could reflect actual independent origins of the distinct groups of archaeal viruses from different nonviral elements, providing important insights into the emergence and evolution of the archaeal virome. (asm.org)
  • RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. (ebi.ac.uk)
  • Recognizing the opportunity to apply this systems-based philosophy to carry out an exhaustive mutagenesis screen of archaeal RNAPs, we recently automated the entire process of assembling recombinant archaeal RNAPs in large numbers on a robotic platform [ 20 ]. (pubmedcentralcanada.ca)
  • This work reveals at a molecular level how reconfiguring a small portion of RNA polymerase can completely alter promoter specificity. (nih.gov)
  • Among these, the addition of non‐templated nucleotides to the 3′ hydroxyl end of RNA (i.e. tailing) is one of the most frequent marks, exhibiting deep conservation and serving diverse molecular functions. (embopress.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)
  • We present different lines of evidence to show that both eukaryotic families perform functions related to RNA metabolism. (pubmedcentralcanada.ca)
  • Based on phyletic patterns and the principle of phylogenetic bracketing, we predict that at least some of the archaeal members may also possess a role in RNA metabolism. (pubmedcentralcanada.ca)
  • The 5′-cap structure, characteristic for RNA polymerase II-transcribed RNAs, plays important roles in RNA metabolism. (royalsocietypublishing.org)
  • Hence, CMTr1-DHX15 cooperation is likely to be important for the metabolism of RNA polymerase II-transcribed RNAs. (royalsocietypublishing.org)
  • The fields of DNA metabolism and RNA metabolism have often been treated separately, although these two areas of research share many common mechanisms and principles. (keystonesymposia.org)
  • STIV has arguably become one of the most studied crenarchaeal archaeal virus systems. (frontiersin.org)
  • RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. (ebi.ac.uk)
  • Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex. (ucdenver.edu)
  • The Ffh protein precipitated from cytosolic cell supernatants with anti-Ffh antibodies, together with an 7 S-alike SRP-RNA, suggesting a stable core ribonucleoprotein composed of both components under native conditions. (portlandpress.com)
  • Small non-coding RNAs (sRNAs) are active in many bacterial cell functions, including regulation of the cell's response to environmental challenges. (semanticscholar.org)
  • We describe the identification of 27 novel Caulobacter crescentus sRNAs by analysis of RNA expression levels assayed using a tiled Caulobacter microarray and a protocol optimized for detection of sRNAs. (semanticscholar.org)
  • The translation and stability of many mRNAs is regulated by small regulatory RNAs (sRNAs). (els.net)
  • Venn diagram illustrating how the (nomenclature of) different types of ncRNA and regulatory RNAs overlap and, in particular, how sRNAs can be assigned to more than one category. (asmscience.org)
  • As phosphorylases, these enzymes use diphosphate nucleotides as substrates and can reversibly polymerize or degrade RNA, depending on the relative concentrations of nucleotides and inorganic phosphate. (nih.gov)
  • Intriguingly, archaeal primase has been demonstrated to possess the ability to synthesize DNA de novo, a property shared with the eukaryotic PrimPol enzymes. (pnas.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)
  • MicroRNAs are regulatory RNAs with a mature length of ~21-nucleotides that are processed from hairpin precursors by Dicer-like enzymes. (salk.edu)
  • RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. (ebi.ac.uk)
  • RNA polymerase II synthesizes precursors of mRNAs and most snRNA and microRNAs. (wikipedia.org)
  • 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. (currentprotocols.com)
  • In particular, transcriptional activators, co-activators, and repressors can interact with the template DNA and/or RNA polymerase to modulate core promoter selection. (nih.gov)
  • Throughout life, factors that interact with RNA polymerase and with sequences close to or within the core promoter itself can alter promoter recognition. (nih.gov)
  • While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form 'nucleosome-like' complexes that continuously wind between 60 and 500 base pairs of DNA ('archaeasomes'), suggested by crystal contacts and analysis of cellular chromatin. (elifesciences.org)
  • Together, this data provides a more detailed global view of archaeal cellular responses to viral infection, demonstrates the power of quantitative two-dimensional differential gel electrophoresis and ABPP using 2D gel compatible fluorescent dyes. (frontiersin.org)
  • In addition to these interactions between the antitoxin and toxin components (RNA-RNA, protein-protein, RNA-protein), TA systems interact with a variety of cellular factors, e.g., toxins target essential cellular components, antitoxins are degraded by RNAses or ATP-dependent proteases. (mdpi.com)
  • As technologies move toward definition of phenotypes by more direct measurement of metabolic status and high-resolution ultrastructural imaging, it is important to develop a rigorous understanding of the quantitative relationship between RNA transcript abundance and broader aspects of cellular physiology, both at the level of bulk populations and at the level of individual cells. (asmscience.org)
  • J. Kjems and R. A. Garrett, "Novel expression of the ribosomal RNA genes in the extreme thermophile and archaebacterium Desulfurococcus mobilis," The EMBO Journal , vol. 6, pp. 3521-3530, 1987. (hindawi.com)
  • Therefore, the prevailing mechanism of archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. (asm.org)
  • Most of the information about cell lysis is based on observations of a decrease in optical density (OD) in an infected culture, plaque assays, or plate growth inhibition assays, but little is known about the actual mechanism of archaeal lysis. (asm.org)
  • The first phosphodiester linkage made during DNA replication is in the context of a short RNA primer synthesized by the dedicated RNA polymerase, primase. (pnas.org)
  • Software.ncrna.org: Web servers for analyses of RNA sequences. (currentprotocols.com)
  • RNAcentral: A vision for an international database of RNA sequences. (currentprotocols.com)
  • Conventional primer pairs are more likely to amplify bacterial sequences than archaeal sequences. (asm.org)
  • Investigating the archaeal population separately from the bacterial population revealed a large number of archaeal sequences in different parts of the human microbiome (see figure, right). (asm.org)
  • In addition to obtaining unidentified archaeal reads from lung samples, the sequences also identified archaeal types previously not known to grow on the human body. (asm.org)
  • None of the archaeal sequences, however, was related to groups previously implicated in anaerobic methane oxidation. (int-res.com)
  • Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. (ebi.ac.uk)
  • Yeast RNA polymerase II core (PDB 1WCM). (wikipedia.org)
  • In the current work, we dissect the functional interplay between DNA and RNA synthetic modes of primase. (pnas.org)
  • Accelerating discovery and functional analysis of small RNAs with new technologies. (currentprotocols.com)
  • DNA replication is critically dependent on the synthesis of short RNA primers by DNA primase ( 1 ). (pnas.org)
  • An RNA primer is required to initiate leading strand synthesis, and primers are also required for every Okazaki fragment synthesized on the lagging strand. (pnas.org)
  • We also performed structure-guided mutational analysis to survey the functions of 36 residues in three component steps of the ligation pathway including ligase-adenylylation (step 1), RNA adenylylation (step 2) and phosphodiester bond synthesis (step 3). (elsevier.com)
  • In type I and III, antitoxins are RNAs that either inhibit the synthesis of the toxin or sequester it. (mdpi.com)
  • Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus," Proceedings of the National Academy of Sciences of the United States of America , vol. 99, no. 11, pp. 7536-7541, 2002. (hindawi.com)
  • Small non-coding RNAs in Caulobacter crescentus. (semanticscholar.org)
  • Novel small RNA‐encoding genes in the intergenic regions of Escherichia coli. (currentprotocols.com)
  • In many cases, these factors interact with only a small surface of RNA polymerase, yet they impose a major specificity change through this contact. (nih.gov)
  • 2001) and proposed a function for Rpb7 in binding the nascent RNA transcript. (trieste.it)
  • We found that CMTr1 binds ATP-dependent RNA DHX15 helicase and that this interaction, mediated by the G-patch domain of CMTr1, has an advantageous effect on CMTr1 activity towards highly structured RNA substrates. (royalsocietypublishing.org)