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.
Ribonucleic acid that makes up the genetic material of viruses.
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).
The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.
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.
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).
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.
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.
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 processes of RNA tertiary structure formation.
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.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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.
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.
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.
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.
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.
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.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.
Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
RNA present in neoplastic 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 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.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A 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.
RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.
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.
Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.
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)
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.
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)
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
Established cell cultures that have the potential to propagate indefinitely.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
A 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.
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.
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 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.
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 biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
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.
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.
Complexes of RNA-binding proteins with ribonucleic acids (RNA).
Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.
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.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
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).
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.
Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
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.
Synthetic transcripts of a specific DNA molecule or fragment, made by an in vitro transcription system. This cRNA can be labeled with radioactive uracil and then used as a probe. (King & Stansfield, A Dictionary of Genetics, 4th ed)
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
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.-.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
The rate dynamics in chemical or physical systems.
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.
Viruses parasitic on plants higher than bacteria.
Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
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.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.
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 sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Cyclic peptides extracted from carpophores of various mushroom species. They are potent inhibitors of RNA polymerases in most eukaryotic species, blocking the production of mRNA and protein synthesis. These peptides are important in the study of transcription. Alpha-amanitin is the main toxin from the species Amanitia phalloides, poisonous if ingested by humans or animals.
The functional hereditary units of VIRUSES.
Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.
An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.
The sum of the weight of all the atoms in a molecule.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Within most types of eukaryotic CELL NUCLEUS, a distinct region, not delimited by a membrane, in which some species of rRNA (RNA, RIBOSOMAL) are synthesized and assembled into ribonucleoprotein subunits of ribosomes. In the nucleolus rRNA is transcribed from a nucleolar organizer, i.e., a group of tandemly repeated chromosomal genes which encode rRNA and which are transcribed by RNA polymerase I. (Singleton & Sainsbury, Dictionary of Microbiology & Molecular Biology, 2d ed)
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
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.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Proteins encoded by a VIRAL GENOME that are produced in the organisms they infect, but not packaged into the VIRUS PARTICLES. Some of these proteins may play roles within the infected cell during VIRUS REPLICATION or act in regulation of virus replication or VIRUS ASSEMBLY.
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.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
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.
Nucleotide sequences located at the ends of EXONS and recognized in pre-messenger RNA by SPLICEOSOMES. They are joined during the RNA SPLICING reaction, forming the junctions between exons.
A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.
A species of ENTEROVIRUS which is the causal agent of POLIOMYELITIS in humans. Three serotypes (strains) exist. Transmission is by the fecal-oral route, pharyngeal secretions, or mechanical vector (flies). Vaccines with both inactivated and live attenuated virus have proven effective in immunizing against the infection.
Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.
A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.
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.
Separation of particles according to density by employing a gradient of varying densities. At equilibrium each particle settles in the gradient at a point equal to its density. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The part of a cell that contains the CYTOSOL and small structures excluding the CELL NUCLEUS; MITOCHONDRIA; and large VACUOLES. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Viruses which produce a mottled appearance of the leaves of plants.
An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.
A compound composed of a two CYCLIC PEPTIDES attached to a phenoxazine that is derived from STREPTOMYCES parvullus. It binds to DNA and inhibits RNA synthesis (transcription), with chain elongation more sensitive than initiation, termination, or release. As a result of impaired mRNA production, protein synthesis also declines after dactinomycin therapy. (From AMA Drug Evaluations Annual, 1993, p2015)
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 determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
A genus of FLAVIVIRIDAE causing parenterally-transmitted HEPATITIS C which is associated with transfusions and drug abuse. Hepatitis C virus is the type species.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.
A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying methionine to sites on the ribosomes. During initiation of protein synthesis, tRNA(f)Met in prokaryotic cells and tRNA(i)Met in eukaryotic cells binds to the start codon (CODON, INITIATOR).
The relationships of groups of organisms as reflected by their genetic makeup.
A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.
Proteins prepared by recombinant DNA technology.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.
Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
A multiribosomal structure representing a linear array of RIBOSOMES held together by messenger RNA; (RNA, MESSENGER); They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A cell line derived from cultured tumor cells.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
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.-
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.
Proteins found in any species of bacterium.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.
A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.
Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.
A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.
A group of uridine ribonucleotides in which the phosphate residues of each uridine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.
Use for nucleic acid precursors in general or for which there is no specific heading.
The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.
Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.
Deletion of sequences of nucleic acids from the genetic material of an individual.
A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.
Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.
Proteins obtained from ESCHERICHIA COLI.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
The infective system of a virus, composed of the viral genome, a protein core, and a protein coat called a capsid, which may be naked or enclosed in a lipoprotein envelope called the peplos.
Highly conserved nuclear RNA-protein complexes that function in RNA processing in the nucleus, including pre-mRNA splicing and pre-mRNA 3'-end processing in the nucleoplasm, and pre-rRNA processing in the nucleolus (see RIBONUCLEOPROTEINS, SMALL NUCLEOLAR).
A defective virus, containing particles of RNA nucleoprotein in virion-like form, present in patients with acute hepatitis B and chronic hepatitis. It requires the presence of a hepadnavirus for full replication. This is the lone species in the genus Deltavirus.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.
Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Elements of limited time intervals, contributing to particular results or situations.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.
Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.
A hemoflagellate subspecies of parasitic protozoa that causes nagana in domestic and game animals in Africa. It apparently does not infect humans. It is transmitted by bites of tsetse flies (Glossina).
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
A genus of plant viruses that infects ANGIOSPERMS. Transmission occurs mechanically and through soil, with one species transmitted via a fungal vector. The type species is Tomato bushy stunt virus.
A purine nucleoside that has guanine linked by its N9 nitrogen to the C1 carbon of ribose. It is a component of ribonucleic acid and its nucleotides play important roles in metabolism. (From Dorland, 28th ed)
The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.
A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)

Evidence on the conformation of HeLa-cell 5.8S ribosomal ribonucleic acid from the reaction of specific cytidine residues with sodium bisulphite. (1/6102)

The reaction of HeLa-cell 5.8S rRNA with NaHSO3 under conditions in which exposed cytidine residues are deaminated to uridine was studied. It was possible to estimate the reactivities of most of the 46 cytidine residues in the nucleotide sequence by comparing 'fingerprints' of the bisulphite-treated RNA with those of untreated RNA. The findings were consistent with the main features of the secondary-structure model for mammalian 5.85S rRNA proposed by Nazar, Sitz, & Busch [J. Biol. Chem (1975) 250, 8591--8597]. Five out of six regions that are depicted in the model as single-stranded loops contain cytidine residues that are reactive towards bisulphite at 25 degrees C (the other loop contains no cytidine). The cytidine residue nearest to the 3'-terminus is also reactive. Several cytidines residues that are internally located within proposed double-helical regions show little or no reactivity towards bisulphite, but the cytidine residues of several C.G pairs at the ends of helical regions show some reactivity, and one of the proposed loops appears to contain six nucleotides, rather than the minimum of four suggested by the primary structure. Two cytidine residues that are thought to be 'looped out' by small helix imperfections also show some reactivity.  (+info)

NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae. (2/6102)

A mutation in NMD3 was found to be lethal in the absence of XRN1, which encodes the major cytoplasmic exoribonuclease responsible for mRNA turnover. Molecular genetic analysis of NMD3 revealed that it is an essential gene required for stable 60S ribosomal subunits. Cells bearing a temperature-sensitive allele of NMD3 had decreased levels of 60S subunits at the nonpermissive temperature which resulted in the formation of half-mer polysomes. Pulse-chase analysis of rRNA biogenesis indicated that 25S rRNA was made and processed with kinetics similar to wild-type kinetics. However, the mature RNA was rapidly degraded, with a half-life of 4 min. Nmd3p fractionated as a cytoplasmic protein and sedimented in the position of free 60S subunits in sucrose gradients. These results suggest that Nmd3p is a cytoplasmic factor required for a late cytoplasmic assembly step of the 60S subunit but is not a ribosomal protein. Putative orthologs of Nmd3p exist in Drosophila, in nematodes, and in archaebacteria but not in eubacteria. The Nmd3 protein sequence does not contain readily recognizable motifs of known function. However, these proteins all have an amino-terminal domain containing four repeats of Cx2C, reminiscent of zinc-binding proteins, implicated in nucleic acid binding or protein oligomerization.  (+info)

A computational screen for methylation guide snoRNAs in yeast. (3/6102)

Small nucleolar RNAs (snoRNAs) are required for ribose 2'-O-methylation of eukaryotic ribosomal RNA. Many of the genes for this snoRNA family have remained unidentified in Saccharomyces cerevisiae, despite the availability of a complete genome sequence. Probabilistic modeling methods akin to those used in speech recognition and computational linguistics were used to computationally screen the yeast genome and identify 22 methylation guide snoRNAs, snR50 to snR71. Gene disruptions and other experimental characterization confirmed their methylation guide function. In total, 51 of the 55 ribose methylated sites in yeast ribosomal RNA were assigned to 41 different guide snoRNAs.  (+info)

Differential transcriptional activity associated with chromatin configuration in fully grown mouse germinal vesicle oocytes. (4/6102)

It was previously shown that fully grown ovarian germinal vesicle (GV) oocytes of adult mice exhibit several nuclear configurations that differ essentially by the presence or absence of a ring of condensed chromatin around the nucleolus. These configurations have been termed, respectively, SN (surrounded nucleolus) and NSN (nonsurrounded nucleolus). Work from our and other laboratories has revealed ultrastructural and functional differences between these two configurations. The aims of the present study were 1) to analyze the equilibrium between the SN and the NSN population as a function of the age of the mice and the time after hCG-induced ovulation and 2) to study the polymerase I (pol I)- and polymerase II (pol II)-dependent transcription in both types of oocytes through the detection of bromouridine incorporated into nascent RNA. We show 1) that ovarian GV oocytes exhibiting the SN-type configuration can be found as soon as 17 days after birth in the C57/CBA mouse strain and 2) that the SN:NSN ratio of ovarian GV oocytes is very low just after hCG-induced ovulation and then increases progressively with the time after ovulation. Furthermore, we demonstrate that the SN configuration correlates strictly with the arrest of both pol I- and pol II-dependent transcription in mice at any age. Finally, we show that ribosomal genes are located at the outer periphery of the nucleolus in the NSN configuration and that pol I-dependent perinucleolar transcription sites correspond to specific ultrastructural features of the nucleolus. Altogether, these results provide clear-cut criteria delineating transcriptionally active GV oocytes from those that are inactive, and confirm that the SN-type configuration is mostly present in preovulatory oocytes.  (+info)

An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes. (5/6102)

Elongation factor 1 alpha (EF-1 alpha) is a highly conserved ubiquitous protein involved in translation that has been suggested to have desirable properties for phylogenetic inference. To examine the utility of EF-1 alpha as a phylogenetic marker for eukaryotes, we studied three properties of EF-1 alpha trees: congruency with other phyogenetic markers, the impact of species sampling, and the degree of substitutional saturation occurring between taxa. Our analyses indicate that the EF-1 alpha tree is congruent with some other molecular phylogenies in identifying both the deepest branches and some recent relationships in the eukaryotic line of descent. However, the topology of the intermediate portion of the EF-1 alpha tree, occupied by most of the protist lineages, differs for different phylogenetic methods, and bootstrap values for branches are low. Most problematic in this region is the failure of all phylogenetic methods to resolve the monophyly of two higher-order protistan taxa, the Ciliophora and the Alveolata. JACKMONO analyses indicated that the impact of species sampling on bootstrap support for most internal nodes of the eukaryotic EF-1 alpha tree is extreme. Furthermore, a comparison of observed versus inferred numbers of substitutions indicates that multiple overlapping substitutions have occurred, especially on the branch separating the Eukaryota from the Archaebacteria, suggesting that the rooting of the eukaryotic tree on the diplomonad lineage should be treated with caution. Overall, these results suggest that the phylogenies obtained from EF-1 alpha are congruent with other molecular phylogenies in recovering the monophyly of groups such as the Metazoa, Fungi, Magnoliophyta, and Euglenozoa. However, the interrelationships between these and other protist lineages are not well resolved. This lack of resolution may result from the combined effects of poor taxonomic sampling, relatively few informative positions, large numbers of overlapping substitutions that obscure phylogenetic signal, and lineage-specific rate increases in the EF-1 alpha data set. It is also consistent with the nearly simultaneous diversification of major eukaryotic lineages implied by the "big-bang" hypothesis of eukaryote evolution.  (+info)

RecA-Mediated gene conversion and aminoglycoside resistance in strains heterozygous for rRNA. (6/6102)

Clinical resistance to aminoglycosides in general is due to enzymatic drug modification. Mutational alterations of the small ribosomal subunit rRNA have recently been found to mediate acquired resistance in bacterial pathogens in vivo. In this study we investigated the effect of 16S rRNA heterozygosity (wild-type [wt] and mutant [mut] operons at position 1408 [1408wt/1408mut]) on aminoglycoside resistance. Using an integrative vector, we introduced a single copy of a mutated rRNA operon (1408 A-->G) into Mycobacterium smegmatis, which carries two chromosomal wild-type rRNA operons; the resultant transformants exhibited an aminoglycoside-sensitive phenotype. In contrast, introduction of the mutated rRNA operon into an M. smegmatis rrnB knockout strain carrying a single functional chromosomal wild-type rRNA operon resulted in aminoglycoside-resistant transformants. Subsequent analysis by DNA sequencing and RNase protection assays unexpectedly demonstrated a homozygous mutant genotype, rRNAmut/rRNAmut, in the resistant transformants. To investigate whether RecA-mediated gene conversion was responsible for the aminoglycoside-resistant phenotype in the rRNAwt/rRNAmut strains, recA mutant strains were generated by allelic exchange techniques. Transformation of the recA rrnB M. smegmatis mutant strains with an integrative vector expressing a mutated rRNA operon (Escherichia coli position 1408 A-->G) resulted in transformants with an aminoglycoside-sensitive phenotype. Subsequent analysis showed stable heterozygosity at 16S rRNA position 1408 with a single wild-type allele and a single resistant allele. These results demonstrate that rRNA-mediated mutational resistance to aminoglycosides is recessive.  (+info)

In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. (7/6102)

Individual cyanobacterial cells are normally identified in environmental samples only on the basis of their pigmentation and morphology. However, these criteria are often insufficient for the differentiation of species. Here, a whole-cell hybridization technique is presented that uses horseradish peroxidase (HRP)-labeled, rRNA-targeted oligonucleotides for in situ identification of cyanobacteria. This indirect method, in which the probe-conferred enzyme has to be visualized in an additional step, was necessary since fluorescently monolabeled oligonucleotides were insufficient to overstain the autofluorescence of the target cells. Initially, a nonfluorescent detection assay was developed and successfully applied to cyanobacterial mats. Later, it was demonstrated that tyramide signal amplification (TSA) resulted in fluorescent signals far above the level of autofluorescence. Furthermore, TSA-based detection of HRP was more sensitive than that based on nonfluorescent substrates. Critical points of the assay, such as cell fixation and permeabilization, specificity, and sensitivity, were systematically investigated by using four oligonucleotides newly designed to target groups of cyanobacteria.  (+info)

Combination of fluorescent in situ hybridization and microautoradiography-a new tool for structure-function analyses in microbial ecology. (8/6102)

A new microscopic method for simultaneously determining in situ the identities, activities, and specific substrate uptake profiles of individual bacterial cells within complex microbial communities was developed by combining fluorescent in situ hybridization (FISH) performed with rRNA-targeted oligonucleotide probes and microautoradiography. This method was evaluated by using defined artificial mixtures of Escherichia coli and Herpetosiphon aurantiacus under aerobic incubation conditions with added [3H]glucose. Subsequently, we were able to demonstrate the potential of this method by visualizing the uptake of organic and inorganic radiolabeled substrates ([14C]acetate, [14C]butyrate, [14C]bicarbonate, and 33Pi) in probe-defined populations from complex activated sludge microbial communities by using aerobic incubation conditions and anaerobic incubation conditions (with and without nitrate). For both defined cell mixtures and activated sludge, the method proved to be useful for simultaneous identification and analysis of the uptake of labeled substrates under the different experimental conditions used. Optimal results were obtained when fluorescently labeled oligonucleotides were applied prior to the microautoradiographic developing procedure. For single-cell resolution of FISH and microautoradiographic signals within activated sludge flocs, cryosectioned sample material was examined with a confocal laser scanning microscope. The combination of in situ rRNA hybridization techniques, cryosectioning, microautoradiography, and confocal laser scanning microscopy provides a unique opportunity for obtaining cultivation-independent insights into the structure and function of bacterial communities.  (+info)

Using a variety of molecular techniques, including immuno-electron microscopy, intermolecular chemical cross-linking, and X-ray crystallography, the location of the 5S rRNA within the large ribosomal subunit has been determined to great precision. In bacteria and archaea, the large ribosomal subunit (LSU) itself is composed of two RNA moieties, the 5S rRNA and another larger RNA known as 23S rRNA, along with numerous associated proteins.[3] In eukaryotes, the LSU contains 5S, 5.8S, and 28S rRNAs and even more proteins.[12][13] The structure of LSU in 3-dimensions shows one relatively smooth surface and the opposite surface having three projections, notably the L1 protuberance, the central protuberance (CP), and the L7/L12 stalk. The L1 protuberance and L7/L12 stalk are arranged laterally surrounding CP. The 5S rRNA is located in the CP and participates in formation and structure of this projection. The other major constituents of the central protuberance include the 23S rRNA (or alternatively ...
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TY - JOUR. T1 - Divergence of primate ribosomal RNA genes as assayed by restriction enzyme analysis. AU - Nelkin, B.. AU - Strayer, D.. AU - Vogelstein, B.. PY - 1980/1/1. Y1 - 1980/1/1. N2 - Primate ribosomal RNA (rRNA) genes have been compared by restriction endonuclease mapping. In all species examined, the restriction map of the reiterated ribosomal DNA is simple (within the limits of detection by hybridization with rRNA) and is consistent with a high degree of homogeneity among the repeats. Within a species, all members have similar rDNA restriction patterns. However, different species of primates have distinctly different rDNA restriction maps; even chimpanzee and man can be discerned by their rDNA restriction patterns. Possible mechanisms for maintenance of homogeneity of the rDNA repeats within a species, while allowing divergence among closely related species, are discussed.. AB - Primate ribosomal RNA (rRNA) genes have been compared by restriction endonuclease mapping. In all species ...
PELP1 activation of ribosomal promoter depends on functional nucleolar domains.(A) Schematic representation of PELP1 nucleolar domains. (B) 293T cells were tran
Hi,. I looked at the GTF file M13 from the GENCODE (https://www.gencodegenes.org/mouse_releases/13.html) and I found the gene name for the 18S ribosomal RNA (Rn18s), but I couldnt find the 28S ribosomal RNA (Rn28s). Does anyone know about it? Does it call in other name?. Thanks. ...
Paenibacillus lentimorbus 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, 5S ribosomal RNA, tRNA-Ile, and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial ...
Aspergillus brasiliensis strain CBS 733.88 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial ...
Quantitative Real Time PCR (qRT-PCR) is an increasingly popular method for the quantitative analysis of gene expression. Despite its high sensitivity, accuracy and wide dynamic range that favour qRT-PCR in gene expression studies, some factors exist that must be taken into account as a possible source of error [1]. A critical element in experimental design is the strategy to quantify the input template cDNA in the sample. Appropriate choice of internal references has been previously shown to be crucial for correct interpretation of expression data [1, 2] and bioinformatic approaches have been developed to increase the accuracy of normalization [3-5]. Although numerous reference genes are currently used for normalization purposes, the most commonly used are still 18 S ribosomal RNA (Rn18S), β-actin (Actb) and glyceraldehyde-3-phosphate dehydrogenase (Gapdh) due to their ubiquitous and relatively high expression levels [6]. Actb and Gapdh are mRNA-encoding housekeeping genes (HKs), and have been ...
Ribosome biogenesis is a very conserved process in the eukaryotic kingdom. In Saccharomyces cerevisiae, the pathway begins with transcription of the 35S and 5S ribosomal RNA (rRNA) precursors by RNA polymerases I and III, respectively. The association of ribosomal proteins and pre-ribosomal factors with nascent pre-rRNAs gives birth to a 90S pre-ribosomal complex that undergoes various steps of maturation. The 90S complex separates into a pre-60S complex, which will generate the large ribosomal subunit containing mature 25S, 5.8S, and 5S rRNAs, and a pre-40S complex, which will generate the small ribosomal subunit containing 18S rRNA. The maturation of both particles follows two distinct pathways, first in the nucleolus and then in the nucleoplasm, and finally in the cytoplasm after Crm1-dependent export through the nuclear pores (Hurt et al., 1999; Moy and Silver, 1999; for review see Johnson et al., 2002). Several factors are necessary for correct modification, cleavage, and processing of ...
MRM1, 50 µg. Mitochondrial rRNA methyltransferase 1 homolog, also known as MRM1, probably methylates the ribose of guanosine G-2270 in the peptidyl transferase center of the mitochondrial large ribosomal RNA (21S).
The product of the PET56 nuclear gene of Saccharomyces cerevisiae was shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase center of the mitochondrial large ribosomal RNA (21S rRNA). Cells reduced in this activity were deficient in formation of functional large subunits of the mitochondrial ribosome. The purified Pet56 protein catalyzed the site-specific formation of 2-O-methylguanosine on in vitro transcripts of both mitochondrial 21S rRNA and Escherichia coli 23S rRNA. These results provide evidence for an essential modified nucleotide in rRNA ...
adshelp[at]cfa.harvard.edu The ADS is operated by the Smithsonian Astrophysical Observatory under NASA Cooperative Agreement NNX16AC86A ...
Plays an essential role in mitochondrial ribosome biogenesis. As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mitochondrial ribosomal RNA (16S mt-rRNA), controls 16S mt-rRNA abundance and is required for intra-mitochondrial translation of core subunits of the oxidative phosphorylation system.
Marker genes are essential for studying microbial diversity. megx.net integrates georeferenced small and large subunit ribosomal RNA (rRNA) sequences form the SILVA ribosomal RNA database project, providing a link between diversity and enviromental data. Details on the available rRNA data can be found on the content page.. The table below lists the sampling sites where rRNA samples have been taken, together with accompanying metadata. The location link will give you details of the sampling site, including number and type of samples taken there, and in situ measurements.. ...
Up till then the dogma, that all biological catalysts are proteins, had not been questioned. Cech and his co-workers demonstrated that the large ribosomal RNA precursor of Tetrahymena thermophilia has the capacity of self-splicing or self-processing. In the complete absence of a protein enzyme, an intervening sequence (IVS or intron) is removed and the remaining RNA pieces are ligated correctly. The only requirement for this reaction is the presence of guanosine (or a derivative thereof, like for instance GMP) and magnesium ions. Cech and his colleagues were able to clarify the mechanistic details of this reaction.. The finding that RNA can act as an enzyme (also called ribozyme) active in breaking and making internucleotide bonds in present-day biological systems, raises the question whether these properties may have played a role in the prebiotic replication and evolution of RNA molecules. Since the substrate oligonucleotides are aligned by a complementary sequence in the IVS RNA itself, the ...
Transcription factor and ribosomal RNA (rRNA). Molecular model showing the 6 zinc fingers of transcription factor IIIA (yellow) bound to RNA (ribonucleic acid, red and blue) from a 5s ribosome sub-unit.
Opens the Highlight Feature Bar and highlights feature annotations from the FEATURES table of the record. The Highlight Feature Bar can be used to navigate to and highlight other features and provides links to display the highlighted region separately. Links in the FEATURES table will also highlight the corresponding region of the sequence. More... ...
We have assembled a sequence database for 80 genera from the Hymenomycete lineage of the Basidiomycota for a small region of the mitochondrial large subunit rRNA gene. Our taxonomic sample is highly biased toward known ectomycorrhizal (EM) taxa, but also includes some related saprobic species. This gene fragment can be amplified directly from mycorrhizae, sequenced, and used to determine the family or subfamily level for many unknown mycorrhizal basidiomycetes. The method is robust to minor sequencing errors, minor misalignments, and method of phylogenetic analysis. ...
1) Partial methylation at Am100 in 18S rRNA of baker´s yeast shows ribosome heterogeneity on the level of eukaryotic rRNA modification. Plos One [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089640 ...
Studies of microbial biodiversity have made astounding discoveries of late due to the use of methodologies based on phylogenetic analyses of small subunit ribosomal RNA sequences. Although there are limitations to these methods, they can nonetheless be very useful if these limitations are kept in mi …
GO:0006364. Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. ...
The metabolism of high-molecular-weight RNA in the nuclear and cytoplasmic fractions of newborn and adult rat brain was investigated after the intracranial administration of [32P]Pi. In young brain, a considerable proportion of the newly synthesized radioactive RNA is transferred to the cytoplasm, in contrast with the adult brain, where there appears to be a high intranuclear turnover. Electrophoretic analysis of the newly synthesized RNA showed that processing of the rRNA precursor to yield the 28S and 18S rRNA may be more rapid in the adult than in the young, although most of the adult rRNA in the nucleus is not transferred to the cytoplasm. In young brain, processing is probably tightly coupled to transport of rRNA into the cytoplasm, so that 28S and 18S rRNA are not subjected to possible degradation within the nucleus. Polyadenylated RNA turns over in concert with high-molecular-weight RNA in the nuclei of the adult rat brain. In the cytoplasm the polyadenylated RNA has a higher turnover ...
Intimacy counselling. Find out more about our free, confidential counselling with medical specialists trained in intimacy, body image, sexual confidence and relationships. Available to all those facing cancer and their partners, including members of the LGBTQI community. ...
Standard experimental techniques for determining the structure of small to moderately-sized molecules are difficult to apply to large macromolecular complexes. These complexes, consisting of multiple protein
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40. Appellants argue that after the publication of Polisky, successful synthesis of protein was still uncertain. They belittle the predictive value of the observation that expression of the transcribed RNA in Polisky produced beta-galactosidase with a greater than normal molecular weight, arguing that since ribosomal RNA is not normally translated, the polypeptide chains that were added to the end of the beta-galactosidase were junk or nonsense proteins. This characterization ignores the clear implications of the reported observations. The Polisky study directly proved that a readthrough transcript messenger RNA had been produced. The preliminary observation showed that this messenger RNA was read and used for successful translation. It was well known in the art that ribosomal RNA was made of the same nucleotides as messenger RNA, that any sequence of nucleotides could be read in groups of three as codons, and that reading these codons should specify a polypeptide chain that would elongate ...
r-RNA is found in the ribosomes in the cell cytoplasm (site of protein synthesis). It is synthesized in the nucleus, but final organization takes place in the cytoplasm. ...
Ribosomal RNA. It is a part of a rybosome and has a very important function in the process of translation. The existence of rRNA is one of the clues whi...
We can design and build Custom CodeSets for your specified gene targets including Gene Expression, CNV, Fusion or Splice Variant detection, Ribosomal RNA, and more.
The precise location of ribosomal RNA (rRNA) synthesis within the nucleolus is the subject of recent controversy; some investigators have detected nascent RNA in the dense fibrillar components (DFCs) while others have localized transcription to the f
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Deregulation of translational control can promote cellular transformation. Protein synthesis and the expression of components of the translation machinery are elevated in cancers and contribute to tumorigenesis (1-5, 7). Here, we show that nuclear ErbB2 promotes binding of RNA Pol I to rDNA, co-occupies the rRNA gene with β-actin and RNA Pol I, and stimulates rRNA production and protein translation independently of traditional ErbB2 downstream PI3-K and ERK signalings, suggesting that nuclear ErbB2 may contribute to oncogenesis by upregulating total cellular translation. rRNA synthesis by RNA Pol I plays a critical role in production of mature ribosomes that are central protein synthesis machinery of the cells. Perturbation of RNA Pol I activity as well as rRNA and protein biosynthesis (i.e., translation control) by oncoproteins such as Myc or tumor suppressors p53, RB, and ADP ribosylation factor has been reported to be associated with tumor development (1, 2, 7-10). The capability of Myc to ...
This, my Cand. Scient. (MS) project, was completed at the Department of Biological Chemistry, Institute of Molecular Biology, University of Copenhagen. My supervisor was Associate Professor Birte Vester who was part of the RNA group led by Professor Roger Garrett. Here I did three years of lab-work investigating posttranscriptional modifications of ribosomal RNA using standard lab methods combined with mass spectrometry. I was able to isolate the part of the 23S ribosomal RNA that constitutes the peptidyl transferase centre using site-directed RNaseH digestion followed by isolation with PAGE. The isolated fragments were analysed by MALDI-MS, where I was so fortunate to collaborate with Associate Professor Finn Kirpekar (University of Southern Denmark) who analyzed the fragments - and taught me to perform this type of analyzis on equipment in Copenhagen. I also screened these fragments for the mass-silent pseudouridines using chemical modification and detection with RT-PCR and visualization on ...
Transcription factor and ribosomal RNA (rRNA). Molecular model showing the 6 zinc fingers of transcription factor IIIA (purple) bound to RNA (ribonucleic acid, pink-beige and green) from a 5s ribosome sub-unit. Transcription factors are proteins that bind to specific DNA sequences, and control the movement (transcription) of genetic information from DNA to mRNA (messenger RNA) during gene expression. Ribosomes are responsible reading the RNA strand and assembling amino acids to form the protein encoded by the gene being read. - Stock Image C008/8514
Abstract: DESCRIPTION (provided by applicant): It is proposed to investigate the hypothesis that chronic ethanol feeding results in decreased levels of hepatic S-adenosy-L-methionine (Adomet) and that this deficiency results in impaired mitochondrial ribosome assembly and depressed protein synthesis. Published data has demonstrated that ethanol has a pronounced effect upon oxidative phosphorylation in the liver. Ethanol consumption results in decreased levels of essential polypeptides encoded for: exclusively by the mitochondrial genome-that are utilized in the assembly of electron transport chain (ETC) complexes. As a consequence, their activities are depressed and ATP production decreases, investigations is to the mechanism(s) responsible for the phenomenon revealed an ethanol-elicited decrease in the number of fully functioning mitochondrial ribosomes (mitoribosomes) along with an increased tendency for them to dissociate upon isolation, This suggests that iethanol-mediated effects at the ...
Conventional sequencing begins with a culture of identical cells as a source of DNA. However, early metagenomic studies revealed that there are probably large groups of microorganisms in many environments that cannot be cultured and thus cannot be sequenced. These early studies focused on 16S ribosomal RNA sequences which are relatively short, often conserved within a species, and generally different between species. Many 16S rRNA sequences have been found which do not belong to any known cultured species, indicating that there are numerous non-isolated organisms out there.. Early molecular work in the field was conducted by Norman R. Pace and colleagues, who used PCR to explore the diversity of ribosomal RNA sequences.[6] The insights gained from these breakthrough studies led Pace to propose the idea of cloning DNA directly from environmental samples as early as 1985.[7] This led to the first report of isolating and cloning bulk DNA from an environmental sample, published by Pace and ...
Humanin is a peptide encoded in the mitochondrial genome by the 16S ribosomal RNA gene, MT-RNR2. Its structure contains a three-turn α-helix, and no symmetry. In in vitro and animal models, it appears to have cytoprotective effects. Humanin is encoded in the mitochondrial genome by the 16S ribosomal RNA gene, MT-RNR2. The expressed peptide contains a three-turn α-helix, and has no symmetry. The length of the peptide depends on where it is produced. If it is produced inside the mitochondria it will be 21 amino acids long. If it is produced outside the mitochondria, in the cytosol, it will be 24 amino acids long. Both peptides have been shown to have biological activity. The rat, Rattus norvegicus, has a gene, rattin, that encodes a 38 amino acid peptide homologous to humanin. The two genes produce cDNAs that show 88% sequence identity. The peptides are 81% identical, with the carboxyl terminal sequence 14 amino acids longer in rattin. Of the 24 amino acids in the rest of the sequence, 20 are ...
Title: Uncultured soil bacterium clone SoilA-18 16S ribosomal RNA gene, partial sequence. Accession Number: DQ906983. Link to Dataset: https://www.ncbi.nlm.nih.gov/nucleotide/DQ906983. Repository: GenBank. Data Type(s): Nucleotide Sequence. Experiment Type(s): Genomic DNA. Organism(s): Bacteria. Summary: Uncultured soil bacterium clone SoilA-18 16S ribosomal RNA gene, partial sequence. Publication(s) associated with this dataset: h4.sbrppubs { padding: 0 5px 2px 5px; border-bottom: 1px solid #bfbeb5; margin: 1px 0 10px 0; text-align: left; } .pubs li { padding-bottom: 14px; } .pubs li img { border: 0px; } ...
Ribosomes are giant molecular machines that produce all proteins necessary for life. In eukaryotic cells, their assembly is a highly elaborate and carefully coordinated process. The Klinge labs research is aimed at understanding the molecular mechanisms that govern early stages of eukaryotic ribosome assembly. Ribosomes are responsible for decoding the information contained in messenger RNA to synthesize proteins used in all domains of life. Ribosome assembly, the process by which ribosomes are synthesized, involves approximately 200 protein and RNA factors in eukaryotes, most of which are essential. These factors are involved in all stages of ribosome assembly, from transcription of ribosomal RNA in the nucleolus to export into the cytoplasm, where the final stages of maturation and quality control occur. As ribosome assembly progresses, more and more of this machinery is released from intermediate complexes until the ribosomal subunits complete maturation.. The structure of this molecular ...
This example of a molecular phylogenetic tree is an unrooted dendrogram. The length of the branches quantitatively represents the evolutionary distance separating gene sequences within these organisms.This particular tree is based on the analysis of small subunit ribosomal RNA sequences. In this tree, the tips of branches are modern organisms. Each node within the tree represents a common ancestor. The last common ancestor (the root) is here marked with the star. How this is determined will be described in a later lecture.. Notice that there is no explicit or implied ranking of above (superior) or below (inferior) in the tree. Evolutionary distance (divergence) is measured along the lengths of the branches connecting species. There are no axes in this graph.. One of the most exciting outcomes of this method early on was the discovery of a new type of organism - the Archaea (a.k.a. archaebacteria). Previously it was thought that all living things were either Bacteria (a.k.a. eubacteria) or ...
In plants, transcription is initiated from a promoter located in the IGS. There are subrepeated regions upstream and downstream of a transcription starting site that have been proposed to have regulatory function (Flavell et al., 1988; Sardana et al., 1993; Komarova et al., 2004). The primary transcript is of variable length (6-9 kb) and is processed into mature 18S, 5.8S, and 26S RNA by excision of ITS1 and ITS2 and a transcribed part of the IGS (called externally transcribed spacer [ETS]). Maturation of primary transcript, post-transcriptional modifications, and ribosome assembly occur in the nucleolus. The regulation of rRNA gene expression occurs through the suppression of whole loci (termed nucleolar dominance) and at genes within the array. Large numbers of repeats are not transcribed and are packed into transcriptionally inactive heterochromatin. Formation of rDNA heterochromatin is believed to be under epigenetic control mediated by modifications of DNA and histones. In mammals, cytosine ...
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Poly(A)-containing mRNA was isolated from Human Universal Reference RNA (Agilent #740000). Libraries were made using the NEBNext Ultra II Directional RNA Kit (plus the NEBNext Poly(A) mRNA Magnetic Isolation Module), Kapa Stranded mRNA-Seq Kit, Kapa mRNA HyperPrep Kit and Illumina TruSeq Stranded mRNA Kit. Libraries were sequenced on an Illumina NextSeq® 500 using paired-end mode (2x76 bp). Read pairs were assessed to be ribosomal RNA (rRNA) if they contain 6 or more 32 base matches to 18S, 28S, 5S, 5.8S, 16S or 12S human rRNA sequences (mirabait 4.9). Percent rRNA remaining was calculated by dividing rRNA reads by the total number of reads passing instrument quality filtering. Average percent rRNA remaining is shown for three replicates. The NEBNext poly(A) Ultra II Directional RNA workflow is the most efficient in removing rRNA from total RNA. ...
We first examined whether there is any change in the expression of ARMS2 and HTRA1 between normal aged and AMD retinas without genotype constraints. The aged retinas were obtained from 20 unrelated individuals (average age=71.8 year), while the AMD group consisted of 12 retinas (average age=77.1 year). Gene expression was measured by real-time qRT-PCR and normalized to rRNA expression, with aged normal retinas as a reference. There was no significant difference in either ARMS2 or HTRA1 mRNA expression levels between the two groups (ARMS2, fold change average=1.051, p=0.487; HTRA1, fold change average=0.991, p=0.918). As predicted, the housekeeping genes (used as controls), HPRT1 and GAPDH, did not show significant change in expression with age (fold change average=0.963, p=0.376 and fold change average=0.997, p=0.934), validating a high quality of RNA from the human retinas for qRT-PCR analysis. To determine changes in RNA expression due to aging, we compared the gene expressions of normal young ...
The second extended Meyer quote youve dug up is just awful. In addition to the whole protein-dominated ribosome, Meyer claims that 1) peptidyl transferase ribozymes are made of ribosomal RNA and 2) that these ribozymes are quite limited because they require another catalyst. (1) is wrong - the Zhang and Cech papers he cites _evolved_ ribozymes from random sequence, they are not free-standing ribosomal RNA. With (2) its hard to tell what Meyer was even thinking: my best guess is that the other catalyst hes referring to is magnesium, which is the only thing that could be considered another catalyst mentioned in the Zhang and Cech paper. If so, thats absurd - first, they dont even show that magnesium is playing a catalytic role, it may just be required for ribozyme folding (as it is for proper folding and function of the protein dominated ribosome); second, even if it is a cofactor involved directly in catalysis, that is incredibly common, not a weakness of the ribozyme. Many enzymes, ...
It has been shown that the overall transcription of ribosomal RNA genes can be stimulated by many signals (41); however, increased transcription is not due to an increased number of actively transcribed rDNA units but instead is due to changes in the rate of transcription, especially of elongation (42, 43). B-WICH is an ATP-dependent chromatin remodeling complex containing SNF2h, a human ISWI ATPase, and it was shown to associate with Pol I facilitating its transcription (30). The SIRT7 interaction with components of the B-WICH complex supports a hypothesis where SIRT7 regulates the rate of elongation of Pol I through the ATP-dependent remodeling activities of B-WICH.. SIRT7 knockdown is known to inhibit rDNA transcription (9, 10), and our results show for the first time that SIRT7 knockdown also leads to a reduction in the large subunit of Pol I at the protein level but not at the mRNA level. A question to be addressed in future studies is whether this regulation of Pol I protein level occurs ...
In the 1980s scientists discovered that, despite microbes invisibility to us, the microbial world is as, or more, diverse than the macroscopic world of plants and animals. Traditional measures of diversity relied on physical traits, but such criteria can not be used to assess relationships between microorganisms and macroorganisms because there are so few physical traits common to both. In the 1980s Carl Woese suggested that the deoxyribonucleic acid (DNA) sequences of certain common genes could be used to measure relatedness among radically different organisms. He picked the genes that encode ribosomal RNA (rRNA). Ribosomes, the protein-RNA complexes that are the scaffold on which proteins are synthesized, are common to all cells, both prokaryotic and eukaryotic. Despite differences in size, the sequences of rRNA molecules contain regions that are highly conserved, thus highly similar. Woese chose the intermediate sized rRNA molecule, 16S rRNA in prokaryotes and 18S rRNA in eukaryotes because ...
Raina, S. N. et al. 2001. Physical mapping of 18S-5.8S-26S and 5S ribosomal RNA gene families in three important vetches (Vicia species) and their allied taxa constituting three species complexes Theor. Appl. Genet. 103:839-845 ...
Sites of transcription of ribosomal RNA in HeLa cells were visualized by electron microscopy. Cells were either incubated with Br-uridine, or permeabilized and then incubated with BrUTP, before sites containing Br-RNA were immunolabeled with gold particles. Short incubations ensured that most incorporated analogue remained at synthetic sites. Fibrillar centres were unlabelled except at their periphery; label was concentrated over certain regions of the surrounding dense fibrillar component. These results suggest that the dense fibrillar component is the site of rRNA transcription. After dispersing the granular component and the dense fibrillar component by a hypotonic treatment, removal of most chromatin and preparation of resinless sections, fibrillar centres remained fixed to a nucleoskeleton. These structural and functional features are incorporated into a model for rRNA transcription. ...
TY - JOUR. T1 - Unsuitable of using ribosomal RNA as loading control fot northen blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors. AU - Solanas, M.. AU - Moral, R.. AU - Escrich, E.. PY - 2001/1/1. Y1 - 2001/1/1. M3 - Article. VL - 288. SP - 99. EP - 102. ER - ...
The overall size of a metazoan is controlled at the cellular level by the coordinate regulation of cell division and cell growth. Although it has long been established that inappropriate cell division can lead to cancer, it is becoming increasingly clear that cell growth, or increase in cell mass, is of equal importance. For example, the oncogenes Myc, Ras and Cyclin D (Prober and Edgar, 2001) and the tumor suppressors retinoblastoma (White, 1997) and Pten (Gao et al., 2000; Goberdhan et al., 1999; Huang et al., 1999) have all been shown to regulate cell growth. Although the factors that regulate cell division have been extensively studied (Sherr and Roberts, 1999), the processes that control cell growth are just beginning to be elucidated (Stocker and Hafen, 2000).. Given the dependence of cell growth on protein synthesis, regulation of translation is likely to play an important role in growth control. In fact, recent studies have shown that one mechanism of cell growth regulation is achieved ...
Ribosomes are large ribonucleoprotein complexes which incorporate amino acids into peptide chains during translational process in all types of living cells. The eukaryotic ribosome is larger compared to its prokaryotic counterpart. The size differences are due to a larger protein part and that the rRNA contains eukaryote specific expansion segments (ES). Cryo-EM reconstruction has visualized many ES on the ribosomal surface which have given clues about function and structural features. However, the secondary structures of most ES are unknown or ill defined. In this thesis, the secondary and also to a certain extent the tertiary structures of several ES are determined by using computational methods and biochemical experimental techniques. The juxtaposition of ES6 close to ES3 in the Cryo-EM image of the yeast ribosome suggested that ES3 and ES6 might interact. A computational analysis of more than 2900 sequences shows that a complementary helical region of seven to nine contiguous base pairs can ...
The sequence of the 16S ribosomal RNA (rRNA) from the archaebacterium Halobacterium volcanii has been determined by DNA sequencing methods.
Using antibodies to various nucleolar and ribosomal proteins, we define, by immunolocalization in situ, the distribution of nucleolar proteins in the different morphological nucleolar subcompartments. In the present study we describe the nucleolar localization of a specific ribosomal protein (S1) by immunofluorescence and immunoelectron microscopy using a monoclonal antibody (RS1-105). In immunoblotting experiments, this antibody reacts specifically with the largest and most acidic protein of the small ribosomal subunit (S1) and shows wide interspecies cross-reactivity from amphibia to man. Beside its localization in cytoplasmic ribosomes, this protein is found to be specifically localized in the granular component of the nucleolus and in distinct granular aggregates scattered over the nucleoplasm. This indicates that ribosomal protein S1, in contrast to reports on other ribosomal proteins, is not bound to nascent pre-rRNA transcripts but attaches to preribosomes at later stages of rRNA ...
Given its unique ability to regulate RNA polymerase I activity and synthesis of rRNA, we investigated the role of the transcription factor TIF-IA in the developing and adult nervous system. We demonstrate that TIF-IA-dependent functions are essential for the survival of both neural progenitors and nondividing neurons of the adult hippocampus. TIF-IA ablation in proliferating cells leads rapidly to activation of the apoptotic machinery. In contrast, in adult hippocampal neurons, significant signs of neurodegeneration are evident only several months after inducing the mutation, although strong interference with pre-rRNA synthesis occurs already early after induction of the mutation.. Increased levels of the p53 protein are found after TIF-IA ablation in rapidly dividing cells as well as in postmitotic neurons. The precise mechanism by which loss of TIF-IA leads to p53 increase requires further investigation. In neural progenitors one possible mechanism regulating p53 protein levels upon TIF-IA ...
Structure and function of ribosomal RNA Biochem Cell Biol. tRNAs are an essential component of translation, where their main function is … We discovered uncharacterized noncoding RNA molecules and identified that ∼30% of total noncoding small RNA transcriptome are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. The function of RNA polymerase: Because RNA pol II is responsible for the synthesis of mRNA, it is functioning in the process of transcription. At the ribosome, these … It occurs in ribosomes, which are made of rRNA and a variety of proteins. Ribosomal RNA (rRNA) The functions of the ribosomal RNAmolecules in the ribosomal particle are notfully understood, but they are necessary forribosomal assembly and seem to play keyroles in the binding of mRNA to ribosomesand its translation Recent studies suggest that an rRNAcomponent performs the peptidyl transferaseactivity and thus is an enzyme (a ribozyme). Functions of RNA. The function of ...
Our research focuses on how ribosomal subunits are assembled in eukaryotic cells. We use the yeast S. cerevisiae as a model organism to study this essential and highly conserved process. Ribosomes are among the largest and most complex macromolecular machines assembled in cells. Ribosomes are assembled from imported ribosomal proteins on nascent rRNA in the nucleolus of the cell. The large and small subunits are then independently exported through nuclear pores at rates that can reach 30 subunits per second. Both subunits require the export receptor Crm1 for export, and both undergo independent post-export maturation events that are required before the subunits are translation-ready. Over 150 proteins that do not end up as constituents of the mature ribosome are necessary for ribosome biogenesis. The molecular details of how most of these non-ribosomal proteins function is unknown. We have focused our work on the late steps of small subunit biogenesis. In particular, we are characterizing the ...
To investigate the function of the nucleolar protein Nop2p in Saccharomyces cerevisiae, we constructed a strain in which NOP2 is under the control of a repressible promoter. Repression of NOP2 expression lengthens the doubling time of this strain about fivefold and reduces steady-state levels of 60S ribosomal subunits, 80S ribosomes, and polysomes. Levels of 40S subunits increase as the free pool of 60S subunits is reduced. Nop2p depletion impairs processing of the 35S pre-rRNA and inhibits processing of 27S pre-rRNA, which results in lower steady-state levels of 25S rRNA and 5.8S rRNA. Processing of 20S pre-rRNA to 18S rRNA is not significantly affected. Processing at sites A2, A3, B1L, and B1S and the generation of 5 termini of different pre-rRNA intermediates appear to be normal after Nop2p depletion. Sequence comparisons suggest that Nop2p may function as a methyltransferase. 2-O-ribose methylation of the conserved site UmGm psi UC2922 is known to take place during processing of 27S ...
Cancer cells have a raised cellular metabolism, including increased protein biosynthesis. Three new studies now show that the oncoprotein Myc, known to drive cell division, also enhances ribosomal RNA synthesis by RNA polymerase I in addition to controlling RNA polymerase II- and III-regulated gene transcription. This suggests that Myc promotes the generation of crucial components of a functional ribosome.
Fingerprint Dive into the research topics of The rRNA Enhancer Regulates rRNA Transcription in Saccharomyces cerevisiae. Together they form a unique fingerprint. ...
Identifying Critical RNA-RNA Interactions during Ribosome Biogenesis is the title of the project that will be based at the U of L and within the Alberta RNA Research and Training Institute (ARRTI), but also include collaborators at the Universities of Sherbrooke and McGill University in Quebec, as well as three German institutions.. What excites me about this project is the intersection between it being medically important and also fundamentally important to understanding life. If you dont understand life, you cannot develop new therapeutic strategies, says Kothe, a professor of biochemistry in the Department of Chemistry & Biochemistry and Board of Governors Teaching Chair.. The CIHR grant has been close to a decade in the making. Kothe has revised and resubmitted her application multiple times over the years, indicating the competitive nature of these grants. By earning this funding, she is among the top 10 per cent of biomedical researchers in Canada. The grant also illustrates the growth ...
RS18_THETH] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [RS4_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [RS14Z_THETH] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [RS15_THETH] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [RS13_THET8] Located at the top of the head of the 30S subunit, it contacts several helices ...
In this issue of Molecular Cell, Bohnsack et al. (2009) identify multiple binding sites of the RNA helicase Prp43 on preribosomal RNA. The target regions suggest distinct functions of Prp43 in ribosome biogenesis.
The phylogeny of ground beetles of supertribe Trechitae is inferred using DNA sequences of genes that code for 28S ribosomal RNA, 18S ribosomal RNA, and wingless. Within the outgroups, austral psydrines are inferred to be monophyletic, and separate from the three genera of true Psydrina (Psydrus, Nomius, Laccocenus); the austral psydrines are formally removed from Psydrini and are treated herein as their own tribe, Moriomorphini Sloane. All three genes place Gehringia with Psydrina. Trechitae is inferred to be monophyletic, and sister to Patrobini.Within trechites, evidence is presented that Tasmanitachoides is not a tachyine, but is instead a member of Trechini. Perileptus is a member of subtribe Trechodina. Against Erwin’s hypothesis of anillines as a polyphyletic lineage derived from the tachyine genus Paratachys, the anillines sampled are monophyletic, and not related to Paratachys. Zolini, Pogonini, Tachyina, and Xystosomina are all monophyletic, with the latter two being sister groups. The
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
The determination of the high-resolution structures of ribosomal subunits in the year 2000 and of the entire ribosome a few years later are revolutionizing our understanding of the role of the ribosome in translation. In the present article, I summarize the main contributions from our laboratory to this worldwide effort. These include the determination of the structure of the 30S ribosomal subunit and its complexes with antibiotics, the role of the 30S subunit in decoding, and the high-resolution structure of the entire 70S ribosome complexed with mRNA and tRNA.. ...
The assignment of specific ribosomal functions toindividual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident
Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.
Ribonucleic Acid. A molecule essential in gene coding, decoding, regulation, and expression. Consists of sequences of the four nucleotide bases: Adenine, Uracil, Guanine, and Cytosine. Types of RNA include messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and other non-coding RNAs. Some viruses including Influenza A and Sars-Cov-2 have RNA genomes.. ...
In situations where the amount of available sample DNA is limited, or where there is a low level of pathogen DNA mixed with a high level of host DNA, and we wish to identify the pathogen, it can be helpful to amplify the target organism by PCR. For bacterial species identification, the 16S ribosomal RNA gene can be amplified from all bacteria non-specifically, without amplifying eukaryotic host DNA, or viruses. As with the whole-genome species ID approach shown in Fig. 1, we have found bead-beating to lyse cells rapidly, yielding DNA with a sufficiently high fragment length for amplification of the 1.5 kb 16S gene. There is no need to purify the extracted DNA before PCR. Fast polymerases are available which can process 1 kb of template in around 30 seconds, meaning that 16S PCR can be performed on a standard thermocycler in 25 minutes. If PCR is performed using Oxford Nanopores modified primers, sequencing adapters can be attached rapidly following amplification, by chemical ligation. This ...
Ribosome production, one of the most energy-consuming biosynthetic activities in living cells, is adjusted to growth conditions and coordinated wit...
Ribosomes are comprised of 65% RNA and 35% proteins. Ribosomes are cellular organelles that are responsible for Protein Synthesis. Ribosomes function
The Archaea / Bacteria division was only recognized relatively recently, however, since the nature of Archaea was not appreciated until the 1970s when ribosomal RNA began to be sequenced. It provided the first primitive molecular sequence that was common to every single form of life and thus provided a metric of diversity and geneology. The great American microbiologist Carl Woese labored to gather these sequences from obscure organisms and bacteria of all sorts. He made the shocking discovery that there were bacteria out there that were very, very different from the usual run of laboratory bacteria- the E. coli and various other disease-causing and easily-cultured bacteria that were the staff of biology since Pasteur. When he plotted out the sequences, these bacteria had ribosomal RNA that was a little more like animal sequences than bacterial, but not terribly similar to either. They werent from another planet, but they were different enough that he took the very bold step of claiming an ...
Ribosomal RNA(rRNA) persists for several days estimates for rRNA half-life in vitro range from ,3 days (human fibroblasts) (primary source), through 3.8 days (18S rRNA moiety in H1299 cells) (3), to about 7.5 days (cultured rat fibroblasts) (4 ...
The possibility exists, yes. Keep in mind that one of the best ways to identify a given bacterium is to sequence its ribosomal RNA genes. If your goal is to identify the bacteria present in a sample, a more affordable approach may be to use primers to amplify these genes from your sample and clone/sequence the fragments. You should be able to use these sequences to create a catalog of some of the more prevalent bacteria in the sample.. ...
Ribosomal RNA must have a strategic and important role that cannot be played by ribosomal proteins, nor perhaps by any other cellular component. The structural complexity of the ribosomal RNAs is not...
Ribosomes, the cellular factories that manufacture proteins, contain both RNA and protein, but exactly how all of the different ribosomal components contribute to protein synthesis is still not clear. Now, as Thomas Cech explains in his Perspective, atomic resolution of the structure of the large ribosomal subunit reveals that, as predicted by those convinced of a prebiotic RNA world, RNA is the catalytic component with proteins being the structural units that support and stabilize it ( Ban et al., Nissen et al., Muth et al.). ...
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Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.. ...
Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.. ...
"ARB-Silva: comprehensive ribosomal RNA database". The ARB development Team. Retrieved January 2, 2016.. ... as a set of 16S ribosomal RNA sequences with less than 85% similarity to already-described phyla.[32] More recently an even ... divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:[12][14] ... Atomic structure of the 30S ribosomal Subunit from Thermus thermophilus of which 16S makes up a part. Proteins are shown in ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.. *^ Johnson, B.J.; Robbins, K.E.; Bailey, R.E.; Cao, B.L.; ... "16S rRNA-based LTP release 111 (full tree)". Silva Comprehensive Ribosomal RNA Database [3]. Retrieved 2013-03-20. ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.. *^ J.P. Euzéby. "Treponema". List of Prokaryotic names with ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.. *^ J.P. Euzéby. "Bacteroidetes". List of Prokaryotic names ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.. *^ See the List of Prokaryotic names with Standing in ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... The CSIs found in DNA-directed RNA polymerase subunit beta and DNA topoisomerase I in Thermales species may be involved in ... Zhang G, Campbell EA, Minakhin L, Richter C, Severinov K, Darst SA (1999). "Crystal structure of Thermus aquaticus core RNA ...
SNORD71: encoding protein Small nucleolar RNA, C/D box 71. *SPSB3: encoding protein SplA/ryanodine receptor domain and SOCS box ... RPS15A: encoding protein 40S ribosomal protein S15a. *RSL1D1: encoding protein Ribosomal L1 domain-containing protein 1 ... LINC00273 encoding protein Long intergenic non-protein coding RNA 273. *LOC124220: encoding protein Zymogen granule protein 16 ... SNAI3-AS1: encoding protein SNAI3 antisense RNA 1. * ... Non-coding RNA genes. Pseudogenes. Source. Release date CCDS. ...
m Ribosomal RNA ‎ (→‎Prokaryotes vs. Eukaryotes) *13:24, 23 September 2007 (diff , hist) . . (0)‎ . . m Ribosomal RNA ‎ (typo: ...
LINC00511: encoding protein Long intergenic non-protein coding RNA 511. *LINC00674 encoding protein Long intergenic non-protein ... RPL23A: encoding protein 60S ribosomal protein L23a. *SC65: encoding protein Synaptonemal complex protein SC65 ...
Positive stranded RNA virus transcription is the method of transcription. Translation takes place by ribosomal skipping. The ... Replication follows the positive stranded RNA virus replication model. ...
The cladogram of Rickettsidae has been inferred by Ferla et al. [3] from the comparison of 16S + 23S ribosomal RNA sequences. ...
Small subunit ribosomal RNAs in several Chlorophyta and euglenid chloroplasts lack motifs for shine-dalgarno sequence ... "Large variations in bacterial ribosomal RNA genes". Molecular Biology and Evolution. 29 (10): 2937-48. doi:10.1093/molbev/ ... The two RNA polymerases may recognize and bind to different kinds of promoters within the chloroplast genome.[85] The ribosomes ... Chloroplasts make all of a cell's purines and pyrimidines-the nitrogenous bases found in DNA and RNA.[158] They also convert ...
RNA is subdivided into many categories, including messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), long non- ... Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA (April 2001). "RNA tertiary interactions in the large ribosomal subunit: the ... Some types of RNA show clear quaternary structure that is essential for function, whereas other types of RNA function as single ... Noller HF (1984). "Structure of ribosomal RNA". Annual Review of Biochemistry. 53: 119-62. doi:10.1146/annurev.bi.53.070184. ...
1,696 sequences RNA Genes: 52 RNA genes rRNAs: 1 5s rRNA, 1 16s rRNA, 1 23s rRNA 5s rRNA: This rRNA is important for ribosomal ... "5S Ribosomal RNA Database". Nucleic Acids Research. 30 (1): 176-178. doi:10.1093/nar/30.1.176. PMC 99124. PMID 11752286. Janda ... 23s rRNA: This rRNA is very important in the process of binding tRNA to ribosomal functional sites. tRNAs: 46 tRNAs ncRNAs: 3 ... "23S rRNA positions essential for tRNA binding in ribosomal functional sites". Proceedings of the National Academy of Sciences ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20. CS1 maint: discouraged parameter (link) Biology portal v t e ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-06-05. CS1 maint: discouraged parameter (link) Kineococcus at ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2018-07-20. Yamada, T.; Sekiguchi, Y.; Hanada, S.; Imachi, H.; Ohashi, A ... 16S ribosomal RNA identity, meaning that they could fall in different families or even orders. Recent phylogenetic analysis of ... divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera Chloroflexus, ... by both the usual phylogenetic means and the identification of shared conserved signature indels in the 50S ribosomal protein ...
"16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. J.P. ... Many of these CSIs in important housekeeping proteins such as Pol1, RecA, and TrpRS, and ribosomal proteins L4, L7/L12, S8, S9 ... 1999). "RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely ...
The All-Species Living Tree' Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA ... Furthermore, it has been found that the GC-content of ribosomal RNA (the traditional phylogenetic marker for prokaryotes) ... One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a ... much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales, even though they are more closely ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20. CS1 maint: discouraged parameter (link). ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. CS1 maint: discouraged parameter (link) J.P. Euzéby. " ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20. CS1 maint: discouraged parameter (link) J.P. Euzéby. " ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2018-07-20.. ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20.. ...
All-Species Living Tree Project."16S rRNA-based LTP release 106 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20. CS1 maint: discouraged parameter (link) Biology portal. ...
Silva Comprehensive Ribosomal RNA Database. Retrieved 2011-11-17. CS1 maint: discouraged parameter (link) Biology portal v t e ...
Transcription of early genes (E genes) by host RNA pol II: these proteins optimize the cellular milieu for viral replication, ... Translation takes place by ribosomal shunting. The virus exits the host cell by nuclear envelope breakdown, viroporins, and ... Transcription of late genes (L genes) by host RNA pol II, mostly encoding structural proteins. Host translation shutoff ...
Positive stranded rna virus transcription is the method of transcription. Translation takes place by -1 ribosomal frameshifting ... Replication of cardioviruses is dependent on a structured RNA element called the Cardiovirus cis-acting replication element ( ... Replication follows the positive stranded RNA virus replication model. ... viral initiation, and ribosomal skipping. The virus exits the host cell by lysis, and viroporins. Human and vertebrates serve ...
3 RNA-Viren *3.1 Doppelsträngige RNA-Viren (dsRNA, double stranded RNA). *3.2 Einzelstrang-RNA-Viren mit negativer Polarität ( ... Orsay virus utilizes ribosomal frameshifting to express a novel protein that is incorporated into virions, in: Virology 450-451 ... 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]. ...
8]-they code for four ribosomal RNAs, 30-31 tRNAs, 21 ribosomal proteins, and four RNA polymerase subunits,[22][23] involved in ... RNA editing in plastidsEdit. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior ... Chloroplasts also contain a mysterious second RNA polymerase that is encoded by the plant's nuclear genome. The two RNA ... The inverted repeat regions usually contain three ribosomal RNA and two tRNA genes, but they can be expanded or reduced to ...
The most important RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of ... Non-coding RNA or "RNA genes". These are a broad class of genes that encode RNA which is not translated into protein. ... RNA polymerase IV synthesizes siRNA in plants.[5]. *RNA polymerase V synthesizes RNAs involved in siRNA-directed ... Grummt I. (1999). "Regulation of mammalian ribosomal gene transcription by RNA polymerase I.". Prog Nucleic Acid Res Mol Biol. ...
... strand RNA genome is replicated through a double-stranded RNA intermediate that is formed using viral RDRP (RNA-Dependent RNA ... 1 ribosomal frameshifting, viral initiation, and ribosomal skipping. The virus exits the host cell by lysis, and viroporins. ... The mRNA encodes RNA dependent RNA polymerase. This polymerase makes complementary minus strands of RNA, then uses them as ... Genomic RNAs of picornaviruses possess multiple RNA elements and they are required for both negative and plus strand RNA ...
... were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular RNA ... although there are many introns in their transfer RNA and ribosomal RNA genes,[146] and introns may occur in a few protein- ... Fox based on the sequences of ribosomal RNA (rRNA) genes.[10] These two groups were originally named the Archaebacteria and ... results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed ...
... where it is initiated by recruitment of the RNA-induced transcriptional silencing (RITS) complex to double stranded RNAs ... Hannon Bozorgmehr J (Oct 2019). "The origin of chromosomal histones in a 30S ribosomal protein". Gene. doi:10.1016/j.gene. ... "Huang R C & Bonner J. Histone, a suppressor of chromosomal RNA synthesis. Proc. Nat. Acad. Sci. US 48:1216-22, 1962" (PDF). ... The formation of this mark is tied to transcription in a rather convoluted manner: early in transcription of a gene, RNA ...
Important information on protein synthesis, ligand binding and RNA interaction can be obtained using this novel technique at ... random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli". Journal of Microscopy. 146 (Pt 2): 113-36 ...
... divided bacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences:[5][6] ... All modern ideas start with the sequence analysis of DNA and RNA. In 1987, Carl Woese, the forerunner of the molecular ...
Schmidt TM, Relman DA (1994). Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods in ... The Ribosomal Database Project[editar , editar a fonte]. The Ribosomal Database Project (RDP) é unha base de datos revisados ... SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. ... Coenye T, Vandamme P (November 2003). "Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced ...
Hedges, S. B. et al. (1990) Tetrapod phylogeny inferred from 18s and 28s ribosomal RNA sequences and a review of the evidence ... Os primeiros estudos de secuencias de ADN mitocondrial e ADN ribosomal nuclear sustentaban unha relación achegada entre as ...
regulation of transcription from RNA polymerase II promoter. • cellular response to UV. • ribosomal large subunit export from ... large ribosomal subunit. • small ribosomal subunit. • nuclear speck. • macromolecular complex. • Ribonucleoprotein. Processo ... ribosomal large subunit binding. • protein homodimerization activity. • ribosomal small subunit binding. • unfolded protein ... ribosomal large subunit biogenesis. • ribosomal small subunit biogenesis. • negative regulation of apoptotic process. • ...
Werner F (2007). "Structure and function of archaeal RNA polymerases". Mol. Microbiol. 65 (6): 1395-404. PMID 17697097. doi: ... a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids". Environ. Microbiol. 9 (4): 1001-16 ... "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, ...
"Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of ... Atkins JF, Gesteland RF, Cech T (2006). The RNA world: the nature of modern RNA suggests a prebiotic RNA world. Plainview, N.Y ... of RNAs with molecular properties predicted for RNAs of the RNA World constitutes an additional argument supporting the RNA ... Properties of RNA[edit]. The properties of RNA make the idea of the RNA world hypothesis conceptually plausible, though its ...
Rowan R, Powers DA (1992) Ribosomal-RNA sequences and the diversity of symbiotic dinoflagellates (zooxanthellae). Proc Natl ... ribosomal e nuclear de copia única. O uso de múltiples marcadores, xunto cunha clasificación filoxenética xerárquica ...
Winker, S; Woese CR (1991). "A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA ... Hansmann, S; Martin W (2000). "Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is ... Achenbach-Richter, L; Woese CR (1988). "The ribosomal gene spacer region in archaebacteria". Syst. Appl. Microbiol. 10: 211-214 ...
They are transfer RNA (tRNA) and ribosomal RNA (rRNA).. tRNA[change , change source]. Transfer RNA (tRNA) is a short molecule ... RNA is physically different from DNA: DNA contains two intercoiled strands, but RNA only contains one single strand. RNA also ... Protein synthesis RNAs[change , change source]. Messenger RNA[change , change source]. The structure of a mature eukaryotic ... This is called RNA interference.[5][6][7]. siRNA[change , change source]. Small interfering RNAs (sometimes called silencing ...
Professor of environmental health engineering best known for the use of 16S ribosomal RNA-targeted techniques and community- ...
ஆர்க்கீயாவின் ரைபோசோமிய ஆர்.என்.ஏ (ribosomal RNA) மற்றும் நகர் ரைபோகருக்காடிகள் பாக்டீரியாவில் உள்ளதை விட வேறான கட்டுமானம் ... 1983), Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type, The EMBO Journal, 2(8): 1291-1294. ...
Non-coding RNA genes Pseudogenes Source Release date CCDS. 63. -. - [2]. 2016-09-08 ... RPS4Y1/RPS4Y2/RPS4X (Ribosomal protein S4). *DDX3Y (helicase) similar to DDX3X on X ...
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. ...
A common non-ribosomal peptide is glutathione, a component of the antioxidant defenses of most aerobic organisms.[9] Other ... RNA, etc.), or to complex macromolecular assemblies.[3] Finally, while aspects of the lab techniques applied to peptides versus ... Some ribosomal peptides are subject to proteolysis. These function, typically in higher organisms, as hormones and signaling ... The peptide families in this section are ribosomal peptides, usually with hormonal activity. All of these peptides are ...
This includes four ribosomal RNAs, approximately 30 tRNAs, 21 ribosomal proteins, and 4 subunits of the plastid-encoded RNA ... RNA editing in plastids[edit]. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript ... Chloroplasts also contain a mysterious second RNA polymerase that is encoded by the plant's nuclear genome. The two RNA ... The inverted repeat regions usually contain three ribosomal RNA and two tRNA genes, but they can be expanded or reduced to ...
... circular RNA, and enhancer RNA, size selection is not applicable for depleting the highly abundant ribosomal RNA molecules (18S ... Standard methods such as microarrays and bulk RNA-seq analysis analyze the expression of RNAs from large populations of cells. ... Current scRNA-seq protocols involve isolating single cells and their RNA, and then following the same steps as bulk RNA-seq: ... However, recent studies are now starting to appreciate the importance of non-poly(A) RNA, such as long-noncoding RNA and ...
... residual ribosomal RNA allows further synthesis of Hb until the reticulocyte loses its RNA soon after entering the vasculature ... this hemoglobin-synthetic RNA in fact gives the reticulocyte its reticulated appearance and name).[33] ... "Characteristics of RNA degradation in the erythroid cell". The Journal of Clinical Investigation. 48 (7): 1266-72. doi:10.1172 ...
Transfer RNA (tRNA), that mediates recognition of the codon and provides the corresponding amino acid, and ribosomal RNA (rRNA ... A 5' cap (also termed an RNA cap, an RNA 7-methylguanosine cap, or an RNA m7G cap) is a modified guanine nucleotide that has ... Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they ... Small interfering RNA (siRNA)Edit. Main article: siRNA. In metazoans, small interfering RNAs (siRNAs) processed by Dicer are ...
An important step was later realization (in 1960) that the messenger RNA was not the same as the ribosomal RNA. None of this, ... DNA → RNA → Protein. Some critics thought that by using the word "dogma", Crick was implying that this was a rule that could ... In 1956, Crick wrote an informal paper about the genetic coding problem for the small group of scientists in Gamow's RNA group. ... George Gamow established a group of scientists interested in the role of RNA as an intermediary between DNA as the genetic ...
A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA ... 9] Sequences within ribosome binding site affecting messenger RNA translatability and method to direct ribosomes to single ... "Ribosomal Binding Site Sequence Requirements". www.thermofisher.com. Retrieved 2015-10-16.. ... The ribosomal protein S1 binds to adenine sequences upstream of the RBS. Increasing the concentration of adenine upstream of ...
The group is defined primarily in terms of ribosomal RNA (rRNA) sequences. ...
The 5S ribosomal RNA (5S rRNA) is an approximately 120 nucleotide-long ribosomal RNA molecule with a mass of 40 kDa. It is a ... "Interaction of the RNA binding fingers of Xenopus transcription factor IIIA with specific regions of 5 S ribosomal RNA". ... Sun, FJ; Caetano-Anollés, G (Nov 2009). "The evolutionary history of the structure of 5S ribosomal RNA". Journal of Molecular ... In bacteria and archaea, the large ribosomal subunit (LSU) itself is composed of two RNA moieties, the 5S rRNA and another ...
28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and ... the Ribosomal Database Project; SILVA, a ribosomal RNA gene database project. Lodish, Harvey F.; Darnell, James E. (1995-01-01 ... "Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers". ... "Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics". RNA. 21 (10): 1719 ...
Variation among human 28S ribosomal RNA genes. I L Gonzalez, J L Gorski, T J Campen, D J Dorney, J M Erickson, J E Sylvester, R ... Variation among human 28S ribosomal RNA genes. I L Gonzalez, J L Gorski, T J Campen, D J Dorney, J M Erickson, J E Sylvester, R ... Variation among human 28S ribosomal RNA genes. I L Gonzalez, J L Gorski, T J Campen, D J Dorney, J M Erickson, J E Sylvester, ... The rapid divergence rates of variable regions in the ribosomal gene may permit answers to the question of time of separation ...
For example, the ribosomal RNA gene rrnD of Escherichia coli has the opposite orientation fro rrnB and rrnE and is separated ... Inversions between ribosomal RNA genes of Escherichia coli. C W Hill and B W Harnish ...
Ribosomal RNA methyltransferase FtsJ domain (IPR002877) *Adrift-type ribose 2-O-methyltransferase domain (IPR025807) ... Ribosomal RNA methyltransferase FtsJ domain (IPR002877). Short name: rRNA_MeTrfase_FtsJ_dom ... RrmJ recognises its methylation target only when the 23 S rRNA is present in 50 S ribosomal subunits. This suggests that the ... RNA methylation under heat shock control.. Mol. Cell 6 349-60 2000 ...
DU-DC2 18S ribosomal RNA genes, partial sequence. *AH009061.2Rhizophydium sp. UGA-F15 18S ribosomal RNA genes, partial sequence ... JEL183 18S ribosomal RNA genes, partial sequence. *AH009065.2Physocladia obscura strain JEL137 18S ribosomal RNA genes, partial ... Fungi 18S ribosomal RNA genes, partial sequence. Fungi 18S ribosomal RNA genes, partial sequence.. PopSet: 1032519594 ... AH009068.2Catenaria anguillulae strain JEL194 18S ribosomal RNA genes, partial sequence. *AH009067.2Harpochytrium sp. JEL94 18S ...
RNA techniques:. Isolation of total RNA from T4-infected cells, primer-extension analysis of soc RNA, and analysis of cDNA ... RNA Cleavage Linked With Ribosomal Action. Haruyo Yamanishi and Tetsuro Yonesaki. Genetics October 1, 2005 vol. 171 no. 2 419- ... RNA Cleavage Linked With Ribosomal Action. Haruyo Yamanishi and Tetsuro Yonesaki. Genetics October 1, 2005 vol. 171 no. 2 419- ... RNA Cleavage Linked With Ribosomal Action. Haruyo Yamanishi and Tetsuro Yonesaki. Genetics October 1, 2005 vol. 171 no. 2 419- ...
Ribosomal RNA (rRNA) is a type of non-coding ribonucleic acid (RNA) that is a primary and permanent component of ribosomes, the ... 5S rRNA is transcribed by RNA polymerase III.. The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been ... is composed of ribosomal RNA and protein. It is at the site of the ribosome that messenger RNAs (mRNA) code for linking amino ... Ribosomal RNA. Encyclopedia of Life Sciences. Retrieved October 4, 2008.. *Smit, S., J. Widmann, and R. Knight. 2007. ...
Entomoplasma melaleucae 16S ribosomal RNA gene, partial sequence Entomoplasma melaleucae 16S ribosomal RNA gene, partial ... Ribosomal Database Project II [Ribosomal Database Project II] Ribosomal Database Project II ...
Ribosomal RNA is a material that combines with proteins to make a structure that transforms mRNA into other proteins. Its main ... Ribosomal ribonucleic acid (ribosomal RNA or rRNA) helps to form the ribosome itself. Unlike messenger RNA (mRNA), it does not ... Ribosomal RNA is just as fundamental and widespread among bacteria as it is in the animal kingdom. As a consequence, many ... Ribosomal RNA appears as two separate parts which operate together. They are the large subunit (LSU) and the small subunit (SSU ...
... a type of RNA synthesized in the nucleolus by RNA polymerase I, is the central component of the ribosome, the protein ... Ribosomal RNA (rRNA), a type of RNA synthesized in the nucleolus by RNA polymerase I, is the central component of the ribosome ... 5S rRNA is transcribed by RNA polymerase III. The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been ... Ribosomal RNA characteristics are important in medicine and in evolution. * rRNA is the target of several clinically relevant ...
ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.. About ASM , Contact Us , Press Room. ASM is a member of. ...
Rapid Diagnosis of Bacteremia by Universal Amplification of 23S Ribosomal DNA Followed by Hybridization to an Oligonucleotide ...
18S RNA) and two of the rRNAs of the large ribosomal subunit (5.8S and 28S RNA) into 1 transcription unit (Figure 1). Because ... Zamb, T. J., and T. D. Petes, 1982 Analysis of the junction between ribosomal RNA genes and single-copy chromosomal sequences ... Ritossa, F. M., 1968 Unstable redundancy of genes for ribosomal RNA. Proc. Natl. Acad. Sci. USA 60: 509-516. ... Organization of the ribosomal RNA (rRNA) genes in eukaryotes. The genes are organized into tandemly repeated units as ...
... dependent methyltransferase responsible for the formation of m5U at U747 and U1939 of 23S ribosomal RNA in Streptococcus ... Ribosomal RNA Is the Subject Area "Ribosomal RNA" applicable to this article? Yes. No. ... RNA structure Is the Subject Area "RNA structure" applicable to this article? Yes. No. ... Transfer RNA Is the Subject Area "Transfer RNA" applicable to this article? Yes. No. ...
Intimacy counselling. Find out more about our free, confidential counselling with medical specialists trained in intimacy, body image, sexual confidence and relationships. Available to all those facing cancer and their partners, including members of the LGBTQI community. ...
... no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the ... Ribosomal RNA: a key to phylogeny FASEB J. 1993 Jan;7(1):113-23. doi: 10.1096/fasebj.7.1.8422957. ... no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the ...
Circular RNAs are widely expressed in eukaryotic cells but their functions and mechanisms of action are still being elucidated ... Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans. *Lesca M. Holdt1, 2. *, Anika ... How to cite this article: Holdt, L. M. et al. Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and ... RNA 19, 141-157 (2013).. **CAS*PubMed*Article*Google Scholar*2.. Memczak, S. et al. Circular RNAs are a large class of animal ...
16S ribosomal RNA. Details. Name. 16S ribosomal RNA. Kind. nucleotide. Organism. Enteric bacteria and other eubacteria. Drug ...
RNA Sequencing. Ribosomal RNA and globin mRNA removal. Efficient ribosomal RNA and globin mRNA removal. To maximize your unique ... QIAseq FastSelect Custom RNA Removal Kits. For rapid removal of unwanted RNAs during RNA-seq library preparation ... For rapid 5S/16S/23S rRNA removal for RNA-seq library preparation from bacterial RNA samples ... you need efficient and near complete ribosomal RNA removal (rRNA removal). Our dedicated kits are specifically designed for ...
RNA Sequencing. Ribosomal RNA and globin mRNA removal. Efficient ribosomal RNA and globin mRNA removal. To maximize your unique ... For rapid 5S/16S/23S rRNA removal for RNA-seq library preparation from bacterial RNA samples ... you need efficient and near complete ribosomal RNA removal (rRNA removal). Our dedicated kits are specifically designed for ... For rapid rRNA and/or globin mRNA removal for RNA-seq library preparation from human, mouse, rat and other mammalian samples ...
RNA-sequencing, and other methods. The Ambion® WT Expression Kit for RNA amplification prior to microarray analysis circumvents ... Enrichment of whole transcriptome RNA by depleting ribosomal RNA (rRNA) species using our RiboMinus™ technology has the ... Enrichment of whole transcriptome RNA by depleting ribosomal RNA (rRNA) species using our RiboMinus™ technology has the ... Drosophila 28S ribosomal RNA is processed into 2 fragments that migrate in a similar manner to the 18S rRNA. ...
... Syst Appl Microbiol. 1998 Jun;21(2): ...
... Benjamin Albert,1,2 Jorge Perez- ... Ribosomal RNA (rRNA) production represents the most active transcription in the cell. Synthesis of the large rRNA precursors ( ... E. Schweizer and H. O. Halvorson, "On the regulation of ribosomal RNA synthesis in yeast," Experimental Cell Research, vol. 56 ... Y. N. Osheim, S. L. French, K. M. Keck et al., "Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior ...
Encyclopedia , Ribosomal RNA. Ribosomal RNA (rRNA), a type of RNA synthesized in the nucleolus by RNA Pol I, is the central ... Guide RNA (gRNA) is a type of RNA that is used in mRNA editing. ... A short hairpin RNA (shRNA) is a sequence of RNA that makes ... Categories: Protein biosynthesis , RNA , Non-coding RNA , Ribosomal RNA Biochemistry is the study of the chemical processes in ... 5S rRNA is transcribed by RNA polymerase III.. The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been ...
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
Ribosomal RNA large subunit methyltransferase CfrAdd BLAST. 349. Amino acid modifications. Feature key. Position(s). ... Ribosomal RNA large subunit methyltransferase CfrUniRule annotation. Manual assertion according to rulesi ... sp,A5HBL2,CFR_STAAU Ribosomal RNA large subunit methyltransferase Cfr OS=Staphylococcus aureus OX=1280 GN=cfr PE=1 SV=1 ... "A new mechanism for chloramphenicol, florfenicol and clindamycin resistance: methylation of 23S ribosomal RNA at A2503.". ...
Computer model showing a bacterial ribosomal protein (green) complexed with a transfer-messenger RNA (tmRNA, orange) and the ... Caption: Ribosomal RNA (ribonucleic acid) complex. Computer model showing a bacterial ribosomal protein (green) complexed with ... ribosomal, ribosome, rna, space-fill, space-filled, spacefill, spacefilled, structure, transfer-messenger, white background ... a transfer-messenger RNA (tmRNA, orange) and the elongation factor G (pink). tmRNA tags incorrectly synthesised proteins for ...
Recognition of the Codon-Anticodon Helix by Ribosomal RNA Message Subject. (Your Name) has forwarded a page to you from Science ... Highly conserved regions of ribosomal RNA (rRNA) form the tRNA-binding sites (5). The codon-anticodon interactions in the ... Experiments are presented that reveal possible contacts between 16S ribosomal RNA and the codon-anticodon complex. N1 ... In the structure of a model RNA oligonucleotide, the N1 positions of A1492 and A1493 point into the minor groove of the RNA (8 ...
  • Ribosomal DNA (rDNA) is not composed of multiple copies of identical transcription units, as commonly believed, but rather of at least seven rDNA variant subtypes that are expressed in somatic cells. (bioone.org)
  • Analysis of transcribed ribosomal DNA (rDNA) after Miller spreading revealed that up to 150 Pol I enzymes simultaneously transcribe rRNA genes in mutant with only 25 rRNA genes [ 1 , 7 ] (Figures 1(c) and 1(d) ). (hindawi.com)
  • The grasshopper Eyprepocnemis plorans harbors B chromosomes containing large amounts of ribosomal DNA (rDNA) units, some of which are eventually active, but the amount of rRNA transcripts contributed by B chromosomes, compared to those of the standard (A) chromosomes, is unknown. (springer.com)
  • The presented method utilizes primers specific for the internal transcribed spacer region (ITS) of ribosomal DNA (rDNA) genes. (jove.com)
  • However, in highly metabolic cells, more than 60% of total cellular transcription results from ribosomal DNA (rDNA) transcription, by the RNA polymerase I (RNAP1), which takes place in the nucleolus. (archives-ouvertes.fr)
  • Chromatin immunoprecipitation assays revealed that ErbB2 enhances binding of RNA Pol I to rDNA. (aacrjournals.org)
  • In addition, ErbB2 associated with rDNA, RNA Pol I, and β-actin, suggesting how it could stimulate rRNA production, protein synthesis, and increased cell size and cell growth. (aacrjournals.org)
  • Epigenetic changes accompanying plant cell dedifferentiation and differentiation are reported in 35S ribosomal DNA (rDNA) of tobacco ( Nicotiana tabacum ). (plantphysiol.org)
  • The data together indicate that the establishment of pluripotency and cell proliferation occurring with callus induction is associated with enhanced ribosomal RNA gene expression and overall rDNA hypomethylation, but is not associated with material-enhanced relaxation of chromatin structure (decondensation) at rDNA loci. (plantphysiol.org)
  • 18S-5.6S-25S and 5S ribosomal DNA (rDNA) sites were located by in situ hybridization to the three main species of the Saccharum genus. (ovid.com)
  • Here we describe the first direct method for the rapid coextraction of RNA and DNA from soil for the comparison of bacterial diversity by 16S rRNA reverse transcription-PCR (RT-PCR) and 16S ribosomal DNA (rDNA)-PCR. (asm.org)
  • Yet, epigenetic features of the ribosomal DNA (rDNA) operon and changes in the ribosome's molecular composition have been associated with disease phenotypes, suggesting that the ribosome itself may possess inherent regulatory capacity. (sciencemag.org)
  • Analyzing whole-genome sequencing data from the 1000 Genomes Project and the Mouse Genomes Project, we find that rDNA copy number varies widely across individuals, and we identify pervasive intra- and interindividual nucleotide variation in the 5 S , 5.8 S , 18 S , and 28 S ribosomal RNA (rRNA) genes of both human and mouse. (sciencemag.org)
  • 20047967 ). Has also an essential role in 40S ribosomal subunit biogenesis independent on its methyltransferase activity, facilitating the incorporation of ribosomal protein S19 during the formation of pre-ribosomes (By similarity). (uniprot.org)
  • One class of the single-stranded non-coding RNAs in the cell's nucleolus, called SNORDs, are known to guide the methyltransferase enzyme fibrillarin to methylate specific bases of ribosomal RNA. (uab.edu)
  • We identified rmtE1 , an uncommon 16S ribosomal methyltransferase gene, in an aminoglycoside- and cephalosporin-resistant Escherichia coli sequence type 448 clinical strain co-harboring bla CMY-2 . (cdc.gov)
  • [11] 5S rRNA together with the ribosomal proteins L5 and L18 and the domain V of 23S rRNA constitute the bulk of the central protuberance (CP). (wikipedia.org)
  • In bacteria and archaea , the large ribosomal subunit (LSU) itself is composed of two RNA moieties, the 5S rRNA and another larger RNA known as 23S rRNA , along with numerous associated proteins. (wikipedia.org)
  • Proteins are shown in blue and RNA in orange. (newworldencyclopedia.org)
  • The formation of proteins by rRNA, mRNA, and tRNA is remarkably complex, involving transcription of the various RNAs from DNA, the movement of RNA within a cell, different types of rRNA, and the process of assembling the amino acids in a precise order. (newworldencyclopedia.org)
  • It is at the site of the ribosome that messenger RNA's (mRNA) code for linking amino acids together to form new proteins and where transfer RNAs (tRNA) transfer specific amino acids to the growing polypeptide chain during the translation of the mRNA into a protein. (newworldencyclopedia.org)
  • The central dogma of cellular biology is that DNA is transcribed into RNA, which is translated into proteins. (wisegeek.com)
  • Ribosomal RNA forms a complex with various proteins in order to bind the amino acids together. (wisegeek.com)
  • Ribosomal RNA is a nucleic acid that, together with proteins , makes up the ribosome . (biology-online.org)
  • Ribosomal RNA, in turn, does not carry the code in making proteins. (biology-online.org)
  • Chloroplasts of the unicellular flagellate eukaryote Euglena gracilis contain several copies of a circular 135-140-kilobase pair DNA 1 which codes for chloroplast-specific stable RNAs (16S, 23S (refs 2, 3), 5S rRNAs 4 and tRNAs 5 ) and for an unknown number of chloroplast-specific proteins. (nature.com)
  • Transcription factors are proteins that bind to specific DNA sequences, and control the movement (transcription) of genetic information from DNA to mRNA (messenger RNA) during gene expression. (sciencephoto.com)
  • This supports a postulate, long debated in biology, that the ribosomal protein factories can be reprogrammed in response to stresses to favor the manufacture of certain proteins. (uab.edu)
  • Ribosomes are macromolecular machines made of ribosomal RNAs and ribosomal proteins, and mammalian cells may have as many as 10 million of them. (uab.edu)
  • The mammalian ribosome is composed of 4 RNA species and approximately 80 different ribsomal proteins (RPs). (humpath.com)
  • Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. (umassmed.edu)
  • Structure of the RNA-tagging machinery shows that only one pair of proteins (blue) can add tags to the RNA (red) at a time. (embl-hamburg.de)
  • To build these factories, other 'machines' inside the cell have to produce specific RNA molecules and fold them into the right shape, then combine the folded RNA with proteins to form a working ribosome. (embl-hamburg.de)
  • Translation of the former, which include translation factors and ribosomal proteins, would favor growth, while translation of the latter, which include genes involved in cell cycle progression, would favor division ( Thomas, 2000 ). (biologists.org)
  • An in vitro transcribed and folded ES6 sequence differed from that observed in situ, suggesting that chaperones, ribosomal proteins, and/or the tertiary rRNA interaction could be involved in the in vivo folding of ES6. (diva-portal.org)
  • Varied and tissue-specific disease phenotypes associated with the perturbation of ribosomal proteins as well as posttranscriptional and posttranslational modifications of ribosomal components ( 1 , 2 ) have renewed interest in the hypothesis that functionally distinct ribosome subpopulations may exist in the cell ( 3 - 5 ), often referred to as specialized ribosomes ( 6 ). (sciencemag.org)
  • While physical heterogeneities in the ribosome arising from differences in the sequences and stoichiometries of ribosomal and ribosome-associated proteins have recently drawn significant attention ( 7 - 9 ), the existence and contribution of sequence variation in ribosomal RNA (rRNA) as a potential source of ribosome heterogeneity has received less consideration. (sciencemag.org)
  • Discovery that the transcriptional output of the human genome is far more complex than predicted by the current set of protein-coding annotations and that most RNAs produced do not appear to encode proteins has transformed our understanding of genome complexity and suggests new paradigms of genome regulation. (biomedcentral.com)
  • [4] [5] Eukaryotic 5S rRNA is synthesized by RNA polymerase III , whereas other eukaryotic rRNAs are cleaved from a 45S precursor transcribed by RNA polymerase I . In Xenopus oocytes , it has been shown that fingers 4-7 of the nine- zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. (wikipedia.org)
  • [6] [7] Binding between 5S rRNA and TFIIIA serves to both repress further transcription of the 5S RNA gene and stabilize the 5S RNA transcript until it is required for ribosome assembly. (wikipedia.org)
  • All lineages organize the single rRNA of the small ribosomal subunit (18S RNA) and two of the rRNAs of the large ribosomal subunit (5.8S and 28S RNA) into 1 transcription unit ( Figure 1 ). (genetics.org)
  • The Ambion® WT Expression Kit for RNA amplification prior to microarray analysis circumvents the need to deplete rRNA by selectively eliminating rRNA from reverse transcription in the amplification process. (thermofisher.com)
  • Ribosomal RNA (rRNA) production represents the most active transcription in the cell. (hindawi.com)
  • The purified factor activates RNA polymerase I (RNA pol I) transcription through direct interactions with either control element. (sciencemag.org)
  • A second RNA pol I transcription factor, designated SL1, participates in the promoter recognition process and is required to reconstitute transcription in vitro. (sciencemag.org)
  • Molecular model showing the 6 zinc fingers of transcription factor IIIA (yellow) bound to RNA (ribonucleic acid, red and blue) from a 5s ribosome sub-unit. (sciencephoto.com)
  • some investigators have detected nascent RNA in the dense fibrillar components (DFCs) while others have localized transcription to the fibrillar centers (FCs). (biomedsearch.com)
  • We traced a movement of RNA from transcription sites through DFCs to granular components. (biomedsearch.com)
  • Reversal of the group I intron self-splicing reaction, termed reverse splicing, coupled with reverse transcription and genomic integration potentially mediate an RNA-based intron mobility pathway. (biomedsearch.com)
  • In this study, we defined a novel function of nuclear ErbB2 in enhancing rRNA gene transcription by RNA polymerase-I (RNA Pol I). Nuclear ErbB2 physically associates with β-actin and RNA Pol I, coinciding with active RNA Pol I transcription sites in nucleoli. (aacrjournals.org)
  • Finally, ErbB2-potentiated RNA Pol I transcription could be stimulated by ligand and was not substantially repressed by inhibition of PI3-K and MEK/ERK (extracellular signal regulated kinase), the main ErbB2 effector signaling pathways. (aacrjournals.org)
  • The only other gene that has so far been shown to negatively regulate RNA polymerase I and III transcription is ncl-1 (for abnormal nucleolus) from the soil nematode Caenorhabditis elegans . (biologists.org)
  • RNA polymerases (RNAPs) contain a conserved 'secondary channel' which binds regulatory factors that modulate transcription initiation. (elifesciences.org)
  • In Escherichia coli , the secondary channel factors (SCFs) GreB and DksA both repress ribosomal RNA (rRNA) transcription, but SCF loading and repression mechanisms are unclear. (elifesciences.org)
  • P.4 right column 2nd paragraph:'A few of the mRNA transcription rates are in the range of speeds typically associated with ribosomal RNA transcription (~70 nt/s) and may be the consequence of regulation by transcriptional elongation factors (primary source). (harvard.edu)
  • Sites of transcription of ribosomal RNA in HeLa cells were visualized by electron microscopy. (biologists.org)
  • After further investigation we could show that c-Myc binds to and activates RNA polymerase I-mediated transcription of the ribosomal RNA (rRNA) genes located in the nucleoli and that proteasomes are involved in this process. (diva-portal.org)
  • lncNB1 binds to the ribosomal protein RPL35 to enhance E2F1 protein synthesis, leading to DEPDC1B gene transcription. (garvan.org.au)
  • Granular particles that were tentatively identified as RNA polymerase molecules were not restricted to the transcription l complexes. (uni-wuerzburg.de)
  • Temporal programming of chloroplast and cytoplasmic ribosomal RNA transcription in the synchronous cell cycle of Chlamydomonas reinhardtii. (rupress.org)
  • While these approaches underscored the complexity of transcriptional output from the human genome [ 10 ], tiling arrays could predict only the complexity, but not the relative mass of 'dark matter' RNA as a fraction of total transcription and, hence, they could not make strong conclusions about its importance. (biomedcentral.com)
  • As non-coding RNA, rRNA itself is not translated into a protein, but it does provide a mechanism for decoding messenger RNA ( mRNA ) into amino acids and interacting with the transfer RNAs ( tRNAs ) during translation by providing peptidyl transferase activity. (newworldencyclopedia.org)
  • Unlike messenger RNA (mRNA), it does not transmit genetic information. (wisegeek.com)
  • The most importance is placed on RNA polymerase II (Pol II), which is responsible for synthesizing mRNA and a large variety of noncoding RNAs. (hindawi.com)
  • An operon is a group of key nucleotide sequences including an operator, a common promoter, and one or more structural genes that are controlled as a unit to produce messenger RNA (mRNA). (statemaster.com)
  • The fidelity of protein synthesis is determined by the interaction of an mRNA codon with the anticodon of the correct (cognate) transfer RNA (tRNA) within the aminoacyl-tRNA site (A site) of the ribosome. (sciencemag.org)
  • In the absence of tRNA fMet , biotin-tRNA Phe binds exclusively to the ribosomal P site in a mRNA-dependent fashion ( 11 ). (sciencemag.org)
  • The canonical translation initiation pathway begins with cap-dependent attachment of the small ribosomal subunit (SSU) to the messenger ribonucleic acid (mRNA) followed by an energy-dependent, sequential 'scanning' of the 5′ untranslated regions (UTRs). (mdpi.com)
  • N6-Methyladenosine (m6A) RNA modification is present in messenger RNAs (mRNA), ribosomal RNAs (rRNA), and spliceosomal RNAs (snRNA) in humans. (inserm.fr)
  • Ribosomal RNA (rRNA) is a type of non-coding ribonucleic acid (RNA) that is a primary and permanent component of ribosomes , the small, cellular particles that form the site of protein synthesis in all living cells . (newworldencyclopedia.org)
  • Ribosomal ribonucleic acid (ribosomal RNA or rRNA) helps to form the ribosome itself. (wisegeek.com)
  • Ribosomal RNA (ribonucleic acid) complex. (sciencephoto.com)
  • Corrie Saux , Chris Simon , and Greg S. Spicer "Phylogeny of the Dragonfly and Damselfly Order Odonata as Inferred by Mitochondrial 12S Ribosomal RNA Sequences," Annals of the Entomological Society of America 96(6), 693-699, (1 November 2003). (bioone.org)
  • Phylogenetic analysis of small-subunit ribosomal RNA gene sequences for gymnamoebae of the families Vexilliferidae, Paramoebidae, and Vannellidae identified two distinct lineages that are supported by gross morphological characters. (columbia.edu)
  • 1980. Molecular and chromosomal organization of DNA sequences coding for the ribosomal RNAs in cereals. (springer.com)
  • Two methylation guide sequences are combined on each guide RNA, the significance of which has remained unclear. (embl-hamburg.de)
  • We show that the two methylation guide sequences are located in different environments in the complex and that the methylation of physiological substrates targeted by the same guide RNA occurs sequentially. (embl-hamburg.de)
  • Phylogenetic relationships of amphibian families inferred from DNA sequences of mitochondrial 12S and 16S ribosomal RNA genes. (nii.ac.jp)
  • Previously identified ribosomal protein S15-interacting RNA leader sequences and structures originating from different phyla of bacteria. (biomedcentral.com)
  • Abstract:'Here, [investigators] report a genome-wide RNA degradation study in Escherichia coli using RNA-seq, and present evidence that the stereotypical exponential RNA decay curve obtained using initiation inhibitor, rifampicin, consists of two phases: residual RNA synthesis, a delay in the interruption of steady state that is dependent on distance relative to the mRNA's 5' end, and the exponential decay. (harvard.edu)
  • This structure is of the 5S rRNA from the Escherichia coli 50S ribosomal subunit and is based on a cryo-electron microscopic reconstruction . (wikipedia.org)
  • For example, the ribosomal RNA gene rrnD of Escherichia coli has the opposite orientation fro rrnB and rrnE and is separated from these genes by roughly 20% of the chromosome. (pnas.org)
  • RIBONUCLEASE LS ( l ate-gene s ilencing in bacteriophage T4) plays a role in Escherichia coli RNA metabolism ( O tsuka and Y onesaki 2005 ), although its effect seems modest in comparison to that of RNase E ( K ushner 2002 ). (genetics.org)
  • Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: the distribution of ribosomal RNA. (rupress.org)
  • 28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. (wikipedia.org)
  • While the ribosomal subunits are quite similar between prokaryotes and eukaryotes, the 70S ribosomes contain proportionally more RNA than protein, while the 80S ribosomes are composed of less RNA than protein. (newworldencyclopedia.org)
  • Larger ribosomes simply contain repeat copies of the same basic ribosomal RNA. (wisegeek.com)
  • Our data demonstrate that in contrast to the E. coli ribosome, which preferentially recognizes the Shine-Dalgarno sequence, eukaryotic ribosomes (such as those found in retic lysate used in in vitro translation systems) can efficiently use either the Shine-Dalgarno or the Kozak ribosomal binding sites. (thermofisher.com)
  • Ribosomes are responsible for 'reading' the RNA strand and assembling amino acids to form the protein encoded by the gene being transcribed. (sciencephoto.com)
  • Altered epigenetic marks on ribosomal RNAs appear to create a pool of specialized ribosomes that can differentially regulate translation of specific messenger RNA. (uab.edu)
  • A messenger RNA is a copy of the DNA gene for that protein, and it carries the gene's information for building a protein from the chromosome to the ribosomes. (uab.edu)
  • They were able to use the VEGF-C IRES to pull down hypoxic ribosomes, and they found that these ribosomes had a pattern of methylation on their 18S, 28S and 5.8S ribosomal RNAs that was distinct from the ribosomal RNAs of cells grown in normal oxygen. (uab.edu)
  • The fact that the pairs of tags have to be added in a particular order could be a way for the cell to control how the RNA is folded, and ultimately when and where ribosomes are formed, the scientists believe. (embl-hamburg.de)
  • Additionally, they have a higher rate of 5S RNA synthesis and probably contain more ribosomes as they contain more protein than do wild-type worms ( Frank and Roth, 1998 ). (biologists.org)
  • [4] The 60S and 40S ribosomal subunits are exported from the nucleus to the cytoplasm where they join to form the mature and translation -competent 80S ribosome. (wikipedia.org)
  • RrmJ recognises its methylation target only when the 23 S rRNA is present in 50 S ribosomal subunits. (ebi.ac.uk)
  • A ) Isolation of chemically modified or mutant 30 S ribosomal subunits that retain their A-site tRNA-binding activity. (sciencemag.org)
  • In the interior of the subunits, a complex distribution of higher mass density is recognized, which is attributed to ribosomal RNA. (rupress.org)
  • RNA methylation under heat shock control. (ebi.ac.uk)
  • 2′-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation? (mdpi.com)
  • Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2′-O-methylation (2′-O-Me). (mdpi.com)
  • 2′-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. (mdpi.com)
  • Researchers led by Rajeev Samant, Ph.D., professor of pathology at the University of Alabama at Birmingham , now report that chronic hypoxia, surprisingly, upregulates RNA polymerase I activity and alters the methylation patterns on ribosomal RNAs. (uab.edu)
  • Rajeev Samant, Ph.D. In additional detailed work, the UAB researchers sought to unravel clues underlying mechanisms that control changes in ribosomal RNA methylation patterns under hypoxia. (uab.edu)
  • We found that the complex has four copies of each protein, and four methylation sites on the RNA, but those methylation sites aren't all the same," Carlomagno says. (embl-hamburg.de)
  • Using RNA immunoprecipitation and sequencing, we further uncovered a non-canonical mechanism of HD2C directly associating with pre-rRNA and small nucleolar RNAs to regulate rRNA methylation. (plantcell.org)
  • The 18S rRNA in most eukaryotes is in the small ribosomal subunit, and the large subunit contains three rRNA species (the 5S, 5.8S and 28S rRNAs). (bionity.com)
  • THE most conserved and most utilized genes in eukaryotes are those encoding ribosomal RNA (rRNA). (genetics.org)
  • Organization of the ribosomal RNA (rRNA) genes in eukaryotes. (genetics.org)
  • 5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. (statemaster.com)
  • Computer model showing a bacterial ribosomal protein (green) complexed with a transfer-messenger RNA (tmRNA, orange) and the elongation factor G (pink). (sciencephoto.com)
  • Utility of Histologic and Histochemical Screening for 16S Ribosomal RNA Gene Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue for Bacterial Endocarditis. (harvard.edu)
  • Thus, TLR13 detects bacterial RNA with exquisite sequence specificity. (elifesciences.org)
  • Li and Chen went on to generate mice lacking TLR13 and showed that immune cells isolated from these mice failed to respond to bacterial RNA. (elifesciences.org)
  • The method described here for analyzing natural bacterial communities circumvents this problem by utilizing ribosomal RNA, found in all life forms, for defining and enumerating the components of natural populations. (oregonstate.edu)
  • Denaturing gradient gel electrophoresis microbial community analysis differentiated the active component (rRNA derived) from the total bacterial diversity (ribosomal DNA derived) down the horizons of an established grassland soil. (asm.org)
  • Ribosomal DNAs, which are the genes coding for ribosomal RNAs, are sequenced in order to identify the taxonomic group of an organism as well as estimate the rate of species divergence. (biology-online.org)
  • Ribosomal RNA depletion or exclusion has negligible effect on the detection of viruses in a pan viral microarray. (surrey.ac.uk)
  • Its enzymatic activity derives from the presence of the ribosomal RNA (rRNA), which performs the catalytic processes for the synthesis. (newworldencyclopedia.org)
  • Synthesis of the large rRNA precursors (35-47S) can be achieved by up to 150 RNA polymerase I (Pol I) enzymes simultaneously transcribing each rRNA gene. (hindawi.com)
  • Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. (statemaster.com)
  • Non-isotopic mapping of ribosomal RNA synthesis and processing in the nucleolus. (biomedsearch.com)
  • We endeavored to resolve this controversy by applying a new technique for non-isotopic labeling of RNA and examined the synthesis and movement of non-isotopically labeled rRNA within the nucleolus. (biomedsearch.com)
  • Scanning through the 5′UTR requires the adenosine triphosphate (ATP)-dependent RNA helicase eukaryotic initiation factor (eIF) 4A and its efficiency contributes to the specific rate of protein synthesis. (mdpi.com)
  • One might expect that hypoxic cells would want to decrease their ribosomal RNA synthesis to save energy, not make more. (uab.edu)
  • RNA interference-mediated knockdown of ErbB2 reduced pre-rRNA and protein synthesis. (aacrjournals.org)
  • rRNA production by RNA polymerase-I (RNA Pol I), the key component of ribosome biogenesis, is the rate-limiting step for translation/protein synthesis and cell growth. (aacrjournals.org)
  • The sequence of 13 residues is located at an active site in the RNA that catalyzes the synthesis of peptide bonds, and changing just one of these residues stops the production of interleukin-1β. (elifesciences.org)
  • Ribosomopathies are diseases arising from aberrations in the assembly, composition, or function of the ribosome, the two-subunit RNA-protein complex responsible for cellular protein synthesis ( 1 ). (sciencemag.org)
  • Such a cell would need to construct ten million copies of each type of ribosomal RNA molecule. (newworldencyclopedia.org)
  • Li and Chen have now discovered that TLR13 is responsible for detecting a certain type of ribosomal RNA called 23S ribosomal RNA that are present in bacteria but not in eukaryotic cells. (elifesciences.org)
  • Finally, elongation factors known to regulate messengers RNA production by RNA polymerase II are also involved in rRNA production and work cooperatively with Rpa49 in vivo . (hindawi.com)
  • Amplification of the ITS2 B amplicon was successful in RNA extracted from all six body parts analyzed, but showed relative quantification (RQ) values four orders of magnitude lower than those obtained for the ITS A+B amplicon. (springer.com)
  • Fragments of 16S ribosomal RNA genes were detected by polymerase chain reaction amplification of DNA extracted from halite samples ranging in age from 11 to 425 Myr (millions of years). (lancs.ac.uk)
  • Similarly, the majority of methods for cDNA sequencing have either used polyA+ selected RNA and/or amplification for library construction, both of which selectively omit significant amounts of RNA and, hence, cannot accurately reflect the profile of all cellular RNAs. (biomedcentral.com)
  • Using a variety of molecular techniques, including immuno-electron microscopy , intermolecular chemical cross-linking , and X-ray crystallography , the location of the 5S rRNA within the large ribosomal subunit has been determined to great precision. (wikipedia.org)
  • As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. (nih.gov)
  • Circular RNAs (circRNAs) are broadly expressed in eukaryotic cells, but their molecular mechanism in human disease remains obscure. (nature.com)
  • The results suggest that the ribosome recognizes the codon-anticodon complex by adenine contacts to the messenger RNA backbone and provide a mechanism for molecular discrimination of correct versus incorrect codon-anticodon pairs. (sciencemag.org)
  • In this lesson, we explore keeping time and dating evolution by tracking genetic mutations in our favorite molecular clocks: mitochondrial DNA and ribosomal RNA. (study.com)
  • The application of ribosomal RNA (rRNA) probes contributes significantly to the assessment of biodiversity at the molecular level. (awi.de)
  • The 5S ribosomal RNA ( 5S rRNA ) is an approximately 120 nucleotide-long ribosomal RNA molecule with a mass of 40 kDa . (wikipedia.org)
  • Like a budding origami artist pencilling in the folds, the cell uses tags called methyl groups to help mark where and how an RNA molecule should be folded. (embl-hamburg.de)
  • m2A2503 modification seems to play a crucial role in the proofreading step occurring at the peptidyl transferase center and thus would serve to optimize ribosomal fidelity. (cusabio.com)
  • Combined with 5.8S rRNA to the 5' side, it is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal RNAs. (wikipedia.org)
  • In eukaryotic cells, ribosomal protein L5 associates and stabilizes the 5S rRNA forming a pre-ribosomal ribonucleoprotein particle (RNP) that is found in both cytosol and the nucleus. (wikipedia.org)
  • To maximize your unique sequencing reads, you need efficient and near complete ribosomal RNA removal (rRNA removal). (qiagen.com)
  • Conclusions The ribodepletion protocol presented here ensures the efficient rRNA removal from low input total planarian RNA, which can be further processed for RNA-Seq applications. (utah.edu)
  • Our understanding of transcriptome biology is undergoing a revolution that is revealing that the regulation of expression and the types and functions of RNA are far more complex than was previously thought. (thermofisher.com)
  • Regulation of Ribosomal RNA Production by RNA Polymerase I: Does Elongation Come First? (hindawi.com)
  • Although it has been known that nuclear RTKs associate with functions in RNA Pol II transcriptional regulation, DNA repair, and DNA replication ( 12-16 , 20 , 26-32 ), the biological significance and functions of the nuclear RTKs, including ErbB2, is still far from clear. (aacrjournals.org)
  • In fact, recent studies have shown that one mechanism of cell growth regulation is achieved through an insulin receptor signaling pathway, one of the most downstream targets of which is the ribosomal protein S6 ( Weinkove and Leevers, 2000 ). (biologists.org)
  • The LSU attracts transfer RNA (tRNA) molecules that carry the necessary amino acids. (wisegeek.com)
  • Living organisms contain several hundred copies of the genes required for the two molecules of ribosomal RNA. (wisegeek.com)
  • Led by Teresa Carlomagno at EMBL, the scientists were able to determine the 3D structure of the complex that adds methyl tags to the RNA, with the RNA molecules attached. (embl-hamburg.de)
  • One initial report [ 14 ] has suggested that nc-RNAs represent only a minor fraction of RNA in a mammalian cell and that most of these non-coding species consisted of intronic by-products generated from unspliced RNAs. (biomedcentral.com)
  • Isolation of total RNA from T4-infected cells, primer-extension analysis of soc RNA, and analysis of cDNA products with polyacrylamide gel electrophoresis were performed as described previously ( K ai and Y onesaki 2002 ). (genetics.org)
  • Total RNA/cDNA was amplified by haptophyte‐specific primers targeting the V4 region of the 18S, and the D1‐D2 region of the 28S rRNA. (uio.no)
  • The large 50S ribosomal subunit contains two rRNA species (the 5S and 23S rRNAs). (bionity.com)
  • 16S ribosomal RNA gene sequence and phylogeny of toxic Microcystis sp. (semanticscholar.org)
  • Phylogeny and dating of some pathogenic keratinophilic fungi using small subunit ribosomal RNA. (semanticscholar.org)
  • The rapid divergence rates of variable regions in the ribosomal gene may permit answers to the question of time of separation of closely related species. (pnas.org)
  • Evolution of the tandemly repeated ribosomal RNA (rRNA) genes is intriguing because in each species all units within the array are highly uniform in sequence but that sequence differs between species. (genetics.org)
  • Using outward-facing primers and PCR analysis of reverse-transcribed RNA, we observed several species of circANRIL isoforms. (nature.com)
  • Enrichment of whole transcriptome RNA by depleting ribosomal RNA (rRNA) species using our RiboMinus™ technology has the potential to enhance discovery using gene expression microarrays, RNA-Seq, and other methods. (thermofisher.com)
  • 2. Physical mapping of 5S and 18S-26S ribosomal RNA gene families in diploid species. (springer.com)
  • When the UAB researchers investigated which RNA species could bind to NMI, "to our excitement," Samant said, "we found that many of the top-ranking RNA entities bound to NMI were SNORDs. (uab.edu)
  • Species-specific repeat units in the intergenic spacer of the ribosomal RNA cistron of Anopheles aquasalis Curry. (ajtmh.org)
  • Using a species-specific polymerase chain reaction (PCR) targeting the small subunit (SSU) ribosomal RNA (rRNA) gene, we detected P. ovale in nearly 4% of the inhabitants of a northeastern Cambodian village. (ajtmh.org)
  • Ribosomal RNA is just as fundamental and widespread among bacteria as it is in the animal kingdom. (wisegeek.com)
  • As a consequence, many antibiotics target ribosomal RNA in bacteria. (wisegeek.com)
  • Since RNA content often increases with growth rate, our findings suggest it is possible to rapidly elucidate active bacteria responding to the addition of uranium in field samples and provides a more targeted approach to stimulate specific populations to enhance radionuclide reduction in contaminated sites. (osti.gov)
  • Here we show that TLR13 detects the 23S ribosomal RNA of both gram-positive and gram-negative bacteria. (elifesciences.org)
  • Highly conserved regions of ribosomal RNA (rRNA) form the tRNA-binding sites ( 5 ). (sciencemag.org)
  • Recent research has revealed the importance of DExD/H-box RHs in many aspects of plant RNA metabolism and physiological processes. (frontiersin.org)
  • The phylogenetic relationships among members of the Odonates were inferred from mitochondrial DNA 12S ribosomal RNA sequence data. (bioone.org)
  • The application of concatenated ribosomal RNA sequence data may prove promising for phylogenetic reconstructions of the Dinophyceae in future. (awi.de)
  • 1 Using messenger RNA as a template, the ribosome traverses each codon and pair it with a specific amino acid linked to a transfer RNA. (biology-online.org)
  • They sequentially read a messenger RNA that directs the ribosome to add specific amino acids, from of a choice of 20 different amino acids, to a growing peptide chain that folds to form the completed protein. (uab.edu)
  • A new marker sequence for systematics of medically important fungi based on amino acid sequence of the largest subunit of RNA polymerase I. (semanticscholar.org)
  • The remaining whole-transcriptome RiboMinus™ RNA is suitable for direct sequencing using any next-generation sequencing platforms or microarray analysis. (thermofisher.com)
  • Thus, RNA interference followed by transcriptome-wide gene expression analysis by RNA-seq is a popular technique to study the impact of any particular planarian gene on regeneration. (utah.edu)
  • However, the frequency and general role of an RNA-based mobility pathway in the spread of natural group I introns is still unclear. (biomedsearch.com)
  • In the eukaryotic ribosomal RNA processing pathway, a complex of ten riboexo nucleases called the exosome that plays a central role in the precise formation of the 3' ends of several types of RNAs . (humpath.com)
  • Moreover, they have shown that a short sequence of 13 residues within the 23S ribosomal RNA triggers this pathway and leads to the production of interleukin-1β. (elifesciences.org)
  • The exosome also destroys excess ribosomal RNA precursors and unused intermediates and degrades poly(A)-mRNAs in the cytoplasm . (humpath.com)
  • We demonstrate that circANRIL regulates the maturation of precursor ribosomal RNA (pre-rRNA), thus controlling ribosome biogenesis and nucleolar stress. (nature.com)
  • Motomasa Ihara , Hung Tseng , and Richard M. Schultz "Expression of Variant Ribosomal RNA Genes in Mouse Oocytes and Preimplantation Embryos," Biology of Reproduction 84(5), 944-946, (5 January 2011). (bioone.org)
  • Fungi 18S ribosomal RNA genes, partial sequence. (nih.gov)
  • Ribosomal RNA (rRNA), a type of RNA synthesized in the nucleolus by RNA polymerase I, is the central component of the ribosome , the protein manufacturing machinery of all living cells . (bionity.com)
  • In the nucleus, the complex appears to function in a regulated m RNA surveillance system that degrades transcripts in response to defects in the m RNA processing and export pathways. (humpath.com)
  • Nuclear run-on assays revealed a 2-fold increase of primary (unprocessed) ribosomal RNA transcripts in callus compared to leaf tissue. (plantphysiol.org)
  • Here our analyses of RNA sequencing data identify the long noncoding RNA lncNB1 as one of the transcripts most over-expressed in MYCN-amplified, compared with MYCN-non-amplified, human neuroblastoma cells and also the most over-expressed in neuroblastoma compared with all other cancers. (garvan.org.au)
  • We show that the relative mass of RNA whose function and/or structure we do not understand (the so called 'dark matter' RNAs), as a proportion of all non-ribosomal, non-mitochondrial human RNA (mt-RNA), can be greater than that of protein-encoding transcripts. (biomedcentral.com)
  • When exactly 5S rRNA is integrated into the ribosome remains controversial, but it is generally accepted that 5S rRNA is incorporated into the 90S particle, which is a precursor to 60S particle, as part of a small ribosome-independent RNP complex formed by 5S rRNA and ribosomal protein L5. (wikipedia.org)
  • Small subunit ribosomal RNA, 5' domain taken from the Rfam database. (newworldencyclopedia.org)
  • In prokaryotes a small 30S ribosomal subunit contains the 16S rRNA. (bionity.com)
  • The tertiary structure of the small subunit ribosomal RNA (SSU rRNA) has been resolved by X-ray crystallography [1] . (bionity.com)
  • This purine-rich 5' UTR sequence is complementary to the UCCU core sequence of the 3'-end of 16S rRNA (located within the 30S small ribosomal subunit). (thermofisher.com)
  • The codon-anticodon interactions in the peptidyl-tRNA site (P site) and A site occur on the small (30 S ) ribosomal subunit ( 6 ). (sciencemag.org)
  • Here, we use a powerful combination of NMR spectroscopy and small angle neutron scattering to solve the structure of the 390 kDa archaeal RNP enzyme bound to substrate RNA. (embl-hamburg.de)
  • In this paper, the association between polymorphism of the small sub-unit ribosomal RNA apicoplastic gene pfssrRNA (PFC10_API0057) and in vitro susceptibilities of P. falciparum isolates to doxycycline were investigated. (biomedcentral.com)
  • The vast majority of RNA production in growing cells is carried out by RNA polymerase I (Pol I), which transcribes the precursor of large rRNA, and by RNA polymerase III (Pol III), which transcribes 5S rRNA, tRNA, and some noncoding RNAs. (hindawi.com)
  • RNA mutations in 16 S rRNA affect the fidelity of translation ( 5 ), and aminoglycoside antibiotics that decrease the fidelity of translation ( 7 ) bind to 16 S rRNA and perturb rRNA structure ( 8 ). (sciencemag.org)
  • Drosophila 28S ribosomal RNA is processed into 2 fragments that migrate in a similar manner to the 18S rRNA. (thermofisher.com)
  • Cryo-EM reconstruction has visualized many ES on the ribosomal surface which have given clues about function and structural features. (diva-portal.org)
  • Interaction of 5S rRNA with the La protein prevents the RNA from degradation by exonucleases in the cell. (wikipedia.org)
  • Interestingly, this RNase triggers RNA degradation more efficiently when the target RNA is translatable than when it is untranslatable. (genetics.org)
  • Our RiboMinus™ technology utilizes specific locked nucleic acid (LNA®) capture probes to bind ribosomal RNA and subsequently remove it from the sample via binding to streptavidin-coated Dynabeads® magnetic beads. (thermofisher.com)
  • Collectively, these findings identify circANRIL as a prototype of a circRNA regulating ribosome biogenesis and conferring atheroprotection, thereby showing that circularization of long non-coding RNAs may alter RNA function and protect from human disease. (nature.com)
  • Ribosome biogenesis is a highly complex process that requires several cofactors, including DExD/H-box RNA helicases (RHs). (frontiersin.org)
  • DExD/H-box RHs are involved in most cellular events associated with RNA, such as ribosome biogenesis, spliceosome assembly, RNA decay, and RNA editing ( Jarmoskaite and Russell, 2014 ). (frontiersin.org)
  • But in accord with the increased RNA polymerase I that the UAB researchers found in hypoxic cells, there was also increased ribosome biogenesis in both the hypoxic model cell lines and the hypoxic regions of spontaneous tumors in mice, as measured by increased nucleoli and another test. (uab.edu)