DNA sequences recognized as signals to end GENETIC TRANSCRIPTION.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. Terminator codons do not specify amino acids.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A protein which effects termination of RNA synthesis during the genetic transcription process by dissociating the ternary transcription complex RNA;-RNA POLYMERASE DNA at the termination of a gene.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A codon that directs initiation of protein translation (TRANSLATION, GENETIC) by stimulating the binding of initiator tRNA (RNA, TRANSFER, MET). In prokaryotes, the codons AUG or GUG can act as initiators while in eukaryotes, AUG is the only initiator codon.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.
The discontinuation of transcription at the end of a transcription unit, including the recognition of termination sites and release of the newly synthesized RNA molecule.
The functional hereditary units of BACTERIA.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is abnormal causing premature termination of protein translation and results in production of truncated and non-functional proteins. A nonsense mutation is one that converts an amino acid-specific codon to a stop codon.
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.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A species of gram-positive bacteria that is a common soil and water saprophyte.
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.
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).
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Proteins found in any species of bacterium.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.
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.
Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.
The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
An enzyme that catalyzes reversibly the formation of galactose 1-phosphate and ADP from ATP and D-galactose. Galactosamine can also act as the acceptor. A deficiency of this enzyme results in GALACTOSEMIA. EC 2.7.1.6.
A process of GENETIC TRANSLATION whereby the terminal amino acid is added to a lengthening polypeptide. This termination process is signaled from the MESSENGER RNA, by one of three termination codons (CODON, TERMINATOR) that immediately follows the last amino acid-specifying CODON.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
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.
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.
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.
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.
A temperate inducible phage and type species of the genus lambda-like viruses, in the family SIPHOVIRIDAE. Its natural host is E. coli K12. Its VIRION contains linear double-stranded DNA with single-stranded 12-base 5' sticky ends. The DNA circularizes on infection.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
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.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
The 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)
Proteins obtained from ESCHERICHIA COLI.
The processes of RNA tertiary structure formation.
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.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
A 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).
Uracil nucleotides which contain deoxyribose as the sugar moiety.
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.
Biochemical identification of mutational changes in a nucleotide sequence.
The process by which a DNA molecule is duplicated.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.
Nucleic acid sequences involved in regulating the expression of genes.
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
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.
A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.
Virulent bacteriophage and type species of the genus T7-like phages, in the family PODOVIRIDAE, that infects E. coli. It consists of linear double-stranded DNA, terminally redundant, and non-permuted.
A tentative species in the genus lambda-like viruses, family SIPHOVIRIDAE.
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.
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)
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.
Protein factors uniquely required during the elongation phase of protein synthesis.
A purine or pyrimidine base bonded to a DEOXYRIBOSE containing a bond to a phosphate group.
A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.
The genetic complement of a BACTERIA as represented in its DNA.
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)
A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
A group of enzymes that catalyzes the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-galactosides. Deficiency of beta-Galactosidase A1 may cause GANGLIOSIDOSIS, GM1.
The sequential set of three nucleotides in TRANSFER RNA that interacts with its complement in MESSENGER RNA, the CODON, during translation in the ribosome.
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
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.
The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.
Mutation process that restores the wild-type PHENOTYPE in an organism possessing a mutationally altered GENOTYPE. The second "suppressor" mutation may be on a different gene, on the same gene but located at a distance from the site of the primary mutation, or in extrachromosomal genes (EXTRACHROMOSOMAL INHERITANCE).
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Deletion of sequences of nucleic acids from the genetic material of an individual.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
Bacteriophages whose genetic material is RNA, which is single-stranded in all except the Pseudomonas phage phi 6 (BACTERIOPHAGE PHI 6). All RNA phages infect their host bacteria via the host's surface pili. Some frequently encountered RNA phages are: BF23, F2, R17, fr, PhiCb5, PhiCb12r, PhiCb8r, PhiCb23r, 7s, PP7, Q beta phage, MS2 phage, and BACTERIOPHAGE PHI 6.
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.
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
A 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.
A series of 7 virulent phages which infect E. coli. The T-even phages T2, T4; (BACTERIOPHAGE T4), and T6, and the phage T5 are called "autonomously virulent" because they cause cessation of all bacterial metabolism on infection. Phages T1, T3; (BACTERIOPHAGE T3), and T7; (BACTERIOPHAGE T7) are called "dependent virulent" because they depend on continued bacterial metabolism during the lytic cycle. The T-even phages contain 5-hydroxymethylcytosine in place of ordinary cytosine in their DNA.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
The functional hereditary units of VIRUSES.
Change brought about to an organisms genetic composition by unidirectional transfer (TRANSFECTION; TRANSDUCTION, GENETIC; CONJUGATION, GENETIC, etc.) and incorporation of foreign DNA into prokaryotic or eukaryotic cells by recombination of part or all of that DNA into the cell's genome.
Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.
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).
Cytosine nucleotides which contain deoxyribose as the sugar moiety.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Any method used for determining the location of and relative distances between genes on a chromosome.
Proteins found in any species of virus.
A family of DNA helicases that participate in DNA REPLICATION. They assemble into hexameric rings with a central channel and unwind DNA processively in the 5' to 3' direction. DnaB helicases are considered the primary replicative helicases for most prokaryotic organisms.
Proteins found in ribosomes. They are believed to have a catalytic function in reconstituting biologically active ribosomal subunits.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
The functional hereditary units of FUNGI.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.
Sequences within RNA that regulate the processing, stability (RNA STABILITY) or translation (TRANSLATION, GENETIC) of RNA.
An enzyme that activates tyrosine with its specific transfer RNA. EC 6.1.1.1.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.
A process of GENETIC TRANSLATION whereby the formation of a peptide chain is started. It includes assembly of the RIBOSOME components, the MESSENGER RNA coding for the polypeptide to be made, INITIATOR TRNA, and PEPTIDE INITIATION FACTORS; and placement of the first amino acid in the peptide chain. The details and components of this process are unique for prokaryotic protein biosynthesis and eukaryotic protein biosynthesis.
Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.
A 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.
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.
Viruses whose hosts are bacterial cells.
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
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.
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.
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.
Biologically functional sequences of DNA chemically synthesized in vitro.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.
A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.
A method (first developed by E.M. Southern) for detection of DNA 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.
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.
A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.
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)
An integration host factor that was originally identified as a bacterial protein required for the integration of bacteriophage Q beta (ALLOLEVIVIRUS). Its cellular function may be to regulate mRNA stability and processing in that it binds tightly to poly(A) RNA and interferes with ribosome binding.
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Nucleosides that have two hydroxy groups removed from the sugar moiety. The majority of these compounds have broad-spectrum antiretroviral activity due to their action as antimetabolites. The nucleosides are phosphorylated intracellularly to their 5'-triphosphates and act as chain-terminating inhibitors of viral reverse transcription.
The rate dynamics in chemical or physical systems.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
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.-.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
The sequential location of genes on a chromosome.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
A species of gram-negative, rod-shaped bacteria belonging to the K serogroup of ESCHERICHIA COLI. It lives as a harmless inhabitant of the human LARGE INTESTINE and is widely used in medical and GENETIC RESEARCH.
The relationships of groups of organisms as reflected by their genetic makeup.
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.
Actual loss of portion of a chromosome.
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
Proteins that are involved in the peptide chain termination reaction (PEPTIDE CHAIN TERMINATION, TRANSLATIONAL) on RIBOSOMES. They include codon-specific class-I release factors, which recognize stop signals (TERMINATOR CODON) in the MESSENGER RNA; and codon-nonspecific class-II release factors.
Family of retrovirus-associated DNA sequences (ras) originally isolated from Harvey (H-ras, Ha-ras, rasH) and Kirsten (K-ras, Ki-ras, rasK) murine sarcoma viruses. Ras genes are widely conserved among animal species and sequences corresponding to both H-ras and K-ras genes have been detected in human, avian, murine, and non-vertebrate genomes. The closely related N-ras gene has been detected in human neuroblastoma and sarcoma cell lines. All genes of the family have a similar exon-intron structure and each encodes a p21 protein.
Members of the beta-globin family. In humans, they are encoded in a gene cluster on CHROMOSOME 11. They include epsilon-globin, gamma-globin, delta-globin and beta-globin. There is also a pseudogene of beta (theta-beta) in the gene cluster. Adult HEMOGLOBIN is comprised of two ALPHA-GLOBIN chains and two beta-globin chains.
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.
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.
An enzyme of the transferase class that catalyzes the reaction RNA(n+1) and orthophosphate to yield RNA(n) and a nucleoside diphosphate, or the reverse reaction. ADP, IDP, GDP, UDP, and CDP can act as donors in the latter case. (From Dorland, 27th ed) EC 2.7.7.8.
An NAD-dependent glyceraldehyde-3-phosphate dehydrogenase found in the cytosol of eucaryotes. It catalyses the dehydrogenation and phosphorylation of GLYCERALDEHYDE 3-PHOSPHATE to 3-phospho-D-glyceroyl phosphate, which is an important step in the GLYCOLYSIS pathway.
The heritable modification of the properties of a competent bacterium by naked DNA from another source. The uptake of naked DNA is a naturally occuring phenomenon in some bacteria. It is often used as a GENE TRANSFER TECHNIQUE.
Viruses whose host is Escherichia coli.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Part of a MESSENGER RNA molecule that undergoes a conformation change upon binding a specific metabolite or other small molecule thereby regulating the messenger RNA's transcription, post-transcriptional processing, transport, translation, or stability in response to varying levels of the metabolite or other small molecule.
Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.
Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.
A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Deoxyribonucleic acid that makes up the genetic material of fungi.
A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 2.7.7.7.
Inorganic salts of phosphoric acid that contain two phosphate groups.
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.
Ribonucleic acid in fungi having regulatory and catalytic roles as well as involvement in protein synthesis.
Proteins that catalyze the unwinding of duplex DNA during replication by binding cooperatively to single-stranded regions of DNA or to short regions of duplex DNA that are undergoing transient opening. In addition DNA helicases are DNA-dependent ATPases that harness the free energy of ATP hydrolysis to translocate DNA strands.
The in vitro fusion of GENES by RECOMBINANT DNA techniques to analyze protein behavior or GENE EXPRESSION REGULATION, or to merge protein functions for specific medical or industrial uses.
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.
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
A reverse transcriptase encoded by the POL GENE of HIV. It is a heterodimer of 66 kDa and 51 kDa subunits that are derived from a common precursor protein. The heterodimer also includes an RNAse H activity (RIBONUCLEASE H, HUMAN IMMUNODEFICIENCY VIRUS) that plays an essential role the viral replication process.
The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
Two-dimensional separation and analysis of nucleotides.
Deoxyribonucleic acid that makes up the genetic material of viruses.
Ribonucleic acid that makes up the genetic material of viruses.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
Enzymes that catalyze the hydrolysis of the internal bonds and thereby the formation of polynucleotides or oligonucleotides from ribo- or deoxyribonucleotide chains. EC 3.1.-.
Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.
Genotypic differences observed among individuals in a population.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
The determination of the concentration of a given component in solution (the analyte) by addition of a liquid reagent of known strength (the titrant) until an equivalence point is reached (when the reactants are present in stoichiometric proportions). Often an indicator is added to make the equivalence point visible (e.g., a change in color).
PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.
The phosphate esters of DIDEOXYNUCLEOSIDES.
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.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Proteins prepared by recombinant DNA technology.
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
The 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.
Adenine nucleotides which contain deoxyribose as the sugar moiety.
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.
A basic polypeptide isolated from Streptomyces netropsis. It is cytotoxic and its strong, specific binding to A-T areas of DNA is useful to genetics research.
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.
Established cell cultures that have the potential to propagate indefinitely.
Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
A pyrimidine nucleoside that is composed of the base CYTOSINE linked to the five-carbon sugar D-RIBOSE.
Enzymes of the transferase class that catalyze the transfer of a pentose group from one compound to another.
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.
The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.
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.
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.-
A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
The difference between two images on the retina when looking at a visual stimulus. This occurs since the two retinas do not have the same view of the stimulus because of the location of our eyes. Thus the left eye does not get exactly the same view as the right eye.
Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.

A premature termination codon interferes with the nuclear function of an exon splicing enhancer in an open reading frame-dependent manner. (1/1018)

Premature translation termination codon (PTC)-mediated effects on nuclear RNA processing have been shown to be associated with a number of human genetic diseases; however, how these PTCs mediate such effects in the nucleus is unclear. A PTC at nucleotide (nt) 2018 that lies adjacent to the 5' element of a bipartite exon splicing enhancer within the NS2-specific exon of minute virus of mice P4 promoter-generated pre-mRNA caused a decrease in the accumulated levels of P4-generated R2 mRNA relative to P4-generated R1 mRNA, although the total accumulated levels of P4 product remained the same. This effect was seen in nuclear RNA and was independent of RNA stability. The 5' and 3' elements of the bipartite NS2-specific exon enhancer are redundant in function, and when the 2018 PTC was combined with a deletion of the 3' enhancer element, the exon was skipped in the majority of the viral P4-generated product. Such exon skipping in response to a PTC, but not a missense mutation at nt 2018, could be suppressed by frame shift mutations in either exon of NS2 which reopened the NS2 open reading frame, as well as by improvement of the upstream intron 3' splice site. These results suggest that a PTC can interfere with the function of an exon splicing enhancer in an open reading frame-dependent manner and that the PTC is recognized in the nucleus.  (+info)

Inhibition of translation and cell growth by minigene expression. (2/1018)

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)

Mutations in the nebulin gene associated with autosomal recessive nemaline myopathy. (3/1018)

The congenital nemaline myopathies are rare hereditary muscle disorders characterized by the presence in the muscle fibers of nemaline bodies consisting of proteins derived from the Z disc and thin filament. In a single large Australian family with an autosomal dominant form of nemaline myopathy, the disease is caused by a mutation in the alpha-tropomyosin gene TPM3. The typical form of nemaline myopathy is inherited as an autosomal recessive trait, the locus of which we previously assigned to chromosome 2q21.2-q22. We show here that mutations in the nebulin gene located within this region are associated with the disease. The nebulin protein is a giant protein found in the thin filaments of striated muscle. A variety of nebulin isoforms are thought to contribute to the molecular diversity of Z discs. We have studied the 3' end of the 20. 8-kb cDNA encoding the Z disc part of the 800-kDa protein and describe six disease-associated mutations in patients from five families of different ethnic origins. In two families with consanguineous parents, the patients were homozygous for point mutations. In one family with nonconsanguineous parents, the affected siblings were compound heterozygotes for two different mutations, and in two further families with one detected mutation each, haplotypes are compatible with compound heterozygosity. Immunofluorescence studies with antibodies specific to the C-terminal region of nebulin indicate that the mutations may cause protein truncation possibly associated with loss of fiber-type diversity, which may be relevant to disease pathogenesis.  (+info)

Mutations in the organic cation/carnitine transporter OCTN2 in primary carnitine deficiency. (4/1018)

Primary carnitine deficiency is an autosomal recessive disorder of fatty acid oxidation caused by defective carnitine transport. This disease presents early in life with hypoketotic hypoglycemia or later in life with skeletal myopathy or cardiomyopathy. The gene for this condition maps to 5q31.2-32 and OCTN2, an organic cation/carnitine transporter, also maps to the same chromosomal region. Here we test the causative role of OCTN2 in primary carnitine deficiency by searching for mutations in this gene in affected patients. Fibroblasts from patients with primary carnitine deficiency lacked mediated carnitine transport. Transfection of patient's fibroblasts with the OCTN2 cDNA partially restored carnitine transport. Sequencing of the OCTN2 gene revealed different mutations in two unrelated patients. The first patient was homozygous (and both parents heterozygous) for a single base pair substitution converting the codon for Arg-282 to a STOP codon (R282X). The second patient was a compound heterozygote for a paternal 1-bp insertion producing a STOP codon (Y401X) and a maternal 1-bp deletion that produced a frameshift creating a subsequent STOP codon (458X). These mutations decreased the levels of mature OCTN2 mRNA and resulted in nonfunctional transporters, confirming that defects in the organic cation/carnitine transporter OCTN2 are responsible for primary carnitine deficiency.  (+info)

Infrequent translation of a nonsense codon is sufficient to decrease mRNA level. (5/1018)

In many organisms nonsense mutations decrease the level of mRNA. In the case of mammalian cells, it is still controversial whether translation is required for this nonsense-mediated RNA decrease (NMD). Although previous analyzes have shown that conditions that impede translation termination at nonsense codons also prevent NMD, the residual level of termination was unknown in these experiments. Moreover, the conditions used to impede termination might also have interfered with NMD in other ways. Because of these uncertainties, we have tested the effects of limiting translation of a nonsense codon in a different way, using two mutations in the immunoglobulin mu heavy chain gene. For this purpose we exploited an exceptional nonsense mutation at codon 3, which efficiently terminates translation but nonetheless maintains a high level of mu mRNA. We have shown 1) that translation of Ter462 in the double mutant occurs at only approximately 4% the normal frequency, and 2) that Ter462 in cis with Ter3 can induce NMD. That is, translation of Ter462 at this low (4%) frequency is sufficient to induce NMD.  (+info)

Heterologous sequences greatly affect foreign gene expression in tobacco mosaic virus-based vectors. (6/1018)

A series of tobacco mosaic virus (TMV)-based hybrid vectors for transient gene expression were constructed with similar designs but differing in the source of heterologous tobamovirus sequence: Odontoglossum ringspot virus, tobacco mild green mosaic virus variants U2 and U5, tomato mosaic virus, and sunn-hemp mosaic virus. These vectors contained a heterologous coat protein subgenomic mRNA promoter and coat protein open reading frame (ORF) and either TMV or heterologous 3' nontranslated region. The foreign ORF, from the jellyfish green fluorescent protein (GFP) gene, was transcribed from the native TMV coat protein subgenomic mRNA promoter, which extended into the coat protein ORF. The presence of an in-frame stop codon within the GFP mRNA leader and the choice of sequence of GFP ORFs substantially affected translational efficiency. However, the major regulatory component of gene expression in these vectors appeared to be transcriptional rather than translational. There was an inverse relationship between expression of GFP and the heterologous coat protein genes that was reflected in accumulation of the respective mRNAs and proteins. The most effective vector in this series (30B) contained sequences encoding the coat protein subgenomic mRNA promoter, coat protein ORF, and 3' nontranslated region from tobacco mild green mosaic virus U5. Expressed from 30B, GFP accumulated up to 10% of total soluble protein in leaves.  (+info)

High frequency of germ-line BRCA2 mutations among Hungarian male breast cancer patients without family history. (7/1018)

To determine the contribution of BRCA1 and BRCA2 mutations to the pathogenesis of male breast cancer in Hungary, the country with the highest male breast cancer mortality rates in continental Europe, a series of 18 male breast cancer patients and three patients with gynecomastia was analyzed for germ-line mutations in both BRCA1 and BRCA2. Although no germ-line BRCA1 mutation was observed, 6 of the 18 male breast cancer cases (33%) carried truncating mutations in the BRCA2 gene. Unexpectedly, none of them reported a family history for breast/ovarian cancer. Four of six truncating mutations were novel, and two mutations were recurrent. Four patients (22%) had a family history of breast/ovarian cancer in at least one first- or second-degree relative; however, no BRCA2 mutation was identified among them. No mutation was identified in either of the genes in the gynecomastias. These results provide evidence for a strong genetic component of male breast cancer in Hungary.  (+info)

Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid. (8/1018)

Replication of the IncL/M plasmid pMU604 is controlled by a small antisense RNA molecule (RNAI), which, by inhibiting the formation of an RNA pseudoknot, regulates translation of the replication initiator protein, RepA. Efficient translation of the repA mRNA was shown to require the translation and correct termination of the leader peptide, RepB, and the formation of the pseudoknot. Although the pseudoknot was essential for the expression of repA, its presence was shown to interfere with the translation of repB. The requirement for pseudoknot formation could in large part be obviated by improving the ribosome binding region of repA, either by replacing the GUG start codon by AUG or by increasing the spacing between the start codon and the Shine-Dalgarno sequence (SD). The spacing between the distal pseudoknot sequence and the repA SD was shown to be suboptimal for maximal expression of repA.  (+info)

Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian readthrough have only recently been uncovered by systems biology and comparative genomics approaches. Previously, our analysis of conserved protein coding signatures that e …
Read about stop codon readthrough, an investigational Duchenne and Becker muscular dystrophy therapy that addresses mutations in the DMD gene.
The mechanisms that regulate oxidative phosphorylation in mammalian cells are largely unknown. To address this issue, cybrids were generated by fusing osteosarcoma cells devoid of mitochondrial DNA (mtDNA) with platelets from a patient with a stop-codon mutation in cytochrome c oxidase subunit I (CO …
Dectin-1, a pattern recognition receptor expressed by the innate immune system, is known to be a major receptor inducing Th17-type adaptive immune responses that have been demonstrated to mediate autoimmunity. In this study, dectin-1 mRNA and protein expression, as well as the recently characterized DECTIN-1 Y238X early stop codon polymorphism, were studied in relation to rheumatoid arthritis (RA) susceptibility and severity. Dectin-1 mRNA expression was measured in synovial tissue specimens of RA, osteoarthritis (OA), and nonrheumatic patients. Dectin-1 protein expression and localization were assessed in RA synovial tissue specimens. Macrophages from individuals with different DECTIN-1 genotypes were examined for differences in cytokine responses on dectin-1 stimulation. Furthermore, clinical parameters of inflammation and bone destruction of 262 RA patients were correlated with the presence of the DECTIN-1 Y238X polymorphism. Evaluation of dectin-1 mRNA expression in synovial tissue biopsies revealed
In Sindbis, Venezuelan equine encephalitis and related alphaviruses, the polymerase is translated as a fusion with other non-structural proteins via readthrough of a UGA stop codon. Surprisingly, earlier work reported that the signal for efficient readthrough comprises a single cytidine residue 3-adjacent to the UGA. However, analysis of variability at synonymous sites revealed strikingly enhanced conservation within the similar to 150 nt 3-adjacent to the UGA, and RNA folding algorithms revealed the potential for a phylogenetically conserved stem-loop structure in the same region. Mutational analysis of the predicted structure demonstrated that the stem-loop increases readthrough by up to 10-fold. The same computational analysis indicated that similar RNA structures are likely to be relevant to readthrough in certain plant virus genera, notably Furovirus, Pomovirus, Tobravirus, Pecluvirus and Benyvirus, as well as the Drosophilia gene kelch. These results suggest that 3 RNA stimulatory ...
During protein translation, a variety of quality control checks ensure that the resulting polypeptides deviate minimally from their genetic encoding template. Translational fidelity is central in...
Ataluren was safe in healthy volunteers. A first trial in Duchenne patients were patients were treated with different daily doses of Ataluren for 4 weeks showed that treatment was well tolerated and that dystrophin expression was increased for treated patients. Trials to test whether this also results in functional improvement after long term treatment have been performed in multiple centers in the USA and Europe.. Unfortunately, treatment did not convincingly lead in to a functional improvement when compared to placebo treated patients using a 6 minute walk test and therefore the trials were put on hold. Patients involved in these trials in the USA and Europe can enrol in an open label trial.. After detailed analysis of the data and further optimization of dosing, a new confirmatory phase 3 trial in 220 DMD patients has been completed in North- and South-America, Asia, Australia and Europe. Translarna treated patients on average walked 15 meters more in 6 minutes compared to placebo treated ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
The Drosophila kelch gene produces a single transcript with a UGA stop codon separating two open reading frames (ORF1 and ORF2). From the transcript, 76 kDa ORF1 and 160 kDa full-length (ORF1 + ORF2) proteins are made. The expression of these two proteins is regulated in a tissue-specific manner causing the ratio of full-length to ORF1 protein to vary in different tissues. The only detected defect for kelch mutants is female sterility, and kelch protein is localized to the ovarian ring canals. kelch mutant ring canals are disorganized and have partly occluded lumens, causing a failure to transport cytoplasm. ORF1 and full-length kelch proteins co-sediment with ring canals suggesting that both proteins are found in the ring canals. Transgenetic analysis reveals that ORF1 kelch protein is sufficient to rescue ring canal morphology and fertility. In addition, we have mutated the UGA stop codon to a UAA stop codon and to three sense codons that allow constitutive readthrough. Analysis of these ...
Frontotemporal lobar degeneration (FTLD) is a devastating and progressive disorder, and a common cause of early onset dementia. Progranulin (PGRN) haploinsufficiency due to autosomal dominant mutations in the progranulin gene (GRN) is an important cause of FTLD (FTLD-GRN), and nearly a quarter of these genetic cases are due to a nonsense mutation. Premature termination codons (PTC) can be therapeutically targeted by compounds allowing readthrough, and aminoglycoside antibiotics are known to be potent PTC readthrough drugs. Restoring endogenous PGRN through PTC readthrough has not previously been explored as a therapeutic intervention in FTLD. We studied whether the aminoglycoside G418 could increase PGRN expression in HEK293 and human induced pluripotent stem cell (hiPSC)-derived neurons bearing the heterozygous S116X, R418X, and R493X pathogenic GRN nonsense mutations. We further tested a novel substituted phthalimide PTC readthrough enhancer in combination with G418 in our cellular models. We next
The process of decoding is the most crucial determinant of the quality of protein synthesis. Ribosomal protein L9 was first implicated in decoding fidelity when a mutant version of L9 was found to increase the translation of a T4 phage gene. Later studies confirmed that the absence of L9 leads to increased translational bypassing, frameshifting, and stop codon readthrough. L9 is part of the large subunit of the prokaryotic ribosome and is located more than 90 Å from the site of decoding, making it difficult to envision how it might affect decoding and reading frame maintenance. Twenty years after the identification of L9s putative function, there is no mechanism for how a remotely located L9 improves translation fidelity. This mystery makes our picture of translation incomplete. Despite the high conservation of L9 in eubacteria, E.coli lacking L9 does not exhibit any obvious growth defects. Thus, the evolutionary advantage conferred by L9 in bacteria is masked under laboratory conditions. In order to
As you can see, mutations which affect STOP codons are very important as they drastically change the protein sequence. This usually disrupts the protein function and causes diseases or inviable embryos. Most of these are removed from populations long-term by natural selection. However, it can rarely lead to entirely new proteins beneficial to the organism and evolutionary changes. This is more likely with duplicated genes where one can change while the other retains the original function. As such, mutations involving STOP codons are among the most biologically important. Another important case is splice functions. Point mutations and frameshifts can also affect intron-exon boundaries, resulting in new splice variants, skipped exons, and reading further into introns (which may contain splice junctions or STOP codons).. ...
Toll-like receptors (TLRs) are evolutionarily conserved pattern-recognition molecules resembling the toll proteins that mediate antimicrobial responses in Drosophila. These proteins recognize different microbial products during infection and serve as an important link between the innate and adaptive immune responses. The TLRs act through adaptor molecules such as MyD88 and TIRAP to activate various kinases and transcription factors so the organism can respond to potential infection. TLR5 recognizes flagellin from both Gram-positive and Gram-negative bacteria and will cause the activation of NF-kappaB, leading to the activation of TNF-alpha and other cytokines. A common TLR5 stop codon polymorphism that disrupts TLR5 signaling is associated with susceptibility to Legionnaires disease and demonstrates the importance of TLR5 in the innate immune response ...
There is a long path from a genetic variant to an organismal phenotype (i.e. one that is observed at the level of the organism). A variant nucleotide can have many effects: Exonic variants may disrupt proper transcription by generating a premature stop-codon, or alter an amino-acid that is crucial for protein function, while intronic variants may affect splicing. Also variants outside the transcribed region can modify the level of expression by altering regulatory sites for chromatin state, as well as transcriptional and post-transcriptional regulation. It is important to realize that regulatory networks have evolved to function robustly under external and internal perturbations. Any effect of a genetic variant on the organismal phenotype is propagated through these networks. This propagation, in particular if it involves crucial cellular functions, is likely to involve compensatory effects mediated by regulatory circuits like feedback loops. Moreover, robust functions are often achieved by ...
Release Factor 1 (RF1) recognizes the termination codons UAA and UAG, and is responsible for stopping translation at these codons. While obviously important for proper functioning of translation, the presence of RF1 also limits the amount of full-length protein produced if the gene contains an in-frame stop codon by competing with the Amber suppressor tRNA at the ribosome. This problem is compounded with each additional Amber in the gene, leading to a rapid dropoff of full-length protein isolated with greater than one stop codon. Until recently, it was thought that RF1 was essential for cell survival. Several methods have recently been used to make RF1 conditionally inessential, enabling its knockout. Mukai et al. introduced all seven essential genes normally ending in Amber codons on a plasmid, instead ending in UAA. [15] Johnson et al. fixed the expression of RF2, the other primary release factor in E. coli.[16] Both these measures enabled the knockout of RF1. The benefit of this knockout ...
Eloxx Pharmaceuticals, Inc. is a clinical-stage biopharmaceutical company developing novel RNA-modulating drug candidates (designed to be eukaryotic ribosomal selective glycosides) that are formulated to treat rare and ultra-rare premature stop codon diseases. Premature stop codons are point mutations that disrupt protein synthesis from messenger RNA.
Nucleotide View When zoomed in, the DNA sequence of the Release 6 (R6) (Hoskins et al, 2015) genome is shown as color-coded blocks, G-orange, A-green, T-red, C-blue. When zoomed in further, the bases are also labeled (GATC). Above and below the base representation, the three-frame translation for the plus and minus strands is shown using the single-letter amino acid code. Start codons (M and L) are indicated in green and stop codons are marked in red. Gene span Shows the extent of all annotated gene models with direction of transcription indicated by a small arrow at the downstream edge. Protein-coding genes are shown in blue with the different shades further indicating direction of transcription. Non-protein-coding genes are shown in red, tRNA genes in purple and pseudogenes in pink. Each gene glyph is hyperlinked to a pop-up window containing an automated gene summary and links to the FlyBase Gene Report and NCBI gene report. Gene: transcript view Shows a condensed transcript summary of all ...
Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. ...
Geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. ...
The overall goal of the Karzai lab is to gain new insights into how the fundamental processes of gene expression are integrated inside the cell. We seek to discover novel integrative links, and explore the biological significance and physiological contributions of these links to the fitness, survival, and virulence of pathogenic bacteria. Our current research is aimed at elucidating the mechanistic details of how the essential processes of protein translation, mRNA stability, and protein degradation are linked. We are particularly interested in investigating: 1) Molecular mechanisms that govern translation quality assurance; 2) Molecular basis for mRNA surveillance and selective nonstop mRNA decay; 3) Biochemical mechanisms of targeted proteolysis and the role of AAA+ proteases in bacterial pathogenesis; 5) Discovery of novel antibiotics and the exploration of new vaccine technologies. We use a combination of protein biochemistry, molecular genetics, functional genomics, bioinformatics, and ...
Because biologization of psychiatric constructs does not involve derivation of laws, or reduce the number of entities involved, the traditional term of
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بعد از نصب همه دستگاه ها اگر روی بلندگو وقتی سورس شما موزیک پخش نمیکنه (حالت STOP) و با چسبوندن گوشتون به بلندگو فقط و فقط نویز سفید یا پینک نویز میشنوید که اون نویز با تغییر ولوم افزایش و کاهش داره میشه گفت کل سیستم سالم هست. صدای نویز سفید یا پینگ نویز تو اینترنت هست و میتونید بشنوید و مثل صدای ششششش هست. یه حالت ملایم داره که همه فرکانسها رو دربر میگیره و این نویز سفيد يا پينك هرچقدر بیشتر باشه نشونه بدي نيست چون دستگاه هایی که فیدبک منفی کمتری دارند این نوع نویز رو میشنویم. هر دو کانال باید نویزشون یه اندازه باشه.. در این حالت اگر وقتی همه دستگاه ها روشنه و ...
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Hi, Could anyone help here, my daughter who has been taking dostinex for over a year, was told to stop taking it, that was 2 months ago, since then she has been...
TY - JOUR. T1 - Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes. AU - Ozawa, Y.. AU - Saito, R.. AU - Washio, T.. AU - Tomita, Masaru. PY - 2003/6/1. Y1 - 2003/6/1. N2 - Translation termination is catalyzed by release factors that recognize stop codons. However, previous works have shown that in some bacteria, the termination process also involves bases around stop codons. Recently, Ito et al, analyzed release factors and identified the amino acids therein that recognize stop codons. However, the amino acids that recognize bases around stop codons remain unclear. To identify the candidate amino acids that recognize the bases around stop codons, we aligned the protein sequences of the release factors of various bacteria and searched for amino acids that were conserved specifically in the sequence of bacteria that seemed to regulate translation termination by bases around stop codons. As a result, species having several highly conserved residues ...
TY - JOUR. T1 - Gentamicin-induced readthrough of stop codons in Duchenne muscular dystrophy. AU - Malik, Vinod. AU - Rodino-Klapac, Louise R.. AU - Viollet, Laurence. AU - Wall, Cheryl. AU - King, Wendy. AU - Al-Dahhak, Roula. AU - Lewis, Sarah. AU - Shilling, Christopher J.. AU - Kota, Janaiah. AU - Serrano-Munuera, Carmen. AU - Hayes, John. AU - Mahan, John D.. AU - Campbell, Katherine J.. AU - Banwell, Brenda. AU - Dasouki, Majed. AU - Watts, Victoria. AU - Sivakumar, Kumaraswamy. AU - Bien-Willner, Ricardo. AU - Flanigan, Kevin M.. AU - Sahenk, Zarife. AU - Barohn, Richard J.. AU - Walker, Christopher M.. AU - Mendell, Jerry R.. PY - 2010/6. Y1 - 2010/6. N2 - Objective: The objective of this study was to establish the feasibility of long-term gentamicin dosing to achieve stop codon readthrough and produce full-length dystrophin. Mutation suppression of stop codons, successfully achieved in the mdx mouse using gentamicin, represents an important evolving treatment strategy in Duchenne ...
Peptide sequence-dependent ribosomal stalling, as occurs after translation of uORF2, has been observed in other eukaryotic and bacterial systems (21, 36, 47). Our results raise the question of whether release factors play a role in other uORF-mediated ribosomal stalling events. The S-adenosylmethionine decarboxylase uORF codes for a sequence-dependent polyamine-responsive peptide that, like uORF2, causes ribosomal stalling specifically at the termination codon and results in accumulation of the uORF peptidyl-tRNA (30, 40). While the critical sequences of this uORF do not include the carboxy-terminal residue, the penultimate and antepenultimate residues have been implicated (35). Thus, it is possible that eRF1 acts in concert with the polyamine effector and the nascent peptide to inhibit the termination reaction. Regulation of the bacterial tryptophanase operon gene tnaC also has intriguing similarities to the uORF2 mechanism (22-24). Toeprinting assays show that ribosomes translating tnaC stall ...
SsrA is a tmRNA involved in tagging polypeptides on stalled ribosomes. The resulting fusion proteins are then degraded. We purified endogenous SsrA-tagged proteins by means of a genetically engineered SsrA and identified some of them. Analysis of the proteins suggested that they are tagged at their C-terminal extremities. One of them, ribokinase, is expressed from a messenger with a poorly efficient stop codon, leading to translational recoding events. A change in the ribokinase coding sequence from a weak to a strong translational stop sequence (UGAc to UAAu) annihilated SsrA tagging. Translational termination by UGA recruits the translational release factor (RF) 2. We observed that SsrA tagging of ribokinase was inversely correlated with RF2 activity, revealing a dynamic competition between translational termination and SsrA tagging.
Termination of protein synthesis in the yeast Saccharomyces cerevisiae occurs when the eukaryotic release factor eRF1 recognises the stop codon. The rate of termination is enhanced by a second release factor, eRF3 (a GTPase). The efficiency of stop codon recognition by eRF1 is influenced by the surrounding nucleotide context of the stop codon, and in yeast, by the structural properties of eRF3, which displays prion-like characteristics. eRF3 in the [PSI+], prion state forms insoluble high molecular weight aggregates that cause inefficient termination (nonsense suppression). This study tested the hypothesis that the [PSI+] state may direct suppression of stop codons, particularly those in weak contexts. This may confer unique phenotypes upon yeast, particularly stress response phenotypes, caused by C-terminal extension of a subset of proteins. Consistent with this hypothesis, the [PSI+] state was found to enhance suppression of all stop codons, with those in weak contexts being most efficiently ...
TY - JOUR. T1 - HMRF1L is a human mitochondrial translation release factor involved in the decoding of the termination codons UAA and UAG. AU - Nozaki, Yusuke. AU - Matsunaga, Noriko. AU - Ishizawa, Toshihiro. AU - Ueda, Takuya. AU - Takeuchi, Nono. PY - 2008/5/1. Y1 - 2008/5/1. N2 - While all essential mammalian mitochondrial factors involved in the initiation and elongation phases of translation have been cloned and well characterized, little is known about the factors involved in the termination process. In the present work, we report the functional analysis of human mitochondrial translation release factors (RF). Here, we show that HMRF1, which had been previously denoted as a human mitochondrial RF, was inactive in in vitro translation system, although it is a mitochondrial protein. Instead, we identified another human mitochondrial RF candidate, HMRF1L, and demonstrated that HMRF1L is indeed a mitochondrial protein that functions specifically as an RF for the decoding of mitochondrial UAA ...
Database of translational recoding events. RECODE is a database of the utilisation of ribosomal rameshifting, translational bypassing and mRNA specific codon redefinition for gene expression.
30S ribosomal subunit, tRNAs, mRNA and release factor RF2 from a crystal structure of the whole ribosomal complex. This file contains the 30S ribosomal subunit, tRNAs, mRNA and release factor RF2 from a crystal structure of the whole ribosomal complex. The entire crystal structure contains one 70S ribosome, tRNAs, mRNA and release factor RF2 and is described in remark 400 ...
N ew versions of the pADL phagemid vectors pADL-20b, pADL-22b, and pADL-23b are now available. The sequence of the Amp(R) gene sequence has been modified, allowing the cloning site to be opened by either SfiI or BglI restriction enzyme. This modification results in lower background during cloning and brings more flexibility for designing libraries. The pADL vector series is a collection of phagemid vectors for controlled display on the minor coat protein III which combines HIS tag for purification, epitope tag for detection and amber stop codon for conditional display. Expression of the fusion protein is tightly controlled, eliminating issues with toxic clones and library misrepresentation.. ...
This system also uses Bak as apoptosis inducing selection marker together with the Tet-on promoter, which is to be stably integrated in the cell-line genome. However, this construct also includes an upstream bacterial attachment site (attB) and a downstream SV40 polyadenylation site (SV40PA). The target gene eGFP is combined with phage attachment site (attP) and another SV40PA but without promoter. The target plasmid is co-transfected with integrase PhiC31o into the cell line. Therefore the target gene can only be expressed if integrated into the cells genome, and the stop-codon and SV40PA following the target gene stop the expression of bak, ensuring the survival of the cell while other cells not expressing the target gene undergo induced apoptosis. For more details of the functional principle, please click: Jump-or-Die Functional Principle ...
Für verschiedene Zwecke sind die verschiedenen Markierungen unterschiedlich gut geeignet. Sie werden im Zuge des Proteindesigns bei der Erzeugung rekombinanter Proteine, bzw. deren Reinigung und Nachweis über die Affinitätschromatografie, über Pulldown-Assays, per Western Blot, per Immunhistochemie, per Fluoreszenzmikroskopie oder im Live-Imaging eingesetzt. Zur Erzeugung eines Protein-Tags wird die codierende DNA-Sequenz des Protein-Tags unter Erhalt des Leserasters in die codierende DNA-Sequenz des Fusionsproteins hinter das Start-Codon oder vor das Stop-Codon eingefügt. Dadurch entsteht ein N-terminales bzw. ein C-terminales Protein-Tag am Protein während der Translation. Gelegentlich muss das Protein-Tag vom Protein nach der Reinigung entfernt werden, was z. B. durch eine Protease-Schnittstelle oder ein induzierbares Intein erreicht werden kann. Der Proteolyse-basierte Ansatz verwendet Proteasen mit längerer Erkennungssequenz, die möglichst nur an der Schnittstelle des Protein-Tags ...
Non-stop decay is a cellular mechanism of mRNA surveillance to detect mRNA molecules lacking a stop codon and prevent these mRNAs from translation. The non-stop decay pathway releases ribosomes that have reached the far 3 end of an mRNA and guides the mRNA to the exosome complex, or to RNase R in bacteria for selective degradation. In contrast to NMD, polypeptides do not release from the ribosome, and thus, NSD seems to involve mRNA decay factors distinct from NMD. Non-stop decay is a cellular pathway that identifies and degrades aberrant mRNA transcripts that do not contain a proper stop codons. Stop codons are signals in messenger RNA that signal for synthesis of proteins to end. Aberrant transcripts are identified during translation when the ribosome translates into the poly A tail at the 3 end of mRNA. A non-stop transcript can occur when point mutations damage the normal stop codon. Moreover, some transcriptions are more likely to preserve low scale of gene expression in a particular ...
Freistroffer, D.V., Pavlov, M.Y., MacDougall, J., Buckingham, R.H. and Ehrenberg, M. (1997). „Release factor RF3 in E. coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner. EMBO J. 16: 4126-4133. PMID 9233821 ...
Second, if the mistake is done, and wrong amino acid was incorporated after all, bacterial class-1 release factors RF1 and RF2 become prone to peptide-release independent of the stop codon, thus removing the product (the growing protein chain). In mitochondria translational system is bacterial-like, but much more insane, and several (as many as 4 in humans!) class-1 release factors are present, with some of them lacking the ability to recognize the stop codon at all (ICT1, for example), and these resolve stalled ribosomal complexes by cutting off the peptide as well as their bacterial counterparts ...
RED20 is a so-called fail-safe genetic code introduced by Calles and colleagues in 2019 [1]. RED20 encodes each of the 20 canonical amino acids with exactly one sense codon and terminates translation with the canonical three stop codons. RED20 therefore leaves 41 of the 64 triplet codons unassociated with any transla
See also: stop codon The codons UAA, UAG and UGA, which signal the end of a polypeptide chain. From the BioTech Dictionary at http://biotech.icmb.utexas...
In Huntingtons Disease (HD), aberrant splicing of the huntingtin protein can produce a highly toxic peptide that accumulates in the brain. The invention describes methods to minimize the toxicity of spliced proteins.
Hi guys, I have a list of protein coding DNA sequences to calculate dN/dS but some of these have mutations which introduce a premature stop codon. So, how to calculate the ratio, just use the sequence before the stop codon or just delete the stop codon? And, is this mutation a mark of strong positive selection ...
IS1A, IS1E, IS1H and IS1I are iso-allelic, indicating that the two recent MG1655(Seq)-specific IS1 insertions originated from either IS1A or IS1E. IS1B, IS1C and IS1D are iso-allelic and have nine DNA substitutions relative to the IS1AEHI alleles, causing L81F polymorphism in InsA2-4 as well as T17P, S18P, L19F, S65R, and H128Y polymorphism in InsB2-4. IS1F has accumulated 77 DNA substitutions relative to the IS1AEHI alleles; the insB6 codon for W98 is replaced by an in-frame stop codon and InsB6 has 16 amino acid differences relative to InsB1,5,8,9 ...
Cold Spring Harbor, NY (PRWEB) September 05, 2012 -- Most people understand genes to be specific segments of DNA that determine traits or diseases that are
The extra Val codon is attached to the 3-end of the ORF, because a Pme I site (GTTTAAAC) is tagged at the 3 end of the ORF instead of the stop codon. The resultant sequence encodes Val-stop in place of stop. By cutting the sequence using Pme I, the stop codon arising in the Pme I site can be omitted. ...
Abstract Researchers have noted that there are portions of the DNA that look similar to functional genes, but contain lesions or premature stop codons. These genes have been assumed to be largely non-functional, but recent research suggests that many of these pseudogenes are actually functional. This paper is an overview of some of the research done…
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An article titled To Err Is Human published in 1999 detailed errors by doctors during surgery and triggered many ... Surgical Errors
Intermittent fasting means that at certain times or on certain days, you dont eat. The two most popular IF methods are Leangains and Eat Stop Eat.
1980) The use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proc. Natl. Acad. Sci. USA 76: 3784-85. ...
A new type of polymerase-III-dependent terminator and its evolutionary implication". J. Mol. Biol. 184 (1): 7-21. doi:10.1016/ ... A dinucleotide deletion produces a frameshift and a termination codon". J. Biol. Chem. 263 (9): 4328-32. PMID 2831226. Marotta ...
This terminator structure forms when no ribosome stalls in the vicinity of the Trp tandem (i.e. Trp or Arg codon): either the ... conservation is observed in these 5 codons whereas mutating the upstream codons do not alter the operon expression. If the ... Binding of trp-activated TRAP to leader RNA results in the formation of a terminator structure that causes transcription ... it will stall at either of the two trp codons. While it is stalled, the ribosome physically shields sequence 1 of the ...
The choice of host is important to ensure that the codon usage will be similar to the donor organism. The host will also need ... Additionally, in expression vectors the promoters and terminators must function within the chosen host organism. The host ... in handy if an individual wants to try functional cloning in a wide range of bacteria to try to combat the issue with codon ... choice may affect transcription and translation due to differing codon usage, transcriptional and translational machinery or ...
The attenuator sequence has its codons translated into a leader peptide, but is not part of the trp operon gene sequence. The ... When RNAP reaches the region of the potential terminator, whether it continues or not is dependent on the position of the ... First, Yanofsky observed that the ORF contained two tandem Trp codons and the protein had a Trp percent composition which was ... This forces region 4 when it is made to be single stranded, preventing the formation of the region 3/4 terminator structure. ...
... codon MeSH D13.444.735.544.355.225 - codon, initiator MeSH D13.444.735.544.355.250 - codon, terminator MeSH D13.444.735.544. ... 355.250.235 - codon, nonsense MeSH D13.444.735.544.500 - rna caps MeSH D13.444.735.544.500.710 - rna cap analogs MeSH D13.444. ...
The terminator requires folding of the mRNA, and by unwinding mRNA structures the ribosome elects the formation of either of ... Transcription outpaces translation when the ribosome pauses or encounters a premature stop codon. This allows the transcription ... the transcription terminator sequence is transcribed. Whether transcription is coupled to translation determines whether this ... the operon encoding enzymes involved in the synthesis of histidine contains a series of histidine codons is the control region ...
The Rho-dependent terminator occurs downstream of translational stop codons and consists of an unstructured, cytosine-rich ... Termination codon Termination factor Terminator gene Transcription (genetics) Richardson, J. P. (1996). "Rho-dependent ... Intrinsic transcription terminators or Rho-independent terminators require the formation of a self-annealing hairpin structure ... The terminator sequence in DNA contains a 20 basepair GC-rich region of dyad symmetry followed by a short poly-A tract or "A ...
A transcriptional terminator is located 69 bases downstream from the translational termination codon. The carboxy terminal ...
... bank Cloned DNA Cloning Cloning vector Coccus Code Code dictionary Coding strand Codominance Codon Codon usage bias aka Codon ... Telomerase Telomere Telophase Temperate phage Template strand Teratogen Teratogenic Teratogens Terminal redundancy Terminator ... Ochre codon Okazaki fragment Oligo Oligogenic Oligonucleotide Oncogene Oncogenes Oncovirus Oocyte Oogenesis Oogonia Opal codon ... Non-disjunction Non-histone protein Non-linear tetrad Non-Mendelian ratio Non-parental Non-recombinant Nonsense codon Nonsense ...
The anticodon that recognizes a codon during the translation process is located on one of the unpaired loops in the tRNA. Two ... This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences. ...
First, Yanofsky observed that the ORF contained two tandem Trp codons and the protein had a Trp percent composition which was ... When RNAP reaches the region of the potential terminator, whether it continues or not is dependent on the position of the ... Without domain 4, translation can continue regardless of the level of tryptophan.[6] The attenuator sequence has its codons ... If the ribosome stalls at the tandem Trp codons, waiting for the appropriate tRNA, region 1 is sequestered within the ribosome ...
A patient's DNA is sequenced from a blood sample with the use of the ABI Big Dye Terminator v.3.0 kit. Since this is a genetic ... This primary mutation can also be paired with a missense at codon 237, where an arginine takes the place of a glycine. When the ... and the most common missense mutation occurs at codon 24, where a glycine takes the place of an arginine. ...
"Alteration of the ATG start codon of the A protein of bacteriophage phi X174 into an ATT codon yields a viable phage indicating ... terminators and one Rho-dependent terminator. ΦX174 encodes 11 proteins. Identification of all ΦX174 proteins using mass ... Only genes A* and K are thought to be non-essential, although there is some doubt about A* because its start codon could be ... April 2017). "Measurements of translation initiation from all 64 codons in E. coli". Nucleic Acids Research. 45 (7): 3615-3626 ...
They inhibit the HIV reverse transcriptase enzyme competitively and act as a chain terminator of DNA synthesis. The lack of a 3 ... The HBV reverse transcriptase gene is 344 amino acids long and occupies codons 349 to 692 on the viral genome. The most ...
In BioBrick assembly, an eight-nucleotide scar sequence, which codes for a tyrosine and a stop codon, is left between every ... and a terminator. For the purpose of Golden Gate Cloning, the internal sequences of level 0 modules should not contain type IIS ... and terminators. Then, second-tier Golden Gate assembly combine several constructs made in first-tier assembly to make a ...
Binding of adenine to the pbuE adenine riboswitch disrupts the structure of a terminator stem that had been blocking access to ... The add gene encodes adenosine deaminase, and the adenine riboswitch that is upstream exposes the gene's start codon and the ... Mandal, M; Breaker RR (2004). "Adenine riboswitches and gene activation by disruption of a transcription terminator". Nat ...
... is a protein signal that mediates the termination of RNA transcription by recognizing a stop codon and ... Boudvillain M, Figueroa-Bossi N, Bossi L (April 2013). "Terminator still moving forward: expanding roles for Rho factor". ...
Importantly, pairing is the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA ... some famous examples are the Rho-independent terminator stem-loops and the tRNA cloverleaf. Active research is on-going to ...
The scar site causes a frame shift which prevents the continuous reading of codons, which is required for the formation of ... Examples of BioBrick parts include promoters, ribosomal binding sites (RBS), coding sequences and terminators. The BioBrick ... but enabling the generation of fusion proteins without altering the reading frame or introducing stop codons and while creating ...
... but in the end chose only the three-letter name after learning about the codons of the genetic code, which can be represented ... which Giger considered derivative from the climaxes from both Alien 3 and Terminator 2: Judgment Day. The designer felt that ...
RC terminator. According to the RTM2 model the 3' terminus of another Helitron serves as an RC terminator of transposition. ... between the first and second nucleotide of a codon (phase 1 introns), or between the second and third nucleotide of a codon ( ... This occurs after a malfunction of the RC terminator. Lastly in the FDNA model portions of genes or non-coding regions can ... Introns can interrupt the reading frame of a gene by inserting a sequence between two consecutive codons (phase 0 introns), ...
High-throughput sequencing is intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator ... Philip Leder revealed the triplet nature of the genetic code and were able to determine the sequences of 54 out of 64 codons in ... The Illumina dye sequencing method is based on reversible dye-terminators and was developed in 1996 at the Geneva Biomedical ... To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are ...
Unfortunately, NRTIs/NtRTIs compete as substrates for not only viral but also host DNA synthesis, acting as chain terminators ... "Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved ... The latter serve as poison building blocks (chain terminators) for both viral and host DNA, causing respectively the desired ...
The RC terminator in the new transposon is formed de novo by a terminator-like signal present in the intron following exon 3. ( ... between the first and second nucleotide of a codon (phase 1 introns), or between the second and third nucleotide of a codon ( ... RC terminator. According to the RTM2 model the 3' terminus of another Helitron serves as an RC terminator of transposition. ... This occurs after a malfunction of the RC terminator. Lastly in the FDNA model portions of genes or non-coding regions can ...
This change in structure can result in the formation or disruption of a terminator, truncating or permitting transcription ... "A model of proto-anti-codon RNA enzymes requiring L-amino acid homochirality". Journal of Molecular Evolution. 73 (1-2): 10-22 ... as any nucleotide of the wrong chirality acts as a chain terminator.[50] ...
Amino acids can have multiple codons that correspond to them. Ribosomes do not directly attach amino acids to mRNA codons. They ... This mRNA strand is synthesized in the 5' to 3' direction.[7] Once the RNA reaches a terminator sequence, it dissociates from ... Ribosomes translate the codons to their respective amino acids.[1] In humans, non-essential amino acids are synthesized from ... This continually occurs until the ribosome reaches a stop codon or receives a signal to stop.[10] A peptide bond forms between ...
A series of codons in part of a mRNA molecule. Each codon consists of three nucleotides, usually representing a single amino ... and the RNA polymerase III terminator.[16] ... Each group of three bases, called a codon, corresponds to a ... form also discounts the difference in acceptance rates between silent mutations that do not alter the meaning of a given codon ...
... giving most amino acids more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of ... It then copies the gene sequence into a messenger RNA transcript until it reaches a region of DNA called the terminator, where ... In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ... The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT ...
... causes ribosomes to have a higher rate of read-through of stop codons, an effect that results in suppression of nonsense ... by giving cells the ability to switch into a PSI+ state and express dormant genetic features normally terminated by stop codon ...
The Illumina dye sequencing method is based on reversible dye-terminators and was developed in 1996 at the Geneva Biomedical ... Philip Leder revealed the triplet nature of the genetic code and were able to determine the sequences of 54 out of 64 codons in ... To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are ... High-throughput sequencing is intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator ...
The Rho-dependent terminator occurs downstream of translational stop codons and consists of an unstructured, cytosine-rich ... Termination codon Termination factor Terminator gene Transcription (genetics) Richardson, J. P. (1996). "Rho-dependent ... Intrinsic transcription terminators or Rho-independent terminators require the formation of a self-annealing hairpin structure ... The terminator sequence in DNA contains a 20 basepair GC-rich region of dyad symmetry followed by a short poly-A tract or "A ...
1980) The use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proc. Natl. Acad. Sci. USA 76: 3784-85. ...
... and variants containing internal stop codons or transcription terminators. Inset in C shows location of toxic sequence element ... Asterisk-marked codons represent the original codon in GFP_170. (C) Growth estimate (OD) of BL21 cells expressing GFP variants ... Many organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. To ... As expected, internal stop codons abrogated GFP protein production (Fig. 2C), but despite the presence of premature stop codons ...
Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian ... Four mRNAs display highly efficient stop codon readthrough, and these mRNAs have a UGA stop codon immediately followed by CUAG ... Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon ... Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol ...
Codon, Terminator* * Methylation * RNA Processing, Post-Transcriptional* * RNA, Messenger / metabolism * RNA, Untranslated / ... We find that m(6)A sites are enriched near stop codons and in 3 UTRs, and we uncover an association between m(6)A residues and ... Comprehensive analysis of mRNA methylation reveals enrichment in 3 UTRs and near stop codons Cell. 2012 Jun 22;149(7):1635-46. ...
2A). Whereas no putative terminator was identified downstream of the ORF, a Rho-independent terminator-like sequence was ... stop codon. Dots are placed every 20 bp. (B) Similarities between the IS1675-encoded protein and Tpases encoded by the IS4 ... putative Rho-independent terminator. The IS1675-A terminator is omitted because orf8 is divergent. BamHI, EcoRI, EcoRV,HindIII ... Additional single-strand sequencing showed that this gene contains more than 291 codons (Fig.1A, orf9). The encoded protein ...
0 (Codon, Terminator); 0 (Organic Cation Transport Proteins); 0 (SLC22A5 protein, human); 0 (Solute Carrier Family 22 Member 5 ...
V. The role of release factors in mRNA terminator codon recognition. Proc Natl Acad Sci USA 64(4):1235-1241. ... codon) (5). This radioactive complex bound to nitrocellulose membranes creating a simple and rapid means of codon/amino acid ... cleavage from the tRNA required one of three codons, UAA, UGA, or UAG, thus completing the assignment of 64 codons to either an ... 1966) Codon-anticodon pairing: The wobble hypothesis. J Mol Biol 19(2):548-555. ...
A transcriptional terminator is located 69 bases downstream from the translational termination codon. The carboxy terminal ...
stop_lost, terminator_codon_variant. rs1000196075. --. 30,754,432(+). C/T. intron_variant. rs1000432477. --. 30,757,828(+). G/C ...
stop_lost, terminator_codon_variant. rs104894683. conflicting-interpretations-of-pathogenicity, likely-benign, benign, Limb- ...
chain terminator 1. Codons which do not code for an amino acid. They signal ribosomes to terminate protein synthesis. The ... See anticodon; initiation codon; termination codon.. codon optimization An experimental strategy in which codons within a ... Also known as stop codons or termination codons. Often two of these codons are found together at the end of a coding sequence ... codon A set of three nucleotides in mRNA, functioning as a unit of genetic coding by specifying a particular amino acid during ...
double STOP codon * transcription terminator Adhesion of Streptococcus mutans to hydroxyapatite (HA) Reference PMID 9062560. ...
"Is a terminator\n" if $myCodonTable-,is_ter_codon(tar); print "Is a unknown\n" if $myCodonTable-,is_unknown_codon(JTG); ... codon is_ter_codon Title : is_ter_codon Usage : $obj-,is_ter_codon(GAA) Function: returns true (1) for all codons that can be ... codon unambiguous_codons Title : unambiguous_codons Usage : @codons = $self-,unambiguous_codons(ACN) Returns : array of ... Example : $myCodonTable-,is_ter_codon(ATG) Returns : boolean Args : codon is_unknown_codon Title : is_unknown_codon Usage : $ ...
Stop codon is there. The terminator comes immediately thereafter, but unfortunately not in frame. What will happen? The manuals ... My vector is self-made and the promoter and terminator are specific. ... Must the terminator be in frame? - posted in Molecular Cloning: I cloned a gene into a vector. ... for some commercial vectors, such as pET, say that the terminator isnt quite necessary. ...
35S, Cauliflower mosaic virus (CaMV) 35S promoter; nos, nopaline synthase terminator; *, start codon of ORF5A. ... the CP start codon present in sgp2 was eliminated by single-nucleotide mutagenesis that converted ATG to AGG, thus ensuring no ... Duplicated sequences were placed downstream of the ORF5A start codon, disrupting the synthesis of an N-terminal CP extension. C ... end by the Agrobacterium tumefaciens nos terminator sequence. ... I restriction enzymes immediately downstream of the stop codon ...
... but note that the promoter is not the same thing as the start codon; nor is the RNA polymerase terminator the stop codon. There ... are needed than the 64 possible codons: 64 codons. 20 amino acids. 30 is the compromise made. ... The A and P sites are so close on the ribosome that tRNAs must fit contiguous codons. tRNAs are brought in by EF-Tu (bacteria) ... Stop codons are bound by cytoplasmic release factors, which add water to tRNApeptidyl, cleaving off the polypeptide. ...
An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. Its occurance is ... A nonsense mutation is one that converts an amino acid-specific codon to a stop codon. ... "Codon, Nonsense" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... This graph shows the total number of publications written about "Codon, Nonsense" by people in Harvard Catalyst Profiles by ...
These precedents, and the fact that the fourpatS missense mutations happened to be in the last five codons (Fig. 2B), led us to ... transcription terminator; P with arrow, external promoter. (B) Nucleotide sequence of the smallest tested DNA fragment that is ... patS potentially encodes a 17-amino acid peptide, starting at the first available ATG codon; however, other in-frame ATG and ... GTG codons are present. PatS has no homologs or sequence motifs in the databases. It contains a stretch of five hydrophobic ...
By default all initiation codons found in the given codon table are used but when start is set to some codon this codon will ... Returns : A Bio::PrimarySeqI implementing object Args : -terminator character for terminator, default * -unknown character ... default false -complete_codons boolean, if true, codons which are incomplete are translated if a suitable amino acid is found. ... For instance, if the incomplete codon is GG, the completed codon is GGN, which is glycine (G). Defaults to false; setting ...
Also called a terminator codon. [from latin anxietas anxiety, from angere to press + -ion indicating an organic group + ...
Also called a terminator codon. Nerve injury is affected. A post shared by Mitch Herbert (@mherbert82) on Aug 13, 2020 at 5: ...
NOSt terminator. Plant specific terminator. Terminates transcription but no stop codon on end.. chloramphenicol. -. link. ... NOSt terminator + stop. Plant specific terminator. Terminates transcription with stop codon on 5 end.. chloramphenicol. -. ...
4. NdeI site : CATATG : this ATG is the initiation codon! • Met- • By placing the Aphos gene right after the NdeI gives a good ... 5. T7 terminator : • T7 polymerase binds to T7 promoter, transcribe mRNA that includes the RBS, and from NdeI to XhoI (which ... Component of mRNA near the 5 end, upstream of the initiation codon, where it is bound by the ribosome for translation. ... proximity to the RBS such that the gene is transcribed right after the ATG codon. • Perfect proximity from the promoter and RBS ...
5. Two strong transcriptional terminators. t0 from phage lambda, and T1 from the rrnB operon of E. coli, to prevent read- ... 4. Translational stop codons In all reading frames for convenient preparation of expression constructs. ...
Using the longer ERECTA terminator (1.9 kb) instead of the 35S terminator (∼200 bp) served the purpose of introducing spacer ... pEPFL2:EPFL2 was generated by amplifying a 4.2-kb fragment including 2.5 kb upstream of the EPFL2 start codon and 1 kb ... All promoter/ERECTA/terminator sequences were cloned into pPZP222 between BamHI and XbaI restriction sites. All created ... The endogenous terminator does not have any regulatory sequences as all regulatory elements are localized in the ERECTA ...
The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon ... and is based on the ability of IF3 to discriminate against translation initiation at the atypical start codon of the reporter ... transcriptional terminators, a promoter, a ribosome binding 5 site, and the coding sequences with the first codon being an ... 15 the first codon of the reporter gene is an atypical start codon. To make a test strain, the native ATG start codon of a ...
The LSL sequence contains loxP-stop codons-3x SV40 polyA-loxP as transcriptional terminator. The vector map is shown in Figure ...
Examples of transcription terminator/polyadenylation signals include those derived from SV40, as described in Sambrook et al., ... The nucleotide sequence can be designed with the appropriate codons for the particular amino acid sequence desired. The ... to result in the codon for the desired amino acid. Such a change can include as little as one base pair, effecting a change in ... The boundaries of the coding sequence can be determined by a start codon at the 5′ (amino) terminus and a translation stop ...
Examples of transcription terminator/polyadenylation signals include those derived from SV40, as described in Sambrook et al. ( ... the use of pVL985 which alters the polyhedrin start codon from ATG to ATT, and which introduces a BamHI cloning site 32 ... 0120] Other control elements which may be included in the yeast expression vectors are terminators, for example, from GAPDH and ... to the translation stop codon. Preferably, a sequence for optimization of initiation of translation, located 5′ to the ...
  • As a result, synonymous mutations are under subtle but nonnegligible selective pressure, which manifests itself in the unequal usage of synonymous codons across genes and genomes ( 9 ⇓ - 11 ). (pnas.org)
  • Previously, our analysis of conserved protein coding signatures that extend beyond annotated stop codons predicted stop codon readthrough of several mammalian genes, all of which have been validated experimentally. (nih.gov)
  • Extending on the identification of this readthrough motif, we here investigated stop codon readthrough, using tissue culture reporter assays, for all previously untested human genes containing UGA_CUAG. (nih.gov)
  • The stop codons of the adjacent genes Ca PMU5 and Ca CCR4 are boxed in the promoter and terminator region, respectively. (nih.gov)
  • I would like to look at this genes promoter/terminator sequence and need a way to do this. (protocol-online.org)
  • Genetic transformation into the Chlamydomonas nucleus has been used in many studies, and methods and reagents including promoters, terminators, enhancers, reporter genes, and auxotrophic and drug-resistance markers are available (for review, see Jinkerson and Jonikas 2015 ). (g3journal.org)
  • PJS43 had a Tn5 inserted 198 bp from the entB termination codon, and pJS100 had the last 25 codons of entB deleted. (elsevier.com)
  • In genetics, a transcription terminator is a section of nucleic acid sequence that marks the end of a gene or operon in genomic DNA during transcription. (wikipedia.org)
  • The Rho-dependent terminator occurs downstream of translational stop codons and consists of an unstructured, cytosine-rich sequence on the mRNA known as a Rho utilization site (rut) for which a consensus sequence has not been identified, and a downstream transcription stop point (tsp). (wikipedia.org)
  • The terminator sequence in DNA contains a 20 basepair GC-rich region of dyad symmetry followed by a short poly-A tract or "A stretch" which is transcribed to form the terminating hairpin and a 7-9 nucleotide "U tract" respectively. (wikipedia.org)
  • The nucleotide sequence in mRNA is recognized in triplets, called codons. (news-medical.net)
  • The ribosome moves along the single strand mRNA, and when a complimentary codon sequence belonging to amino acid bearing tRNA bonds with the mRNA, the amino acid is added to the chain. (news-medical.net)
  • The mRNA possesses a stop codon, a sequence of three nucleotides that indicates that translation is complete. (news-medical.net)
  • The DNA sequence of this gene was modified by optimizing the codon usage and reducing CpG motifs to 16 without changing the amino acid sequence of the wild type protein. (invivogen.com)
  • In bacteria, the stop codons in the mRNA sequence are recognized by two release factors: RF1 and RF2. (pubmedcentralcanada.ca)
  • A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). (genomicglossaries.com)
  • 15. The plant of claim 14, wherein the polynucleotide sequence further comprises a stop codon. (patentgenius.com)
  • Normalized per-cell fluore-scence measured from three replicate cultures, grown in LB and resuspended in PBS before measurement, with each of the 64 codons as the start codon in the GFP coding sequence. (asmblog.org)
  • However, in other retroelements, translational readthrough of the gag stop codon can be directed by its flanking sequence, including a 3' pseudoknot. (nih.gov)
  • [1] High levels of uncharged tRNA promote the anti-terminator sequence leading to increased concentrations of charged tRNA. (wikipedia.org)
  • Direct mapping of adeno-associated virus capsid proteins B and C: a possible ACG initiation codon. (semanticscholar.org)
  • Component of mRNA near the 5' end, upstream of the initiation codon, where it is bound by the ribosome for translation. (coursehero.com)
  • this ATG is the initiation codon! (coursehero.com)
  • The identification of the triplet codons was made by a second in vitro assay (P. Leder and S. Peska), which measured the binding of radioactive aminoacyl transfer RNA (tRNA) to ribosomes by a triplet (not doublet) synthetic RNA molecule (codon) ( 5 ). (pnas.org)
  • Hungry codons promote frameshifting in human mitochondrial ribosomes. (mitomap.org)
  • Our results show that RF1 associates with similar association rate constants to ribosomes programmed with a stop or sense codons. (pubmedcentralcanada.ca)
  • Interestingly, the affinity of RF1 for ribosomes programmed with different sense codons does not correlate with the defects in peptide release. (pubmedcentralcanada.ca)
  • Earlier studies from several laboratories had established that the ability of ribosomes to reinitiate translation at an internal AUG codon depends on having a terminator codon in frame with the preceding AUG triplet and upstream from the intended restart site. (asm.org)
  • But how can ribosomes distinguish between AUG codons that signal addition of methionine (M, or Met) to a nascent peptide chain and those that are 'meant' to be start codons? (asmblog.org)
  • Although stop codon readthrough is used extensively by viruses to expand their gene expression, verified instances of mammalian readthrough have only recently been uncovered by systems biology and comparative genomics approaches. (nih.gov)
  • Four mRNAs display highly efficient stop codon readthrough, and these mRNAs have a UGA stop codon immediately followed by CUAG (UGA_CUAG) that is conserved throughout vertebrates. (nih.gov)
  • We find that m(6)A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m(6)A residues and microRNA-binding sites within 3' UTRs. (nih.gov)
  • An amino acid-specifying codon that has been converted to a stop codon (CODON, TERMINATOR) by mutation. (harvard.edu)
  • A nonsense mutation is one that converts an amino acid-specific codon to a stop codon. (harvard.edu)
  • Stop codon is there. (protocol-online.org)
  • Furthermore, after stop codon, no 'frame' longer exists actually. (protocol-online.org)
  • Terminates transcription but no stop codon on end. (igem.org)
  • Terminates transcription with stop codon on 5' end. (igem.org)
  • Upon reaching the stop codon, the ribosome ceases translation and releases the mRNA and newly generated polypeptide. (news-medical.net)
  • mRNA must interact with ribosomal RNA (rRNA), the central component of ribosomal machinery that recognizes the start and stop codons of mRNA, and tRNA, which provides the amino acid once bound with a complimentary mRNA codon. (news-medical.net)
  • As the ribosome moves along the mRNA, it encounters one of the three stop codons for which there is no corresponding tRNA. (news-medical.net)
  • Terminator proteins present at the stop codon bind to the ribosome and trigger the release of the newly synthesized polypeptide chain. (news-medical.net)
  • However, in 2010 Temperley showed that human mitochondria use only UAA and UAG stop codons. (mitomap.org)
  • Ribosome rescue and translation termination at non-standard stop codons by ICT1 in mammalian mitochondria. (mitomap.org)
  • Recognition of stop codons by class I release factors is a fundamental step in the termination phase of protein synthesis. (pubmedcentralcanada.ca)
  • Since premature termination is costly to the cell, release factors have to efficiently discriminate between stop and sense codons. (pubmedcentralcanada.ca)
  • In order to understand the mechanism of discrimination between stop and sense codons, we developed a new, pre-steady state kinetic assay to monitor the interaction of RF1 with the ribosome. (pubmedcentralcanada.ca)
  • However, dissociation of RF1 from sense codons is as much as three orders of magnitude faster than from stop codons. (pubmedcentralcanada.ca)
  • Termination of protein synthesis is triggered when the nearly universal stop codons UAA, UAG, or UGA enter the decoding center of the small ribosomal subunit ( 1 ). (pubmedcentralcanada.ca)
  • Recognition of a stop codon by class I release factors (RF) leads to peptidyl-tRNA hydrolysis and the release of the newly synthesized protein from the ribosome ( 2 ). (pubmedcentralcanada.ca)
  • In eukaryotes, a single release factor (eRF1) recognizes all three stop codons ( 4 ). (pubmedcentralcanada.ca)
  • Stop codons are recognized by RFs with remarkably high accuracy (error frequency of 1 × 10 -3 to 1 × 10 -6 ), even without a proofreading mechanism, indicating that the RFs have a sophisticated mechanism for distinguishing the three stop codons from the sixty-one sense codons ( 5 ) ( 6 ). (pubmedcentralcanada.ca)
  • Genetic and biochemical studies identified a 'tripeptide anticodon' motif in domain 2 of RF1 and RF2 [P(A/V)T in RF1 and SPF in RF2] that is important for stop codon recognition ( 9 ). (pubmedcentralcanada.ca)
  • Recent x-ray crystal structures of RF1 or RF2 bound to the ribosome have revealed in exquisite detail the structural basis for stop codon recognition ( 19 ) ( 20 , 21 ). (pubmedcentralcanada.ca)
  • The 'anticodon tripeptide' motif in RF1 and RF2 interact precisely with the stop codons in the decoding center ( Figure 1 ). (pubmedcentralcanada.ca)
  • Interestingly, the structures showed that other residues in RF1 and RF2, in addition to the tripeptide motif, are also important for stop codon recognition. (pubmedcentralcanada.ca)
  • The first position of the stop codon (U1) interacts with a conserved glycine in domain 2 of RF1 or RF2. (pubmedcentralcanada.ca)
  • A ) Intron-exon structure and location of translational start (AUG) and in-frame stop (*) codons. (sciencemag.org)
  • It dives deeper into 'translational initiation' and is, therefore, arranged like a messenger RNA (mRNA) with proper ribosome-binding site (RBS), AUG start codon, open reading frame (orf), and amber (UAG) stop codon. (asmblog.org)
  • Maybe you were even told the fun story that the first identified 'non-sense' or 'translational termination' or simply stop codon (UAG) was called amber stop for Harris Bernstein (German for amber), a grad student who helped with the experiments that led to its detection. (asmblog.org)
  • With a wink, the other two stop codons were called ochre (UAA) and opal (UGA). (asmblog.org)
  • This mechanism depends on several core factors in the exon junction complex (EJC), eIF4A3, RBM8a, Magoh, and BTZ, as well as peripheral factors to distinguish premature stop codons (PTCs) from normal stop codons in transcripts. (elsevier.com)
  • In the C. albicans retrotransposon Tca2, the gag and pol ORFs are separated by a UGA stop codon, 3' of which is a potential RNA pseudoknot. (nih.gov)
  • The hypothesis was tested that in Tca2, gag stop codon flanking sequences direct translational readthrough and synthesis of a gag-pol fusion protein. (nih.gov)
  • Although downstream of UGA, luc was expressed, but its expression was unaffected by inserting additional stop codons at the 3' end of lacZ. (nih.gov)
  • This is the first demonstration that the LTR promoter directs Tca2 pol protein expression, and that pol proteins are translated from a gag-pol RNA, which thus requires a mechanism for stop codon bypass. (nih.gov)
  • Constructs tested all contain 5xEK repeats upstream of the gag stop codon (see Figure 1). (nih.gov)
  • The sanL is located on the upstream of sanK, it has 1281 nucleotides with ATG at 345 position as start codon and TGA at 623 position as stop codon. (elsevier.com)
  • A translational stop codon situated downstream from the site(s) used for cloning and preceding and in frame with the ATG start codon of the neo gene ensures the detection of transcriptional, rather than translational, fusions. (springer.com)
  • When the upstream "minicistron" terminated 79 nucleotides before the preproinsulin start site, the synthesis of proinsulin was as efficient as if there were no upstream AUG codons. (asm.org)
  • These results suggest that sense codons inhibit conformational changes necessary for RF1 to stably bind to the ribosome and catalyze peptide release. (pubmedcentralcanada.ca)
  • These widely distributed sequences are responsible for triggering the end of transcription upon normal completion of gene or operon transcription, mediating early termination of transcripts as a means of regulation such as that observed in transcriptional attenuation, and to ensure the termination of runaway transcriptional complexes that manage to escape earlier terminators by chance, which prevents unnecessary energy expenditure for the cell. (wikipedia.org)
  • By placing the Aphos gene right after the NdeI gives a good proximity to the RBS such that the gene is transcribed right after the ATG codon. (coursehero.com)
  • The assay uses a reporter gene system in whole cells, and is based on the ability of IF3 to discriminate against translation initiation at the atypical start codon of the reporter gene. (google.es)
  • The figure is a schematic diagram of the pAUU-CAT reporter gene construct in which the CAT gene has its ATG initiator codon replaced with ATT. (google.es)
  • The E. coli rnpb terminator allows efficient transcription termination of the Puro-lowCpG gene. (invivogen.com)
  • Eleven out of 17 Drosophila splice sites map within two codons of splice sites in the human NF1 gene ( 29 ). (sciencemag.org)
  • Each tRNA is read as a ribonucleotide triplet called an anticodon that is complementary to an mRNA codon. (news-medical.net)
  • tRNA carry a particular amino acid, which is added to the growing polypeptide chain if complimentary codons bond. (news-medical.net)
  • The initiator tRNA which is equipped with the anticodon (UAC) also binds to the start codon (AUG) of the mRNA. (news-medical.net)
  • Following initiation, a new tRNA-amino acid complex enters the codon next to the AUG codon. (news-medical.net)
  • If the anticodon of the new tRNA matches the mRNA codon, base pairing occurs and the two amino acids are linked by the ribosome through a peptide bond. (news-medical.net)
  • If the anticodon does not match the codon, base pairing cannot happen and the tRNA is rejected. (news-medical.net)
  • Then, the ribosome moves one codon forward making space for a new tRNA-amino acid complex to enter. (news-medical.net)
  • Termination complex containing fMet-Phe-Thr-Ile-tRNA Ile bound in the P site with a UAA codon in the A site was prepared as described by Freistroffer et al. (asmscience.org)
  • The tightly folded, L-shaped tRNA molecules have two ' business ends ', an exposed 3‑letter 'anticodon' that matches the 3-letter codon for an amino acid on one end, and the respective amino acid cova-lent-ly linked to the other end. (asmblog.org)
  • Specifically, they expose a mRNA codon in their 'A site' for binding to the cognate tRNA while the growing polypeptide chain remains covalently attached to the tRNA that had been previously bound to the A-site and now, after one move-ment of the gear, sits 'next door' in their 'P site' (see here for a schematic diagram of the trans-lation cycle). (asmblog.org)
  • if the ribosome pauses due to insufficient charged tRNA then the anti-terminator structure is favoured. (wikipedia.org)
  • An efficient transcriptional terminator from E. coli phage fd has been inserted upstream of the neo coding region to prevent significant transcriptional read-through from vector promoters. (springer.com)
  • Rho-dependent transcription terminators require a large protein called a Rho factor which exhibits RNA helicase activity to disrupt the mRNA-DNA-RNA polymerase transcriptional complex. (wikipedia.org)
  • In eukaryotic transcription of mRNAs, terminator signals are recognized by protein factors that are associated with the RNA polymerase II and which trigger the termination process. (wikipedia.org)
  • Exon 18b includes a translational terminator after a single codon, and cDNAs harboring this exon predict a protein ending in PTDKAA. (sciencemag.org)
  • Frontpage: Image of an agar plate streaked with 16 diffe-rent strains of E.coli , each containing a green fluorescent protein with a different start codon (annotated along the edge of the plate). (asmblog.org)
  • Protein-RNA interactions may prevent or stabilize the formation of an anti-terminator structure. (wikipedia.org)
  • histidine-rich protein 2 terminator. (nih.gov)
  • In the present studies, the position of the upstream terminator codon relative to the preproinsulin restart site has been systematically varied. (asm.org)
  • The only differences are in available initiator codons. (ubuntu.com)
  • esponds to a transcription terminator. (psu.edu)
  • This structure has a DG value of 224.4 kcal mol21 =-=(30)-=- and probably corresponds to a transcription terminator. (psu.edu)
  • Initiation codons in mammalian mitochondria: differences in genetic code in the organelle. (mitomap.org)
  • Maybe you had to struggle, a little, to come to terms with degeneracy of the genetic code, meaning that it is redundant yet not ambi-guous: there are four codons for proline (P or Pro) but none of them codes for another amino acid. (asmblog.org)
  • When you add to this the fact that the genetic code lacks a 'word divider' (a comma or a space) for the codon triplets, it is immediately obvious that ribo-so-mes better start translating mRNA in the 'correct' reading frame, because the two other possible reading frames can easily result in peptide gibberish. (asmblog.org)
  • Of course, this had to be done quickly because a second competition was now fueled with Professor Gobind Khorana, an extraordinary chemist at the University of Wisconsin, who was ready with the material and intellectual resources to test each of the possible 64 triplet codons for their activity. (pnas.org)
  • Our data indicated that the difference in expression was not due to rare codons, stretches of certain bases or a putative downstream box. (diva-portal.org)
  • Potential start codons are underlined. (sciencemag.org)
  • Transcription start sites are marked by an upward arrow, a polyadenylation site in the terminator is marked by a downward arrow. (nih.gov)
  • This case highlights multiple abnormalities to the ossicular chain in a patient with a start codon variant in NOG . (hindawi.com)
  • PacI sites were introduced 15 bp after the NdeI site encompassing the start codon of lacZI, and 5' of the SV40 PA terminator. (addgene.org)
  • Numbers refer to the nucleotide positions relative to the ATG start codon. (nih.gov)
  • Codon tables are also called translation tables or genetic codes since that is what they represent. (ubuntu.com)
  • Instead, in vitro transcription/translation experiments suggest a role of the first 20 codons of the native prfA -mRNA for maximal expression. (diva-portal.org)
  • Translation initiation from all 64 codons. (asmblog.org)
  • Recognizes the appropriate codons on the mRNA and bonds to them with H-bonds. (powershow.com)
  • 1980) The use of the UGA terminator as a tryptophan codon in yeast mitochondria. (wikipedia.org)
  • Have anticodons that are complementary to mRNA codons. (powershow.com)
  • Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. (genomicglossaries.com)
  • Codon, Nonsense" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)
  • Different pattern of codon recognition by mammalian mitochondrial tRNAs. (mitomap.org)
  • Downward pointing arrows indicate amino acids encoded by the last complete codon in each exon. (sciencemag.org)
  • In either case you were certainly shown the famous codon table that specifies which of the 64 possible triplets in messenger RNA (mRNA) are transla-ted into one of the 20 canonical or 'proteinogenic' L-amino acids . (asmblog.org)
  • Intrinsic transcription terminators or Rho-independent terminators require the formation of a self-annealing hairpin structure on the elongating transcript, which results in the disruption of the mRNA-DNA-RNA polymerase ternary complex. (wikipedia.org)
  • This radioactive complex bound to nitrocellulose membranes creating a simple and rapid means of codon/amino acid assignments. (pnas.org)
  • Rho-dependent terminators are found in bacteria and phages. (wikipedia.org)
  • Many organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. (pnas.org)
  • T1 and T2, putative Rho-independent terminator. (asm.org)
  • A bit more complete picture of the full complexity of codon usage in various taxonomic groups is presented at the NCBI Genetic Codes Home page. (ubuntu.com)
  • The number of CpG dinucleotides has been reduced to 16 and the codon usage optimized. (invivogen.com)