RNA: 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)RNA, Small Interfering: 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.RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.RNA Editing: 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).RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.DNA-Directed RNA Polymerases: Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).RNA Viruses: Viruses whose genetic material is RNA.RNA Interference: 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, Messenger: 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, Double-Stranded: 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, Catalytic: 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.RNA Folding: The processes of RNA tertiary structure formation.RNA Polymerase II: 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.RNA, Fungal: Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.RNA Stability: 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.RNA Helicases: A family of proteins that promote unwinding of RNA during splicing and translation.RNA, Antisense: 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.RNA Processing, Post-Transcriptional: 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.RNA, Transfer: The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.RNA, Small Nuclear: 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 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, Untranslated: 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.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.RNA Caps: 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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.RNA, Protozoan: Ribonucleic acid in protozoa having regulatory and catalytic roles as well as involvement in protein synthesis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.RNA, Neoplasm: RNA present in neoplastic tissue.RNA Ligase (ATP): 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.DEAD-box RNA Helicases: 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.RNA Polymerase III: 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.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.RNA Polymerase I: 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, Nuclear: RNA molecules found in the nucleus either associated with chromosomes or in the nucleoplasm.RNA, Guide: Small kinetoplastid mitochondrial RNA that plays a major role in RNA EDITING. These molecules form perfect hybrids with edited mRNA sequences and possess nucleotide sequences at their 5'-ends that are complementary to the sequences of the mRNA's immediately downstream of the pre-edited regions.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.RNA Transport: The process of moving specific RNA molecules from one cellular compartment or region to another by various sorting and transport mechanisms.RNA, Spliced Leader: 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).RNA, Satellite: 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)RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.RNA, Archaeal: Ribonucleic acid in archaea having regulatory and catalytic roles as well as involvement in protein synthesis.Nucleic Acid Hybridization: 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)Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Virus Replication: 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.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.RNA Cleavage: 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.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Oligoribonucleotides: 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.RNA, Heterogeneous Nuclear: 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.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.RNA, Small Cytoplasmic: Small RNAs found in the cytoplasm usually complexed with proteins in scRNPs (RIBONUCLEOPROTEINS, SMALL CYTOPLASMIC).RNA 3' End Processing: 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.Templates, Genetic: 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.RNA, Small Untranslated: Short RNA, about 200 base pairs in length or shorter, that does not code for protein.HeLa Cells: 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.Ribonucleoproteins: Complexes of RNA-binding proteins with ribonucleic acids (RNA).Ribonucleases: Enzymes that catalyze the hydrolysis of ester bonds within RNA. EC 3.1.-.Poly A: 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.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).RNA, Long Noncoding: 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.RNA, Small Nucleolar: Small nuclear RNAs that are involved in the processing of pre-ribosomal RNA in the nucleolus. Box C/D containing snoRNAs (U14, U15, U16, U20, U21 and U24-U63) direct site-specific methylation of various ribose moieties. Box H/ACA containing snoRNAs (E2, E3, U19, U23, and U64-U72) direct the conversion of specific uridines to pseudouridine. Site-specific cleavages resulting in the mature ribosomal RNAs are directed by snoRNAs U3, U8, U14, U22 and the snoRNA components of RNase MRP and RNase P.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.RNA Virus InfectionsProtein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.RNA, Complementary: 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)UridinePromoter Regions, Genetic: 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.Endoribonucleases: A family of enzymes that catalyze the endonucleolytic cleavage of RNA. It includes EC 3.1.26.-, EC 3.1.27.-, EC 3.1.30.-, and EC 3.1.31.-.Cell Nucleus: 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)RNA, Chloroplast: Ribonucleic acid in chloroplasts having regulatory and catalytic roles as well as involvement in protein synthesis.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Plasmids: 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.Reverse Transcriptase Polymerase Chain Reaction: 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.Kinetics: The rate dynamics in chemical or physical systems.Single-Strand Specific DNA and RNA Endonucleases: 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.Base Pairing: Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.RNA, Helminth: Ribonucleic acid in helminths having regulatory and catalytic roles as well as involvement in protein synthesis.Plant Viruses: Viruses parasitic on plants higher than bacteria.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Gene Expression Regulation: 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.Saccharomyces cerevisiae: 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.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.RNA, Transfer, Phe: A transfer RNA which is specific for carrying phenylalanine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, Lys: A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.Ribosomes: Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.Blotting, Northern: 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.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Oligonucleotides: 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)Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.5' Untranslated Regions: 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.RNA, Transfer, Tyr: A transfer RNA which is specific for carrying tyrosine to sites on the ribosomes in preparation for protein synthesis.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Amanitins: 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.Genes, Viral: The functional hereditary units of VIRUSES.Nucleic Acid Denaturation: 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.Transfection: 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.Ribonuclease T1: An enzyme catalyzing the endonucleolytic cleavage of RNA at the 3'-position of a guanylate residue. EC 3.1.27.3.Molecular Weight: The sum of the weight of all the atoms in a molecule.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Cell Nucleolus: 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)HIV-1: The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.Cell-Free System: 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)Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.DNA, Complementary: 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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Genes: 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.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Viral Nonstructural Proteins: 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.RNA, Transfer, Amino Acyl: 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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Introns: 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.RNA Splice Sites: 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.RNA, Transfer, Ala: A transfer RNA which is specific for carrying alanine to sites on the ribosomes in preparation for protein synthesis.Poliovirus: 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, Cultured: 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.Tobacco: A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.Ribonuclease P: An RNA-containing enzyme that plays an essential role in tRNA processing by catalyzing the endonucleolytic cleavage of TRANSFER RNA precursors. It removes the extra 5'-nucleotides from tRNA precursors to generate mature tRNA molecules.Centrifugation, Density Gradient: 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)Cytoplasm: 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)Nucleotides: 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)Mosaic Viruses: Viruses which produce a mottled appearance of the leaves of plants.RNA-Directed DNA Polymerase: 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.Dactinomycin: 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)Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Hepacivirus: 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, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.RNA, Transfer, Asp: A transfer RNA which is specific for carrying aspartic acid to sites on the ribosomes in preparation for protein synthesis.TritiumRNA, Transfer, Met: 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).Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Bromovirus: A genus of tripartite plant viruses in the family BROMOVIRIDAE. Transmission is by beetles. Brome mosaic virus is the type species.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Ribonuclease H: 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.Nuclear Proteins: 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.Models, Genetic: 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.Regulatory Sequences, Ribonucleic Acid: Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.Polyribosomes: 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)Cell Line, Tumor: A cell line derived from cultured tumor cells.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Exoribonucleases: 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.-Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Bacterial Proteins: Proteins found in any species of bacterium.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.RNA, Transfer, Gly: A transfer RNA which is specific for carrying glycine to sites on the ribosomes in preparation for protein synthesis.RNA, Transfer, His: A transfer RNA which is specific for carrying histidine to sites on the ribosomes in preparation for protein synthesis.Saccharomyces cerevisiae Proteins: 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.RNA, Transfer, Val: A transfer RNA which is specific for carrying valine to sites on the ribosomes in preparation for protein synthesis.Poly U: 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.Nodaviridae: A family of RNA viruses infecting insects and fish. There are two genera: Alphanodavirus and Betanodavirus.Nucleic Acid Precursors: Use for nucleic acid precursors in general or for which there is no specific heading.Virus Assembly: The assembly of VIRAL STRUCTURAL PROTEINS and nucleic acid (VIRAL DNA or VIRAL RNA) to form a VIRUS PARTICLE.Defective Viruses: 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.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.RNA, Transfer, Arg: A transfer RNA which is specific for carrying arginine to sites on the ribosomes in preparation for protein synthesis.RNA, Algal: Ribonucleic acid in algae having regulatory and catalytic roles as well as involvement in protein synthesis.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Heterogeneous-Nuclear Ribonucleoproteins: 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.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.Alternative Splicing: 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.Virion: 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.Ribonucleoproteins, Small Nuclear: 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).Hepatitis Delta Virus: 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.Ribosomal Proteins: Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.RNA, Transfer, Trp: A transfer RNA which is specific for carrying tryptophan to sites on the ribosomes in preparation for protein synthesis.Oligonucleotide Array Sequence Analysis: 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.Terminator Regions, Genetic: DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.Recombinant Fusion Proteins: 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.Macromolecular Substances: 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.Plants: 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.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Levivirus: A bacteriophage genus of the family LEVIVIRIDAE, whose viruses contain the short version of the genome and have a separate gene for cell lysis.Blotting, Western: 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.PolynucleotidesTrypanosoma brucei brucei: 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).DNA Restriction Enzymes: 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.Models, Biological: 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.Exons: 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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Tombusvirus: 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.Guanosine: 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)Polyadenylation: 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.RNA, Transfer, Leu: A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Structure-Activity Relationship: 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.

Chlamydia pneumoniae infection in human monocytes. (1/10063)

Chlamydia pneumoniae infection has been associated with cardiovascular diseases in seroepidemiological studies and by demonstration of the pathogen in atherosclerotic lesions. It has the capacity to infect several cell types, including monocyte-derived macrophages, which play an essential role in the development of atherosclerosis. However, the persistence of C. pneumoniae in mononuclear cells is poorly understood. To study the morphology and biological characteristics of the infection, human peripheral blood monocytes were infected with C. pneumoniae. Freshly isolated monocytes resisted the development of infectious progeny, and confocal and transmission electron microscopy showed that the morphology of the inclusions and chlamydial particles was abnormal. Addition of tryptophan or antibodies against gamma interferon did not diminish the inhibition of C. pneumoniae, suggesting that other factors are involved in the chlamydiostatic activity of the monocytes. Chlamydial mRNA was expressed at least 3 days after infection, however, and a capability for infected monocytes to induce a positive lymphocyte proliferative response was detected for up to 7 days, indicating that C. pneumoniae remains metabolically active in the monocytes in vitro. These results are in accordance with the hypothesis that C. pneumoniae may participate in the maintenance of local immunological response and inflammation via infected monocytes and thus enhance atherosclerosis.  (+info)

Synthesis of bacteriophage phi6 double-stranded ribonucleic acid. (2/10063)

Uracil was incorporated into all three bacteriophage phi6 dsRNA segments throughout the infection cycle; the rates of incorporation into each of the three segments were approx. constant for the first 15 to 20 min and then increased rapidly until 50 min after infection. The medium and small dsRNA segments were produced in greater amounts than the large dsRNA segment at all times in the infection cycle. Inhibition of host RNA and protein synthesis with rifampin and chloramphenicol revealed that virus dsRNA synthesis immediately after infection was independent of either host function.  (+info)

Characterization of an insertion sequence element associated with genetically diverse plant pathogenic Streptomyces spp. (3/10063)

Streptomycetes are common soil inhabitants, yet few described species are plant pathogens. While the pathogenicity mechanisms remain unclear, previous work identified a gene, nec1, which encodes a putative pathogenicity or virulence factor. nec1 and a neighboring transposase pseudogene, ORFtnp, are conserved among unrelated plant pathogens and absent from nonpathogens. The atypical GC content of nec1 suggests that it was acquired through horizontal transfer events. Our investigation of the genetic organization of regions adjacent to the 3' end of nec1 in Streptomyces scabies 84.34 identified a new insertion sequence (IS) element, IS1629, with homology to other IS elements from prokaryotic animal pathogens. IS1629 is 1,462 bp with 26-bp terminal inverted repeats and encodes a putative 431-amino-acid (aa) transposase. Transposition of IS1629 generates a 10-bp target site duplication. A 77-nucleotide (nt) sequence encompassing the start codon and upstream region of the transposase was identified which could function in the posttranscritpional regulation of transposase synthesis. A functional copy of IS1629 from S. turgidiscabies 94.09 (Hi-C-13) was selected in the transposon trap pCZA126, through its insertion into the lambda cI857 repressor. IS1629 is present in multiple copies in some S. scabies strains and is present in all S. acidiscabies and S. turgidiscabies strains examined. A second copy of IS1629 was identified between ORFtnp and nec1 in S. acidiscabies strains. The diversity of IS1629 hybridization profiles was greatest within S. scabies. IS1629 was absent from the 27 nonpathogenic Streptomyces strains tested. The genetic organization and nucleotide sequence of the nec1-IS1629 region was conserved and identical among representatives of S. acidiscabies and S. turgidiscabies. These findings support our current model for the unidirectional transfer of the ORFtnp-nec1-IS1629 locus from IS1629-containing S. scabies (type II) to S. acidiscabies and S. turgidiscabies.  (+info)

Inhibition of translation and cell growth by minigene expression. (4/10063)

A random five-codon gene library was used to isolate minigenes whose expression causes cell growth arrest. Eight different deleterious minigenes were isolated, five of which had in-frame stop codons; the predicted expressed peptides ranged in size from two to five amino acids. Mutational analysis demonstrated that translation of the inhibitory minigenes is essential for growth arrest. Pulse-labeling experiments showed that expression of at least some of the selected minigenes results in inhibition of cellular protein synthesis. Expression of the deleterious minigenes in cells deficient in peptidyl-tRNA hydrolase causes accumulation of families of peptidyl-tRNAs corresponding to the last minigene codon; the inhibitory action of minigene expression could be suppressed by overexpression of the tRNA corresponding to the last sense codon in the minigene. Experimental data are compatible with the model that the deleterious effect of minigene expression is mediated by depletion of corresponding pools of free tRNAs.  (+info)

Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. (5/10063)

We examined the effectiveness of antisense RNA (as RNA) strategies for metabolic engineering of Clostridium acetobutylicum. Strain ATCC 824(pRD4) was developed to produce a 102-nucleotide asRNA with 87% complementarity to the butyrate kinase (BK) gene. Strain ATCC 824(pRD4) exhibited 85 to 90% lower BK and acetate kinase specific activities than the control strain. Strain ATCC 824(pRD4) also exhibited 45 to 50% lower phosphotransbutyrylase (PTB) and phosphotransacetylase specific activities than the control strain. This strain exhibited earlier induction of solventogenesis, which resulted in 50 and 35% higher final concentrations of acetone and butanol, respectively, than the concentrations in the control. Strain ATCC 824(pRD1) was developed to putatively produce a 698-nucleotide asRNA with 96% complementarity to the PTB gene. Strain ATCC 824(pRD1) exhibited 70 and 80% lower PTB and BK activities, respectively, than the control exhibited. It also exhibited 300% higher levels of a lactate dehydrogenase activity than the control exhibited. The growth yields of ATCC 824(pRD1) were 28% less than the growth yields of the control. While the levels of acids were not affected in ATCC 824(pRD1) fermentations, the acetone and butanol concentrations were 96 and 75% lower, respectively, than the concentrations in the control fermentations. The lower level of solvent production by ATCC 824(pRD1) was compensated for by approximately 100-fold higher levels of lactate production. The lack of any significant impact on butyrate formation fluxes by the lower PTB and BK levels suggests that butyrate formation fluxes are not controlled by the levels of the butyrate formation enzymes.  (+info)

In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. (6/10063)

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)

The use of terminal blocking groups for the specific joining of oligonucleotides in RNA ligase reactions containing equimolar concentrations of acceptor and donor molecules. (7/10063)

Under the conditions that RNA ligase converts the tetranucleotide, pA-A2-A, to larger polynucleotides, no such polymerization can be detected with the derivative, pA-A2-A(MeOEt), that possesses a terminal 2'-0-(alpha-methoxyethyl) group. The protection against self condensation offered by the methoxyethyl group in this system allows the specific joining of donor and acceptor oligonucleotides in reaction mixtures containing equimolar concentrations of the two species. Thus, the enzyme, together with ATP, converts equimolar quantities of A-A2-A and pA-A2-A(MeOEt) to A-A6-A(MeOEt) in 55% yield, while a similar reaction with A-A2-A and pU-U2-U(MeOEt) results in a 40% yield of A-A3-U3-U(MeOEt). The intermediate in these ligations is a disubstituted pyrophosphate composed of the donor molecule and the adenylate moiety deriving from ATP. In the case of the intermediate arising from the blocked adenosine tetranucleotide, the assigned structure, A5'pp5'A-A2-A(MeOEt), has been confirmed by chemical synthesis. The pyrophosphate derivative is able to participate in joining reactions in the absence of ATP. These observations constitute an efficient approach to the synthesis of larger polynucleotides from a specific series of oligonucleotide blocks since (i), the methoxyethyl group can be easily introduced into each oligonucleotide using the single addition reaction catalyzed by polynucleotide phosphorylase in the presence of a 2'-0-(alpha-methoxyethyl)nucleoside 5'-diphosphate, and (ii), the blocking group may be readily removed under mild conditions after each successive ligation reaction. Two other octanucleotides, I-I2-A-U3-U and U-U2-C-I3-A, have also been synthesized by this method, and these molecules correspond (with I substituting for G) to sequences appearing near the 3' terminus of the 6S RNA transcribed from phage lambda DNA. The terminal 3'-phosphate group serves equally well as a blocking group for specific ligation reactions in that the ligase converts equimolar amounts of A-A2-A and pA-A2-Ap to A-A6-Ap in 50% yield.  (+info)

An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. (8/10063)

Current global phylogenies are built predominantly on rRNA sequences. However, an experimental system for studying the evolution of rRNA is not readily available, mainly because the rRNA genes are highly repeated in most experimental organisms. We have constructed an Escherichia coli strain in which all seven chromosomal rRNA operons are inactivated by deletions spanning the 16S and 23S coding regions. A single E. coli rRNA operon carried by a multicopy plasmid supplies 16S and 23S rRNA to the cell. By using this strain we have succeeded in creating microorganisms that contain only a foreign rRNA operon derived from either Salmonella typhimurium or Proteus vulgaris, microorganisms that have diverged from E. coli about 120-350 million years ago. We also were able to replace the E. coli rRNA operon with an E. coli/yeast hybrid one in which the GTPase center of E. coli 23S rRNA had been substituted by the corresponding domain from Saccharomyces cerevisiae. These results suggest that, contrary to common belief, coevolution of rRNA with many other components in the translational machinery may not completely preclude the horizontal transfer of rRNA genes.  (+info)

Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1. In trans-translation, tmRNA and its associated proteins bind to bacterial ribosomes which have stalled in the middle of protein biosynthesis, for example when reaching the end of a messenger RNA which has lost its stop codon. The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. In the majority of bacteria these functions are carried out by standard one-piece tmRNAs. In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing. tmRNA was first designated 10Sa RNA ...
A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the green algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags.. ...
Small RNAs (sRNAs) are post-transcriptional regulators of gene expression that play fundamental roles in the response of bacterial cells to environmental cues. We study the response of genetic networks and architectural motifs that include sRNAs, as well as the cell-to-cell variability in the expression of genes controlled by sRNAs. To do so, we use fluorescence microscopy and microfluidic techniques that allow us to measure directly the concentrations of fluorescently-tagged target proteins in individual cells as they respond to controlled stimuli, as well as single-molecule fluorescence in-situ hybridization to monitor the response at the target transcript level.. ...
Methods of producing macromolecular compositions and using same are provided. The method includes preparing a resin material; forming an acetyl group on the resin material; and oxidizing the acetyl group via a one-step reaction including reacting a sulfoxide and an acid with the acetyl group to form a ketoaldehyde group. The macromolecular compositions are capable of removing an effective amount of one or more constituents from a physiological solution, such as urea during dialysis therapy.
Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. MOLECULAR EVOLUTION. ...
Here we show that most macromolecular biosynthesis reactions in growing bacteria are sub-saturated with substrate. The experiments should in part test predictions from a previously proposed model (Jen
... Curr Opin Microbiol. 2017 Feb 01;36:14-19 Authors: Ignatova Z, Narberhaus F Abstract RNA folds into intricate structures. Recent discoveries using next-generation sequencing (NGS) approaches have revealed unprecedented structural complexity with a pivotal role in regulating RNA function and stability...
ZR-96 Quick-RNA™ Kit (4 x 96 Preps) [[Includes E1009 x 8: DNase I Set (250 U) w/ 10X Reaction Buffer (1 ml)] Quick-RNA™ MiniPrep Kit (50 Preps) w/Zymo-Spin™ IIICG Columns (Capped) & Spin-Away™ Filters [Includes E1009 x 1: DNase I Se Sample: Quick-RNA™ MiniPrep Kit (10 Preps) Quick-RNA™ MiniPrep Kit (200 Preps) w/Zymo-Spin™ IIICG Columns (Capped) & Spin-Away™ Filters [Includes E1009 x 4: DNase I Set (250 U) w/ 10X Reaction Buffer (1 ml)] ZR small-RNA™ PAGE Recovery Kit (20 Preps) ZR-96 RNA Clean & Concentrator™ Kit (2 x 96 Preps) RNA Shield Purification Kit (50 prep) supplied w/ 50 ml RNA Shield RNA Shield Purification Kit (50 prep) Without RNA Shield ZR Fungal/Bacterial RNA MicroPrep™ Kit (50 Preps) ZR Fungal/Bacterial RNA MiniPrep™ Kit (50 Preps) ZR Tissue & Insect RNA MicroPrep™ Kit (50 Preps) ZR Soil/Fecal RNA MicroPrep™ Kit (50 Preps) Direct-zol™ RNA MiniPrep (50 Preps) w/ Zymo-Spin™ IIC Columns (Capped) [Includes E1009 x 1: DNase I Set (250 U) w/ 10X Reaction ...
GERALD FINK, RICHARD BRIMACOMBE; Synthesis and Applications of a Two-Step Reagent Forming Cross-links between Ribonucleic Acid and Protein. Biochem Soc Trans 1 December 1975; 3 (6): 1014-1015. doi: https://doi.org/10.1042/bst0031014. Download citation file:. ...
Detection of circulating ribonucleic acid (cRNA) from blood is an unmet need in clinical diagnostics. Here we describe methods that...
இரைபோ கருவமிலம் அல்லது ஆர்.என்.ஏ. (RNA - Ribonucleic acid) என்பது ஒரு கருவமிலம் ஆகும். இதனை இரைபோக் கருக்காடி, ஐங்கரிமவினியக் கருக்காடி, ஐவினியக் கருக்காடி, ஐங்கரிமவினியக் கருவமிலம், ஐவினியக் கருவமிலம் என்ற பெயர்கள் கொண்டும் அழைக்கலாம். இது அனைத்து உயிரினங்களுக்கும் தேவையான நான்கு பெரிய பிரிவுகளில் அடங்கும் பருமூலக்கூறுகளில் ஒன்றான கருவமிலங்களில் ஒன்றாகும். இவையும் டி.என்.ஏ யைப் ...
Although basement membranes are ubiquitous structures throughout the body, basement membranes have distinct compositions that are specific to their location. This basement membrane heterogeneity may, in part, reflect functional differences among various basement membranes. We examined basement membrane heterogeneity in normal, healthy mouse kidneys to assess the similarities and differences between glomerular and tubular basement membrane composition. It was demonstrated that mouse glomerular and tubular basement membrane share similar compositions but differ with respect to specific amounts of some components. In diabetes mellitus and passive Heymann nephritis (PHN) , damage to the glomerular barrier occurs and is accompanied by an increase in penneability to proteins the size of albumin and larger: Presumably, the biochemical nature of the filter is not maintained. The acute effects of streptozotocin diabetes and PHN on the macromolecular composition of rat GBM was investigated to determine if ...
casSAR Dugability of Q03AJ7 | smpB | SsrA-binding protein - Also known as SSRP_LACP3, smpB. Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a tag peptide, a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the tag peptide encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation.
casSAR Dugability of B7MYQ8 | smpB | SsrA-binding protein - Also known as SSRP_ECO81, smpB. Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene; the 2 termini fold to resemble tRNA(Ala) and it encodes a tag peptide, a short internal open reading frame. During trans-translation Ala-aminoacylated tmRNA acts like a tRNA, entering the A-site of stalled ribosomes, displacing the stalled mRNA. The ribosome then switches to translate the ORF on the tmRNA; the nascent peptide is terminated with the tag peptide encoded by the tmRNA and targeted for degradation. The ribosome is freed to recommence translation, which seems to be the essential function of trans-translation.
Ribosomes translate the genetic information contained in mRNAs into protein by linking together amino acids with the help of aminoacyl-tRNAs. In bacteria, protein synthesis stalls when the ribosome reaches the 3-end of truncated mRNA transcripts lacking a stop codon. Trans-translation is a conserved bacterial quality control process that rescues stalled ribosomes. Transfer-messenger RNA (tmRNA) and its protein partner SmpB mimic a tRNA by entering the A site of the ribosome and accepting the growing peptide chain. The ribosome releases the truncated mRNA and resumes translation on the tmRNA template. The open reading frame found on tmRNA encodes a peptide tag that marks the defective nascent peptide for proteolysis. A stop codon at the end of the open reading frame allows the ribosome to be recycled and engage in future rounds of translation.The entry of tmRNA into stalled ribosomes presents a challenge to our understanding of ribosome function because during the canonical decoding process, the
Waters et al (2017) build on previous work from the Tollervey group who originally developed cross‐linking, ligation, and sequencing of hybrids (CLASH) to discover new snoRNA-rRNA interactions on snoRNA‐related yeast proteins (Kudla et al, 2011). An earlier attempt to apply this proximity ligation method to Hfq in enterohemorrhagic E. coli (EHEC) yielded few RNA hybrids (Tree et al, 2014); however, encouraged by the observation that RNase E recognizes the short seed helix formed between an sRNA and its target (Bandyra et al, 2012), the authors now focused on ligation to RNase E, which much elevated the proportion of RNA hybrids (Waters et al, 2017). Since these hybrids are significantly enriched in pairs of known sRNA seed regions and co‐regulated targets, they likely represent bona fide sRNA-mRNA interactions. What recruits RNase E to these many duplexes cannot be directly concluded from the data. However, plenty of coincidences with Hfq sites suggest a model whereby RNase E is recruited ...
Introductory biochemistry. Protein structure and folding, enzyme mechanisms, kinetics, and allostery; nucleic acid structure; macromolecular biosynthesis with emphasis on specificity and fidelity; lipids and membrane structure; vitamins and coenzymes; introduction to intermediary metabolism. Three hours lecture, one hour discussion, four hours lab.. ...
This model describes the SsrA-binding protein, also called tmRNA binding protein, small protein B, and SmpB. The small, stable RNA SsrA (also called tmRNA or 10Sa RNA) recognizes stalled ribosomes such as occur during translation from message that lacks a stop codon. It becomes charged with Ala like a tRNA, then acts as mRNA to resume translation started with the defective mRNA. The short C-terminal peptide tag added by the SsrA system marks the abortively translated protein for degradation. SmpB binds SsrA after its aminoacylation but before the coupling of the Ala to the nascent polypeptide chain and is an essential part of the SsrA peptide tagging system. SmpB has been associated with the survival of bacterial pathogens in conditions of stress. It is universal in the first 100 sequenced bacterial genomes ...
The transfer-messenger ribonucleoprotein (tmRNP), which is composed of RNA and a small protein, small protein B (SmpB), recycles ribosomes that are stalled on broken mRNAs lacking stop codons and tags the partially translated proteins for degradation. Although it is not yet understood how the ribosome gets from the 3 end of the truncated message onto the messenger portion of the tmRNA to add the tag, a recent study in BMC Biology has shed some light on this astonishing feat.
Ribosome stalling during translation has recently been shown to cause neurodegeneration, yet the signaling pathways triggered by stalled elongation complexes are unknown. To investigate these pathways we analyzed the brain of C57BL/6J-Gtpbp2(nmf205)(-/-) mice in which neuronal elongation complexes are stalled at AGA codons due to deficiencies in a tRNA(Arg)UCU tRNA and GTPBP2, a mammalian ribosome rescue factor. Increased levels of phosphorylation of eIF2α (Ser51) were detected prior to neurodegeneration in these mice and transcriptome analysis demonstrated activation of ATF4, a key transcription factor in the integrated stress response (ISR) pathway. Genetic experiments showed that this pathway was activated by the eIF2α kinase, GCN2, in an apparent deacylated tRNA-independent fashion. Further we found that the ISR attenuates neurodegeneration in C57BL/6J-Gtpbp2(nmf205)(-/-) mice, underscoring the importance of cellular and stress context on the outcome of activation of this pathway. These results
Demo, G, Svidritskiy E, Madireddy R, Diaz-Avalos R, Grant T, Grigorieff N, Sousa D, Korostelev AA. 2017. Mechanism of ribosome rescue by ArfA and RF2. eLife. 6(e23687):1-18. Abstract ...
Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory. ...
Affiliation:北海道大学,医学研究院,講師, Research Field:General medical chemistry,Pathological medical chemistry,Tumor biology and related fields,Tumor biology, Keywords:転写,RNAポリメラーゼII,発現制御,腫瘍,転写制御,がん,転写因子,ユビキチン,転写伸長因子,腫瘍性疾患, # of Research Projects:9, # of Research Products:70, Ongoing Project:新規の転写伸長制御因子Med26を標的とした腫瘍治療シーズ開発基盤の確立
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Unique bacterial process, trans-translation, has been studied to be an important process in many bacteria. However, there was nothing known about the significance of this process in mycobacteria, especially in relation to drug susceptibility. Consistent with findings in Escherichia coli, Salmonella typhimurium, and Synechocystis sp., we found that interfering with the expression of tmRNA and the smpB gene (critical components of trans-translation) in Mycobacterium smegmatis caused increased bactericidal activity of antimicrobial agents that target the ribosomes. Moreover, exposure to ribosome inhibitors increased the expression of tmRNA. This increase was driven by the tmRNA gene promoter which activity seemed to utilize a de-repression mechanism. Not only is trans-translation important to the bacterial response to ribosome inhibitors, evidence from this laboratory suggests that trans-translation is essential in mycobacteria. Thus, we believe that trans-translation may represent a new important ...
Staphylococcus aureus quickly develops resistance to antibiotics and poses a significant health threat to humans. New antibiotic targets are needed for the development of new antibiotics. Trans-translation has important roles in maintaining bacterial viability. Small molecules, KKL-35 and KKL-40, were recently identified as specific inhibitors of trans-translation. We have investigated the roles of trans-translation on S. aureus viability and the potential of KKL-35 and KKL-40 as antibiotics. We find that KKLs show bactericidal activity against multiple S. aureus strains at relatively low concentration. We also find that sub-lethal doses of KKLs make S. aureus more susceptible to antimicrobials. Neither KKL-35 nor KKL-40 are cytotoxic to human HeLa cells. Unfortunately, KKL-40 is inactivated by human serum. Therefore, new inhibitors will need to be identified in future studies. Notably, the development of resistance by S.aureus against KKLs remains at a low level. Therefore trans-translation is ...
In contrast to btuB and thiM, our results show that the lysC riboswitch employs a different regulation mechanism, by directly modulating the cleavage of RNase E (Fig. 6B). Our data indicate that, in the absence of ligand, the riboswitch folds into the ON state that not only allows ribosome binding but also sequesters RNase E cleavage sites, thus ensuring efficient mRNA translation. However, in its ligand-bound form, the lysC riboswitch adopts the OFF state that concomitantly sequesters the RBS and exposes RNase E cleavage sites, thus effectively inhibiting translation and initiating mRNA decay. The location of RNase E cleavage sites in the riboswitch expression platform, and not in the ORF, strongly suggests that the lysC riboswitch directly controls the cleavage of the mRNA as a function of ligand binding. In such cases, the transcript stability and concomitant translation are reduced directly through endoribonucleolytic action, a situation referred to as "nucleolytic repression" (Fig. 6B) ...
The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in Escherichia coli. It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein (type II toxin-antitoxin). The hok/sok system involves three genes: hok, host killing - a long lived (half-life 20 minutes) toxin sok, suppression of killing - a short lived (half-life 30 seconds) RNA antitoxin mok, modulation of killing - required for hok translation When E. coli undergoes cell division, the two daughter cells inherit the long-lived hok toxin from the parent cell. Due to the short half-life of the sok antitoxin, daughter cells inherit only small amounts and it quickly degrades. If a daughter cell has inherited the R1 plasmid, it has inherited the sok gene and a strong promoter which brings about high levels of transcription. So much so that in an ...
TY - PAT. T1 - Therapeutics for Drug-Resistant Bacterial Infections: Inhibitors of Bacterial RNA Polymerase. AU - Ebright, Richard. AU - Feng, Yu. AU - Zhang, Yu. PY - 2017/1. Y1 - 2017/1. N2 - Invention Summary: Bacterial infectious diseases kill 100,000 persons each year in the US and 11 million persons each year worldwide, representing nearly a fifth of deaths each year worldwide. For six decades, antibiotics have been our bulwark against bacterial infectious diseases. However, now this bulwark is collapsing. For all major bacterial pathogens, strains resistant to at least one current antibiotic have arisen, and, for several bacterial pathogens, strains resistant to all current antibiotics have arisen. There is an urgent national and international need for new classes of antibacterial agents effective against bacterial pathogens resistant to current antibacterial agents. Rutgers researchers have identified five new "drug targets" within the structure of bacterial RNA polymerase, the enzyme ...
In 1995, the release of the first fully sequenced bacterial genome heralded a new era of bacterial genomic research (21). Over the past 20 years, the number of sequenced bacterial genomes has risen exponentially, and new research strategies, techniques, and applications have emerged to exploit the opportunities that these resources provide. While raw genomic sequence data are valuable, the availability of fully annotated genome sequences, outlining the positions of known genes and genomic features, dramatically increases their utility. Global expression analysis techniques such as microarrays and RNA-seq depend heavily on annotated genome sequences as a reference source for genes in the bacterial cell. These techniques have proved extremely useful; however, recently, certain limitations to their application are becoming apparent. A major concern in this regard is that they do not provide expression data for genes that are not included in genome annotation files. Bacterial sRNAs represent a class ...
In this thesis, we first investigated the regulon of the alternative sigma factor E by employing next-generation sequencing of both the genome and the transcriptome of N. meningitidis wildtype and an overexpression mutant. Its small regulatory repertoire compared to E. coli and its lack of regulating proteins involved in the outer membrane stress response is a prime example of divergent evolution of superficially similar regulatory systems in these two gram-negative bacteria. Second, the chaperon protein Hfq and its role in riboregulation by facilitating RNA-RNA interactions between a sRNA and its mRNA target(s) was investigated by studying its regulatory proteome in depth. Finally, the regulatory roles of two sRNAs, NmsRs and NrrF are described; showing their extensive involvement in the related cell biological processes of carbohydrate metabolism and oxidative phosphorylation by simultaneously downregulating multiple enzymes involved in these pathways ...
Christine Ward (mjward at vt.edu) wrote: : Greetings Netters: : I could really use some input from those of you with experience doing : Northerns on bacterial RNA. I have been using the Chomczynski (sp?) : and Sacchi procedure (AGPC procedure, Analytical Biochem.) to isolate : total RNA from a Gram negative organism. I have upscaling the original : procedure by a factor of 10 to isolate RNA from about 1 x 10e9 organisms. : When I do my Northerns, all I see is one really good smear. : When I stain the total RNA on the membrane with methylene blue, my markers : look OK, and I can clearly see the 23S and 16S rRNA bands in my RNA prep. : I believe my technique is quite good--using clean pipettors, DEPCd solutions, : storing RNA in formamide etc. OD260/OD280 is about 1.8, which supposedly : indicates pure RNA. My gut instinct is that I have some residual : protein (and therefore RNAse carryover), OR that the particular RNA I am : trying to detect has a very rapid turnover rate (even though the ...
Interlink Scientific Services Limited Biomiga Bacterial RNA Kit - R6616-01 [R6616-01] - Description : Introduction The EZgeneTM total RNA kit provides an easy and fast method for isolating total RNA from Gram-positive (B. subtilis) Or Gram-negative (E. coli) Bacteria within 30 min. Only trace genomic DNA exists in the purified RNA, which can be eliminated by DNase I treatment (See detail in the protocol) when it is necessary. Storage and StabilityDNase I (optional) and lysozyme should be stored at -20℃. All other components can be stored at room temperature. All kit components are guaranteed for 12 monthsr from the date of purchasing.Kit ContentsCatalog#R6616-00R6616-01R6616-02Preps450250Buffer LY 2.4 mL28 mL135 mLBuffer RB3 mL30 mL135 mLRNA Wash Buffer *2 mL20 mL3 x 24 mLDEPC-Treated dH2O 500 µL10 mL30 mLDNase Stop Buffer 200 µL2.4 mL12 mLezBind Columns450250Collection Tubes8100500Lysozyme 1.2 mg15 mg75 mgUser Menu111Note4DNase I are not supplied. They could be purchased from Biomiga. Before
It is nowadays widely accepted that non-coding RNAs play important roles in post-transcriptional regulation of genes in all kingdoms of life. In bacteria, the largest group of RNA regulators are the small RNAs (sRNAs). Almost all sRNAs act through anti-sense base-pairing with target mRNAs, and by doing so regulate their translation and/or stability. As important modulators of gene expression, sRNAs are involved in all aspects of bacterial physiology. My studies aimed to deepen our understanding of the mechanisms behind sRNA-mediated gene regulation. We have shown that translation of the di-guanylate-cyclase YdaM, a major player in the biofilm regulatory cascade, is repressed by the sRNAs OmrA and OmrB. OmrAB require the RNA chaperone protein Hfq for efficient regulation. Interestingly, our results suggest a non-canonical mechanism for Hfq-mediated ydaM-OmrA/B base-pairing. Instead of serving as RNA interaction platform, Hfq restructures the ydaM mRNA to enable sRNA binding. We also addressed the ...
Turnover of Endogenous SsrA-tagged Proteins Mediated by ATP-dependent Proteases in Escherichia coli*[S with combining enclosing square]: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516991 ...
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Transfer RNA molecule. Computer artwork of the double helix of tRNA (transfer ribonucleic acid), formed by spiralling paired strands of sugar phosphates, linked by nucleotide base pairs. Transfer RNA carries amino acid groups to ribosomes for protein synthesis. Protein synthesis is controlled by DNA (deoxyribonucleic acid, not seen) in the nucleus of a cell. - Stock Image G110/0742
Transfer RNA molecule. Computer artwork of the double helix of tRNA (transfer ribonucleic acid), formed by spiralling paired strands of sugar phosphates, linked by nucleotide base pairs. Transfer RNA carries amino acid groups to ribosomes for protein synthesis. Protein synthesis is controlled by DNA (deoxyribonucleic acid, not seen) in the nucleus of a cell. - Stock Image G110/0740
The vast majority of currently known ProQ‐binding sRNAs are of unknown function (Smirnov et al, 2016). We have previously observed that asRNAs are enriched in the ProQ interactome, suggesting that this protein may be involved in gene expression regulation via perfect base pairing with cis‐encoded mRNA targets. Some of these asRNAs and their regulatory mechanisms have been characterized, including members of the Sib, Rdl, and IstR families of type I antitoxins, the transposon‐associated art200 and the intergenic cis‐acting SraG sRNAs (Darfeuille et al, 2007; Ellis et al, 2015; Fontaine et al, 2016; Han et al, 2010; Kawano, 2012; Mok et al, 2010). Some other ProQ‐associated sRNAs are derived from transcriptional attenuators (SraF, rimP leader) or have been proposed to function as trans‐encoded base‐pairing sRNAs (SraL) (Argaman et al, 2001; Naville & Gautheret, 2010; Nechooshtan et al, 2009; Plumbridge et al, 1985; Silva et al, 2013; Sittka et al, 2008). Recently, one of the ...
The first two times we went, he didn´t show up. I stared to wonder if it was a sign that I shouldn´t go. But my friend said, that he was just super busy and sometimes just forgets, as he is Peruvian.. Well, the third time we went he was there. No, let me rephrase that. The third time we went, he came to „his office" after an hour of waiting. „His office" because it is basically his house, where he reserved a room to welcome his patients. It is a big door on the street, you go in and set foot into a backyard. Here are several buildings, the house of his family, some small stables and a house for visitors. The room I went into to talk to him looked like it had been a stable and he decorated it differently, it was dark and had no windows, oh wait, it had one tiny window, but it didn´t really let the sunlight in.. I had exected a very spiritual person, you know the ones you see on pictures. They have long hair and wear these special clothes, but he was just a normal person. A farmer, comming ...
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. ...
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Everyone* knows that DNA codes for proteins. In between the DNA and the protein though, there is an intermediate molecule called RNA - ribonucleic acid (DNA is deoxyribonucleic acid). RNA is similar to DNA in many respects - long chain of bases that we can consider letters, which form a code - but its less…
Ribonucleic acid (RNA) interference is a relatively new technique in which small molecules called short interfering RNA (siRNA) can be inserted into cells to turn off a chosen gene.
TY - JOUR. T1 - Desulfotomaculum genus-and subgenus-specific 16S rRNA hybridization probes for environmental studies. AU - Hristova, Krassimira R.. AU - Mau, Margit. AU - Zheng, Dandan. AU - Aminov, Rustam I.. AU - Mackie, Roderick I.. AU - Gaskins, H. Rex. AU - Raskin, Lutgarde. PY - 2000/1/1. Y1 - 2000/1/1. N2 - Based on comparative analysis of 16S rRNA sequences and the recently established phylogeny of the genus Desulfotomaculum, a set of phylogenetically nested hybridization probes was developed and characterized. A genus-specific probe targets all known Desulfotomaculum species (with the exception of Desulfotomaculum acetoxidans), and five specific probes target subclusters within the Desulfotomaculum genus. The dissociation temperature of each probe was determined experimentally. Probe specificities were verified through hybridizations with pure culture rRNA isolated from a wide variety of target and non-target organisms and through an evaluation of probe nesting using samples obtained ...
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods
TY - JOUR. T1 - Interaction of the tylosin-resistance methyltransferase RlmA II at its rRNA target differs from the orthologue RlmA I. AU - Douthwaite, Stephen. AU - Jakobsen, Lene. AU - Yoshizawa, Satoko. AU - Fourmy, Dominique. PY - 2008/5/16. Y1 - 2008/5/16. N2 - RlmA(II) methylates the N1-position of nucleotide G748 in hairpin 35 of 23 S rRNA. The resultant methyl group extends into the peptide channel of the 50 S ribosomal subunit and confers resistance to tylosin and other mycinosylated macrolide antibiotics. Methylation at G748 occurs in several groups of Gram-positive bacteria, including the tylosin-producer Streptomyces fradiae and the pathogen Streptococcus pneumoniae. Recombinant S. pneumoniae RlmA(II) was purified and shown to retain its activity and specificity in vitro when tested on unmethylated 23 S rRNA substrates. RlmA(II) makes multiple footprint contacts with nucleotides in stem-loops 33, 34 and 35, and does not interact elsewhere in the rRNA. Binding of RlmA(II) to the rRNA ...
Another ribosome rescue pathway for resolving pauses at tandem rare codons involves cleavage of the mRNA in the A-site of the ribosome and subsequent binding by tmRNA and SmpB to carry out trans-translation. The authors fail to note that this cleavage is a prerequisite for tmRNA activity, as the tmRNA-SmpB complex recognizes only ribosomes with an A-site devoid of mRNA (Pech, 2012; Shimizu, 2012). Furthermore, other studies using the same PURExpress in vitro translation system featured in this manuscript have observed no evidence of cleavage. For example, rescue of ribosomes stalled in a similar fashion cannot be rescued by ArfA, which also requires an empty A-site (Shimizu, 2012). The presence of tmRNA and SmpB is not believed to be sufficient to promote cleavage, as they are dispensable in vivo (Garza-Sánchez, 2009). If this study did a better job of demonstrating that the higher molecular weight product is indeed the result of cleavage and tagging, the search for the as of yet unidentified ...
The invention relates to a method for the synthesis of ribonucleic acid (RNA) starting from deoxyribonucleic acid (DNA). In the method of the invention, a double stranded DNA molecule is cleaved with a restriction endonuclease so as to generate a free 3-end. The resultant DNA molecule is then denatured and hybridized with a primer that anneals to the 3-end of the denatured DNA. The primer used in the hybridization contains a T7 promoter sequence at its 5-end. Following the hybridization step, the 3-ends of the resultant hybrid DNA molecule are extended with DNA polymerase to generate a template suitable for T7 RNA polymerase mediated RNA synthesis.
"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 ... Protein synthesis within chloroplasts relies on two RNA polymerases. One is coded by the chloroplast DNA, the other is of ...
For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase so it ... ICTV classification of prokaryotic (bacterial and archaeal) viruses[1] Order. Family. Morphology. Nucleic acid. Examples ... RNA phage such as MS2 have the smallest genomes of only a few kilobases. However, some DNA phages such as T4 may have large ... "Novel Phage Therapy Saves Patient with Multidrug-Resistant Bacterial Infection". UC Health - UC San Diego. Retrieved 2018-05-13 ...
Some bacterial heat shock proteins are upregulated via a mechanism involving RNA thermometers such as the FourU thermometer, ... Narberhaus F (2010). "Translational control of bacterial heat shock and virulence genes by temperature-sensing mRNAs". RNA ... 7 (1): 84-9. doi:10.4161/rna.7.1.10501. PMID 20009504.. *^ Walter S, Buchner J (April 2002). "Molecular chaperones--cellular ... HSF1 inhibition by a potent RNA aptamer attenuates mitogenic (MAPK) signaling and induces cancer cell apoptosis.[34] ...
... Bacterial small RNA. (Lister 1873). Schleifer et al. 1986. Subspecies. ... "RNA Biology. 13 (3): 353-366. doi:10.1080/15476286.2016.1146855. ISSN 1547-6286. PMC 4829306 . PMID 26950529.. ... "Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon ... Hundreds of novel small RNAs were identified by Meulen et al. in the genome of L. lactis MG1363. One of them: LLnc147 was shown ...
Bacterial small RNAs (sRNA) are an important class of regulatory molecules. Many Brucella sRNAs have been identified. Infection ...
"Tertiary structure of bacterial selenocysteine tRNA". Nucleic Acids Research. 41 (13): 6729-6738. doi:10.1093/nar/gkt321. PMC ... A transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA[1]) is an adaptor molecule composed of RNA, ... doi:10.4161/rna.27177. PMC 3917982 . PMID 24351723.. *^ a b Shigematsu Megumi; et al. (2014). "Transfer RNA as a source of ... In eukaryotic cells, tRNAs are transcribed by RNA polymerase III as pre-tRNAs in the nucleus.[50] RNA polymerase III recognizes ...
Lactis-leu-phe leader RNA motif Attenuation in eukaryotes[edit]. Research conducted on microRNA processing showed an evidence ... Attenuation (in genetics) is a proposed mechanism of control in some bacterial operons which results in premature termination ... When the RNA polymerase binds and transcribes the trp gene, the ribosome will start translating. (This differs from eukaryotic ... In this situation RNA polymerase is dependent on (lagging) ribosome activity; if the ribosome pauses due to insufficient ...
Mehta, Preeti; Woo, Perry; Venkataraman, Krithika; Karzai, A. Wali (2012). Bacterial Regulatory RNA. Methods in Molecular ...
March 2007). "Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial ... Rose, L. J.; O'Connell, H. (2009-05-01). "UV Light Inactivation of Bacterial Biothreat Agents". Applied and Environmental ...
It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. It is ... RNA polymerase holoenzyme complex consisting of core RNA polymerase and a sigma factor executes transcription of a DNA template ... Finally, structural models of RNA polymerase complexes predict that, as the growing RNA product becomes longer than ~15 ... It was previously believed that the RNA polymerase holoenzyme initiates transcription, while the core RNA polymerase alone ...
"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity". Science. 337 (6096): 816-21. Bibcode:2012Sci ... July 2010). "Creation of a bacterial cell controlled by a chemically synthesized genome". Science. 329 (5987): 52-6. Bibcode: ...
Bacterial small RNA Wen, Y; Feng, J; Scott, DR; Marcus, EA; Sachs, G (January 2011). "A cis-encoded antisense small RNA ... In molecular biology, 5' ureB sRNA is a small RNA. It is located at the 5' end of the ureB gene in the urease gene cluster, and ... Wen, Y; Feng, J; Sachs, G (February 2013). "Helicobacter pylori 5'ureB-sRNA, a cis-encoded antisense small RNA, negatively ...
"An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in ... Bacterial small RNA Tsui, HC; Mukherjee, D; Ray, VA; Sham, LT; Feig, AL; Winkler, ME (Jan 2010). "Identification and ... "The small regulatory RNA FasX controls pilus expression and adherence in the human bacterial pathogen group A Streptococcus". ... RNA. 18 (3): 530-546. doi:10.1261/rna.027359.111. PMC 3285940 . PMID 22274957. Perez, N; Treviño, J; Liu, Z; Ho, SC; Babitzke, ...
"New target for inhibition of bacterial RNA polymerase: 'switch region'". Current Opinion in Microbiology. 14 (5): 532-43. doi: ... Most target bacterial functions or growth processes.[53] Those that target the bacterial cell wall (penicillins and ... bacterial, on Oxford Dictionaries *^ a b Moloney MG (August 2016). "Natural Products as a Source for Novel Antibiotics". Trends ... an antibiotic target may be absent from the bacterial genome. Acquired resistance results from a mutation in the bacterial ...
Bacterial small RNAs play critical roles in virulence and stress/adaptation responses. Although their specific functions have ... "Bacterial small RNAs in the Genus Rickettsia". BMC Genomics. 16: 1075. doi:10.1186/s12864-015-2293-7. ISSN 1471-2164. PMC ... The cladogram of Rickettsidae has been inferred by Ferla et al. [13] from the comparison of 16S + 23S ribosomal RNA sequences. ... In March 2010, Swedish researchers reported a case of bacterial meningitis in a woman caused by Rickettsia helvetica previously ...
Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge ... Both DNA and RNA viruses can undergo recombination. When two or more viruses, each containing lethal genomic damage infect the ... "Bacterial genetics". Nature. Macmillan Publishers Limited. Retrieved 8 November 2015.. *^ Chen I, Dubnau D (2004). "DNA uptake ... Bacterial conjugation has been extensively studied in Escherichia coli, but also occurs in other bacteria such as Mycobacterium ...
Napoli, Lemieux and Jorgensen discover the principle of RNA interference (1990).. Chemistry[edit]. *Blaise Pascal carries a ... Herbert Boyer and Stanley Cohen selectively clone genes in bacteria, using bacterial plasmids cut by specific endonucleases ( ... Nirenberg and Matthaei experiment demonstrating in vitro protein synthesis using synthetic RNA as to substitute for messenger ... Nirenberg and Leder experiment, binding tRNA to ribosomes with synthetic RNA to decipher the genetic code (1964). ...
Other RNA-guided Cas proteins cut foreign RNA.[9] CRISPR are found in approximately 50% of sequenced bacterial genomes and ... "RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex". Cell. 139 (5): 945-56. doi:10.1016/j.cell.2009.07.040. PMC ... doi:10.4161/rna.24023. PMC 3737337. PMID 23445770.. *^ a b c Erdmann S, Garrett RA (September 2012). "Selective and hyperactive ... Sashital DG, Jinek M, Doudna JA (June 2011). "An RNA-induced conformational change required for CRISPR RNA cleavage by the ...
"A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity". Science. 337 (6096): 816-21. Bibcode:2012Sci ... Chen I, Dubnau D (March 2004). "DNA uptake during bacterial transformation". Nature Reviews. Microbiology. 2 (3): 241-9. doi: ... In 2010, scientists at the J. Craig Venter Institute created the first synthetic genome and inserted it into an empty bacterial ... July 2010). "Creation of a bacterial cell controlled by a chemically synthesized genome". Science. 329 (5987): 52-6. Bibcode: ...
Kortmann J, Narberhaus F (March 2012). "Bacterial RNA thermometers: molecular zippers and switches". Nature Reviews. ... Upstream activation sequence RNA List of cis-regulatory RNA elements Polyadenylation signals, mRNA AU-rich element, mRNA Other ... Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and ... Walczak R, Westhof E, Carbon P, Krol A (April 1996). "A novel RNA structural motif in the selenocysteine insertion element of ...
Lim, K; Furuta, Y; Kobayashi, I (October 2012). "Large variations in bacterial ribosomal RNA genes". Molecular Biology and ... tRNA replication origin regions tRNA small RNA ribosomal protein replication origin regions ribosomal RNA tRNAs ribosomal RNA ... The two RNA polymerases may recognize and bind to different kinds of promoters within the chloroplast genome. The ribosomes in ... While similar to bacterial ribosomes, chloroplast translation is more complex than in bacteria, so chloroplast ribosomes ...
An RNA transcript of MGEs is copied by reverse transcriptase. Then, the DNA sequence can be inserted back to a random location ... Check date values in: ,date= (help) Hausner, Georg; Hafez, Mohamed; Edgell, David R. (2014-03-10). "Bacterial group I introns: ... Plasmids of bacteria are a transferable genetic element through bacterial conjugation. This is a mechanism of horizontal gene ... Strategies to combat certain bacterial infections by targeting these specific virulence factors and mobile genetic elements ...
Bacterial clocks[edit]. In bacterial circadian rhythms, the oscillations of the phosphorylation of cyanobacterial Kai C protein ... "RNA-methylation-dependent RNA processing controls the speed of the circadian clock". Cell. 155 (4): 793-806. doi:10.1016/j.cell ... More recently, however, it was reported that only 22% of messenger RNA cycling genes are driven by de novo transcription.[29] ... also employed a genome-wide small interfering RNA screen in U2OS cell line to identify additional clock genes and modifiers ...
... works by binding to a site on the bacterial 30S and 50S ribosome, preventing formation of the 70S complex.[7] As a ... However, there seems to be no indication that Tobramycin binds to natural RNAs or other nucleic acids. ... A proprietary formulation of micronized, nebulized tobramycin has been tested as a treatment for bacterial sinusitis.[3] Tobrex ... Tobrex and TobraDex are indicated in the treatment of superficial infections of the eye, such as bacterial conjunctivitis. ...
"Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes". FEMS Microbiology ... "The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses". PLoS One 8 (2 ... "Comparative RNA function analysis reveals high functional similarity between distantly related bacterial 16 S rRNAs". ... Schmidt TM, Relman DA (1994). Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods in ...
RNA editing in plastidsEdit. RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA transcript prior ... Because it is similar to bacterial amino acid transporters and the mitochondrial import protein Tim17[38] (translocase on the i ... Chloroplasts also contain a mysterious second RNA polymerase that is encoded by the plant's nuclear genome. The two RNA ... Among land plants, the contents of the chloroplast genome are fairly similar[8]-they code for four ribosomal RNAs, 30-31 tRNAs ...
... Shahram Mori smori at nmsu.edu Mon Mar 13 02:39:14 EST 1995 *Previous message: Need ... RNA. : Does anyone know of any compounds I could add to my growing culture : to slow the RNA turnover rate without killing my ... Northerns on bacterial RNA. I have been using the Chomczynski (sp?) : and Sacchi procedure (AGPC procedure, Analytical Biochem ... When I stain the total RNA on the membrane with methylene blue, my markers : look OK, and I can clearly see the 23S and 16S ...
The RNA landscape of all sequenced bacteria is littered with regulatory noncoding small RNAs (sRNA). Understanding the ... Nguyen TC, Cao X, Yu P et al (2016) Mapping RNA-RNA interactome and RNA structure in vivo by MARIO. Nat Commun 7:12023CrossRef ... Han K, Tjaden B, Lory S (2016) GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by ... Wong J., Pang I., Wilkins M., Tree J.J. (2018) Systems-Level Analysis of Bacterial Regulatory Small RNA Networks. In: Rajewsky ...
Given that similar RNA thermometer-like structures exist upstream of related toxin genes in various bacterial pathogens, we ... This regulation depends on a temperature-responsive RNA structure, an RNA thermometer, in the 5-untranslated region of the ... Preventing melting of the RNA structure at 37°C by nucleotide substitutions that stabilize base pairing resulted in avirulent ... propose that RNA thermometer-mediated toxin production is an evolutionary conserved mechanism. Interfering with opening of such ...
DNA/RNA tunnel of bacterial DNA dependent RNA polymerase (IPR021975). Short name: RNApol_Rpb2_rif ... This domain is part of the beta subunit of bacterial DNA dependent RNA polymerase. This domain is the binding site for the ... antibacterial drug rifampin (and its analogues) which blocks the DNA/RNA tunnel and prevents initiation of transcription. ...
Bacterial control of host gene expression through RNA polymerase II. Nataliya Lutay,1 Ines Ambite,1 Jenny Grönberg Hernandez,1 ... Here, we identify a new mechanism of bacterial adaptation through broad suppression of RNA polymerase II-dependent (Pol II- ... Effects on RNA Pol II-dependent transcription. RNA Pol II controls eukaryotic gene expression through mRNA precursors, most ... Such bacterial modulation of host gene expression may be essential to sustain asymptomatic bacterial carriage by ensuring that ...
2012) Accessibility and conservation: General features of bacterial small RNA-mRNA interactions? RNA Biol 9(7):954-965. ... RNA-RNA interaction. Small RNAs (sRNAs) are ubiquitous and important regulators of gene expression in bacteria. The most common ... 2011) Bacterial small RNA regulators: Versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 3(12): ... 2011) Quantifying the sequence-function relation in gene silencing by bacterial small RNAs. Proc Natl Acad Sci USA 108(30): ...
Systems biology of bacterial small RNAs. Small RNAs (sRNAs) are post-transcriptional regulators of gene expression that play ... fundamental roles in the response of bacterial cells to environmental cues. We study the response of genetic networks and ...
RNA can also serve in these capacities. For example, RNA has sufficient structural plasticity to form ribozyme1,2 and receptor3 ... It has also been proposed7,8,9,10,11,12 that certain messenger RNAs might use allosteric mechanisms to mediate regulatory ... Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. *Wade Winkler1. , ... Winkler, W., Nahvi, A. & Breaker, R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. ...
RNA-seq) have enabled tremendous leaps forward in our understanding of bacterial transcriptomes. However, computational methods ... for analysis of bacterial transcriptome data have not kept pace with the large and growing data sets generated by RNA-seq … ... Computational analysis of bacterial RNA-Seq data Nucleic Acids Res. 2013 Aug;41(14):e140. doi: 10.1093/nar/gkt444. Epub 2013 ... Our results suggest that Rockhopper can be used for efficient and accurate analysis of bacterial RNA-seq data, and that it can ...
RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 139, 945 (2009). doi:10.1016/j.cell.2009.07.040 pmid:19945378 ... Structures of the RNA-guided surveillance complex from a bacterial immune system. Nature 477, 486 (2011). doi:10.1038/ ... A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity Message Subject. (Your Name) has forwarded a ... A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. By Martin Jinek, Krzysztof Chylinski, Ines ...
Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the ... This article belongs to the Special Issue Bacterial RNA Polymerase) View Full-Text , Download PDF [941 KB, uploaded 21 May 2015 ... Zhang, N.; Buck, M. A Perspective on the Enhancer Dependent Bacterial RNA Polymerase. Biomolecules 2015, 5, 1012-1019. ... Zhang N, Buck M. A Perspective on the Enhancer Dependent Bacterial RNA Polymerase. Biomolecules. 2015; 5(2):1012-1019. ...
The GenElute Bacterial Genomic Kit provides a simple and convenient technique to isolate high quality DNA from both Gram(-) and ... Figure 3. Purified genomic DNA was isolated from various bacterial species using the GenElute Bacterial Genomic DNA kit. A 1 µg ... Typical DNA Yields with the GenElute Bacterial Genomic DNA Kit.. Source. Type of Media. Amount of Overnight Culture. OD600 per ... The GenElute Bacterial Genomic DNA Kit contains all of the reagents needed to purify genomic DNA from Gram negative bacteria ( ...
Bacterial,RNA,Isolation,From,Infected,Eukaryotic,Hosts,biological,advanced biology technology,biology laboratory technology, ... Works with any bacterial species ... Seamless integration with MICROB Express ... Enables microarray expression analysis with ... Remove 90% of mammalian RNA from ... Simple procedure takes less than 2 hours ... ... Mammalian and Bacterial Expression in One Vector. 3. Bacterial mRNA Isolation, Fast and Easy. 4. Bacterial RNA Isolation From ...
For the extraction of protein and nucleic acids from bacterial cell cultures ... Home − Shop − Sample Technologies − RNA − Total RNA − Allprep Bacterial DNA/RNA/Protein Kit ... Easy-to-use, the AllPrep Bacterial DNA/RNA/Protein Kit isolates total nucleic acids and cellular proteins from bacterial ... The Allprep Bacterial DNA/RNA/Protein Kit is intended for molecular biology applications. This product is not intended for the ...
... modified RNA from bacteria. This approach identified covalent cap-like linkage of a s … ... The absence of capped RNA is considered as a hallmark of prokaryotic gene expression. Recent developments combine next- ... Cap-like structures in bacterial RNA and epitranscriptomic modification Curr Opin Microbiol. 2016 Apr;30:44-49. doi: 10.1016/j. ... modified RNA from bacteria. This approach identified covalent cap-like linkage of a specific set of small RNAs to the ...
The bacterial Sm-like protein Hfq: a key player in RNA transactions.. Valentin-Hansen P1, Eriksen M, Udesen C. ... The recent findings that Hfq assists in bimolecular RNA-RNA interactions and is similar structurally and functionally to ... The conserved RNA-binding protein Hfq, originally discovered in Escherichia coli as a host factor for Qbeta replicase, has ... control has been an area of increasing focus because the protein has been linked to the action of many versatile RNA-based ...
Bacterial small RNAs (sRNA) are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, ... How ribonucleases dictate the rules in the control of small non-coding RNAs". RNA Biol. 5 (4): 230-43. doi:10.4161/rna.6915. ... a Staphylococcus regulatory RNA database". RNA. 21 (5): 1005-1017. doi:10.1261/rna.049346.114. ISSN 1469-9001. PMC 4408781 . ... Vogel J, Papenfort K (December 2006). "Small non-coding RNAs and the bacterial outer membrane". Curr. Opin. Microbiol. 9 (6): ...
RNA-Seq) offers an unbiased approach for analyzing and quantifying bacterial, viral, and other microbial transcripts. ... RNA-Seq for Microbial Transcript Analysis. Bacterial, viral, and other microbial RNA-Seq experiments enable annotation and ... Note: If using the TruSeq RNA library prep kit, you will NOT need to extract RNA and transcribe to cDNA. If you use an RNA ... Next-generation RNA sequencing (RNA-Seq) of bacteria, viruses, and other microbes has become a standard method for analyzing ...
... is the only kit available for bacterial RNA enrichment from mixed host-bacterial RNA populations. A robust yet simple procedure ... MICROBEnrich depletes mammalian (host cell) RNA selectively, leaving behind highly enriched bacterial RNA. ... is the only kit available for bacterial RNA enrichment from mixed host-bacterial RNA populations. A robust yet simple procedure ... because no method has existed to isolate bacterial RNA away from host cell RNA, the corresponding analyses of bacterial ...
2017 Feb 01;36:14-19 Authors: Ignatova Z, Narberhaus F Abstract RNA folds into intricate structures. Recent discoveries using ... approaches have revealed unprecedented structural complexity with a pivotal role in regulating RNA function and stability... ... Systematic probing of the bacterial RNA structurome to reveal new functions. Curr Opin Microbiol. ... Systematic probing of the bacterial RNA structurome to reveal new functions. Curr Opin Microbiol. 2017 Feb 01;36:14-19 Authors ...
Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among ... Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.. Lamichhane ... Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage-Display Libraries ... Selection of Peptides Targeting Helix 31 of Bacterial 16S Ribosomal RNA by Screening M13 Phage-Display Libraries ...
In turn, bacterial RNA polymerase (RNAP), a proven target for broad-spectrum antibacterial therapy [7,8,9], is structurally and ... Figure 2. Docking scores for previously reported triazole NNRTIs (1-11) [6], known bacterial RNA polymerase inhibitor (12) [14 ... Figure 2. Docking scores for previously reported triazole NNRTIs (1-11) [6], known bacterial RNA polymerase inhibitor (12) [14 ... Chopra, I. Bacterial RNA polymerase: A promising target for the discovery of new antimicrobial agents. Curr. Opin. Investig. ...
RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA. Nat ... A two plasmid system for editing bacterial genomes using an RNA-guided Cas9 nuclease. ...
Bacterial RNA from Infected Host RNA * An easy method of removing ,90% of host RNA from complex mixtures of host-bacterial ... input RNA amount, RNA quality, the bacterial species from which the RNA was isolated, and incubation time of the in vitro ... Enrich for Bacterial RNA- Even from Mixed Host-Pathogen Samples MICROBExpress™ to Purify Bacterial mRNA * The only system ... Linear Bacterial RNA Amplification MessageAmp II-Bacteria is based on a linear amplification method (Figure 1) in which the RNA ...
Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation ... Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus Phi6 from De Novo Initiation ... Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation ... RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, ...
  • Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries. (nih.gov)
  • Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. (nih.gov)
  • Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. (nih.gov)
  • 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)
  • Other forms of ribosomal RNA are unable to trigger the production of interleukin-1β. (elifesciences.org)
  • Aminoglycosides antibiotics provoke lethal translation errors by specifically binding to the bacterial ribosomal A-site. (jbsdonline.com)
  • To estimate the contribution of demand for RNA polymerase to the cost of resistance in rifampicin-free environments, we measured the fitness of 53 rifampicin-resistant mutants of Pseudomonas aeruginosa across a range of environments where we experimentally manipulated demand for RNA polymerase by adding sublethal doses of ribosomal inhibitors. (genetics.org)
  • Initially, three ranges (Type I, Type II, and Type III) of precursor 16S ribosomal RNA levels were defined by whole cell fluorescence in situ hybridization of a pure culture of Acinetobacter calocaceticusT prepared in three culture conditions. (bepress.com)
  • Low levels of precursor 16S ribosomal RNA (Type I) corresponded to a stationary phase culture prepared overnight in Luria-Bertani medium. (bepress.com)
  • Intermediate levels of precursor 16S ribosomal RNA (Type II) corresponded to a culture transferred into fresh Luria-Bertani medium, and high levels of precursor 16S ribosomal RNA (Type III) corresponded to a culture treated with the growth inhibiting antibiotic chloramphenicol. (bepress.com)
  • This mutation significantly alters cell growth, folding of 16S ribosomal RNA, and translational fidelity. (mendeley.com)
  • Barquist L, Westermann AJ, Vogel J (2016) Molecular phenotyping of infection-associated small non-coding RNAs. (springer.com)
  • Treatment of bacterial/HIV-1 co-infection is even more challenging due to potential drug-drug interactions and the ongoing prevalence of resistant strains in HIV-1 populations [ 4 ]. (mdpi.com)
  • In the context of myeloid-specific deletion of Ttp, the potentiation of neutrophil deployment protected mice against lethal soft tissue infection with Streptococcuspyogenes and prevented bacterial dissemination. (ovid.com)
  • IsrM RNA is expressed in vitro under conditions resembling those during infection in the gastrointestinal tract. (prolekare.cz)
  • Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children. (ox.ac.uk)
  • Because clinical features do not reliably distinguish bacterial from viral infection, many children worldwide receive unnecessary antibiotic treatment, while bacterial infection is missed in others.To identify a blood RNA expression signature that distinguishes bacterial from viral infection in febrile children.Febrile children presenting to participating hospitals in the United Kingdom, Spain, the Netherlands, and the United States between 2009-2013 were prospectively recruited, comprising a discovery group and validation group. (ox.ac.uk)
  • Each group was classified after microbiological investigation as having definite bacterial infection, definite viral infection, or indeterminate infection. (ox.ac.uk)
  • RNA expression signatures distinguishing definite bacterial from viral infection were identified in the discovery group and diagnostic performance assessed in the validation group. (ox.ac.uk)
  • 62% male) included 52 with definite bacterial infection, of whom 36 (69%) required intensive care, and 92 with definite viral infection, of whom 32 (35%) required intensive care. (ox.ac.uk)
  • Analysis of RNA expression data identified a 38-transcript signature distinguishing bacterial from viral infection. (ox.ac.uk)
  • Of the children in the indeterminate groups, 46.3% (63/136) were classified as having bacterial infection, although 94.9% (129/136) received antibiotic treatment.This study provides preliminary data regarding test accuracy of a 2-transcript host RNA signature discriminating bacterial from viral infection in febrile children. (ox.ac.uk)
  • Furthermore, we demonstrate that viral infection of the placenta may sensitize the pregnant mother to bacterial products and promote preterm labor. (jimmunol.org)
  • We use the infection of E. coli cells by bacteriophage lambda, whose DNA integrates at a unique site into the bacterial genome, when following the lysogenic pathway. (weizmann.ac.il)
  • As of 2017, he is the Founding Director of the Helmholtz Institute for RNA -based Infection Research in Würzburg. (helmholtz-hzi.de)
  • A cooperative study conducted by University of Jyväskylä and Natural Resources institute Finland (Luke), revealed that enriched rearing of juvenile fish significantly enhances the survival of fish from bacterial infection commonly seen in rearing conditions. (phys.org)
  • 14. The method of claim 13 in which a formulation comprised of the RNA is applied on or adjacent to a plant, and disease associated with nematode infection of the plant is thereby reduced. (google.com)
  • Despite antibiotic stewardship programs and increased awareness, clinicians continue to prescribe antibiotics without clear evidence of bacterial infection, especially in high risk populations such as immunocompromised patients, children, and the elderly. (biomedcentral.com)
  • total RNA from a Gram negative organism. (bio.net)
  • For microarray analysis and other sensitive applications, Ambion also recommends a DNase treatment (such as with DNA free Treatment and Removal Reagents ) to remove contaminating genomic DNA from the total RNA prior to the MICROB Enrich procedure. (bio-medicine.org)
  • In the first step of the MICROB Enrich procedure, host-bacterial total RNA is incubated with an optimized mixture of capture oligonucleotides that bind to the mammalian 18S and 28S rRNAs and polyadenylated RNAs. (bio-medicine.org)
  • Rat liver total RNA (25 g) and E. coli total RNA (2 g) were mixed together and subjected to the MICROB Enrich procedure. (bio-medicine.org)
  • Another mixed sample of total RNA was subjected to a mock MICROB Enrich procedure in which the capture oligonucleotide mix was left out of the reaction. (bio-medicine.org)
  • Even with a short 6 hour IVT incubation time, 100 ng of input total RNA results in sufficient aRNA for several replicate array experiments. (thermofisher.com)
  • Second, the proportion of reads representing rare transcripts can be increased by depleting abundant transcripts from total RNA and/or depleting cDNAs representing these abundant transcripts from cDNA libraries. (biomedcentral.com)
  • How I can to remove specific sequence from a fungu of a plant-fungu interaction of total RNA-Seq data? (usegalaxy.org)
  • This method involves fusing RNA aptamers that bind metabolites to Spinach 2 , a 98-nt RNA that switches on the fluorescence of 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), an otherwise nonfluorescent small molecule. (pubmedcentralcanada.ca)
  • Previous research has shown that six Hfq subunits combine to form a ring-shaped structure and has also provided some clues about the way in which Hfq can recognise a short stretch of a small RNA molecule, but the precise details of the interaction between them are not fully understood. (elifesciences.org)
  • have used a technique called X-ray crystallography to visualize the interaction between Hfq and a small RNA molecule called RydC. (elifesciences.org)
  • propose a model for how the RydC:Hfq complex is likely to interact with a messenger RNA molecule. (elifesciences.org)
  • In March 2020, astronomer Tomonori Totani presented a statistical approach for explaining how an initial active RNA molecule might have been produced randomly in the universe sometime since the Big Bang . (wikipedia.org)
  • One version of the hypothesis is that a different type of nucleic acid , termed pre-RNA , was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. (wikipedia.org)
  • The aminoacyl-tRNA synthetase (also known as aminoacyl-tRNA ligase) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction [ PMID: 10704480 , PMID: 12458790 ]. (ebi.ac.uk)
  • They did this with great success: About one third of all typical 'common colds' and some cases of diarrhoea as well are caused by these RNA Viruses, which are the largest of their kind. (helmholtz-hzi.de)
  • Treatment with binase was shown to improve survival of laboratory animals infected with different RNA viruses. (biomedcentral.com)
  • High-throughput sequencing of cDNA libraries (RNA-Seq) has proven to be a highly effective approach for studying bacterial transcriptomes. (biomedcentral.com)
  • In order to generate comprehensive transcriptome profiles using RNA-Seq one must therefore obtain a sufficiently large number of reads to detect those biologically relevant transcripts that comprise a relatively small proportion of the cDNA library. (biomedcentral.com)
  • Should Rna-Seq Reads Map To One Strand Of Cdna Reference? (biostars.org)
  • long RNAs are first converted into a library of cDNA fragments through either RNA fragmentation or DNA fragmentation. (rna-seqblog.com)
  • Altuvia S, Weinstein-Fischer D, Zhang A et al (1997) A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator. (springer.com)
  • Barquist L, Vogel J (2015) Accelerating discovery and functional analysis of small RNAs with new technologies. (springer.com)
  • These defense systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids. (sciencemag.org)
  • This approach identified covalent cap-like linkage of a specific set of small RNAs to the ubiquitous redox cofactor NAD, and a profound influence of this modification on RNA turnover. (nih.gov)
  • The small RNA nitrogen stress-induced RNA 1 (NsiR1) is produced by Cyanobacteria under conditions of nitrogen deprivation. (wikipedia.org)
  • The lack of an appropriate method for bacterial RNA amplification has hampered studies that rely on rare or limited samples, such as environmental collections, small volume cultures, and bacterial RNA isolated from host cells. (thermofisher.com)
  • Strong σ70 promoters were predicted upstream of all novel small RNAs, indicating the potential for transcriptional activity. (biomedcentral.com)
  • Is illumina small RNA-Seq strand specific? (biostars.org)
  • Because they are able to accurately make DNA copies of almost any type of RNA from very small amounts of starting material, they would do a better job of catching biomarkers for disease than anything currently available in an RNA-based liquid biopsy. (medicalautomation.org)
  • There has recently been a surge in studies, including one by Waters et al ( 2017 ) in this issue of The EMBO Journal , that have used clever variations of the RNA ‐seq technique to comprehensively map small RNA -target networks. (embopress.org)
  • While these processes are well understood in the messenger RNA of cells in higher organisms, Prof. Dr Andres Jäschke and his bioorganic chemistry working group now revealed these mechanisms in bacterial RNA. (xonl.de)
  • Chao Y, Li L, Girodat D et al (2017) In vivo cleavage map illuminates the central role of RNase E in coding and non-coding RNA pathways. (springer.com)
  • CLASH: Following in vivo cross‐linking, RNase E is pulled down using a FLAG‐tag, the bound RNA is trimmed, and the complex is purified under denaturing conditions using a His‐tag. (embopress.org)
  • In vivo cross‐linked Hfq is pulled down using a FLAG‐tag, followed by RNA trimming and ligation of the interacting RNAs with T4 ligase. (embopress.org)
  • Detection and quantification of low abundance transcripts by RNA-Seq can be enhanced in two main ways. (biomedcentral.com)
  • The upgrades increase throughput and performance of the Sequel in applications such as de novo assembly, structural variant detection, targeted sequencing, and RNA sequencing. (genomeweb.com)
  • Holmqvist et al , 2016 ), showing more precisely where Hfq recognizes its RNA targets. (embopress.org)
  • Thus, it was necessary to eliminate the human RNA, which could be done by hybridization capture using MICROBEnrich (Ambion). (asm.org)
  • Degraded human RNA cannot be removed by hybridization capture and could affect microarray analysis. (asm.org)
  • Soukup, G. A. & Breaker, R. R. Engineering precision RNA molecular switches. (nature.com)
  • Here, we use explicit solvent molecular dynamics (MD) simulations to map ions (NH 4 + , K + ) and water binding sites of a free bacterial A-site and their aminoglycoside complexes. (jbsdonline.com)
  • RNA‑based regulation in type I toxin-antitoxin systems and its implication for bacterial persistence Bork A. Berghoff 0 1 E. Gerhart H. Wagner 0 0 Department of Cell and Molecular Biology, Uppsala University , 75124 Uppsala , Sweden 1 Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität , 35392 Giessen , Germany 2 E. Gerhart H. Wagner Bacterial dormancy is a valuable survival strategy upon challenging environmental conditions. (paperity.org)
  • Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. (unil.ch)
  • This book is a valuable resource for molecular biologists and other investigators collecting the large number of reported DNA and RNA sequences and making them available in computer-readable form. (elsevier.com)
  • I hope that this Commentary inspires exciting new questions that can be tested in the near future as new ways of studying RNA secondary and tertiary structure are developed (for a review of methods, see Ignatova and Narberhaus, 2017 ). (biologists.org)
  • Previously, we found that the truncated RNase E lacking the C-terminal scaffold region no longer supports the rapid degradation of target mRNAs mediated by SgrS or RyhB RNA ( 9 , 12 ). (pnas.org)
  • Was wondering which would be the best mapper for strand-specific RNA-seq mapping for bacterial transcriptomics? (biostars.org)
  • I am looking for mapping software to analyze directional/strand-specific RNA-seq. (biostars.org)
  • Could I map strand specific RNA-seq with non-strand specific? (biostars.org)
  • Does the order of input files matter when mapping paired-end strand specific RNA-seq reads? (biostars.org)
  • And to that end, biochemists at the University of Texas at Austin have found that a bacterial enzyme (of a group of enzymes known as thermostable group II intron reverse transcriptases) are much more efficient in determining a cell's health state. (medicalautomation.org)
  • RNA methyltransferases comprise a superfamily of highly specialized enzymes that accomplish a wide variety of modifications. (biomedcentral.com)
  • These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in 6 RdRp, and pinpoint the previously unresolved Mn(2+)-dependent step in replication. (rcsb.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)
  • Here, we review recent insights concerning RNA-based control of toxin synthesis, and discuss possible implications for persister generation. (paperity.org)
  • Recent discoveries using next-generation sequencing (NGS) approaches have revealed unprecedented structural complexity with a pivotal role in regulating RNA function and stability. (medworm.com)
  • For many RNA-Seq-based projects, the budget for sequencing costs, and thus the total number of reads that can be obtained, is constrained. (biomedcentral.com)
  • Thus, researchers designing RNA-Seq experiments must often determine the correct balance between sequencing depth (the number of reads per sample) and breadth (the number of samples sequenced). (biomedcentral.com)
  • The new release also improves the sensitivity of Iso-Seq, PacBio's RNA sequencing method, while software enhances help simplify the analytics for multiplexed samples, according to the company. (genomeweb.com)