Codon
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).
Codon, Terminator
Base Sequence
Rho Factor
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Codon, Initiator
Transcription, Genetic
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Operon
Transcription Termination, Genetic
Nucleic Acid Conformation
RNA, Bacterial
Codon, Nonsense
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.
Plasmids
Amino Acid Sequence
Cloning, Molecular
Mutation
DNA-Directed RNA Polymerases
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
Gene Expression Regulation, Bacterial
RNA, Messenger
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Protein Biosynthesis
Promoter Regions, Genetic
Genes, Regulator
Genetic Code
Restriction Mapping
Galactokinase
Peptide Chain Termination, Translational
Sequence Analysis, DNA
Genes
RNA, Transfer
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Templates, Genetic
Bacteriophage lambda
RNA Polymerase I
Sequence Homology, Nucleic Acid
RNA, Ribosomal
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Models, Genetic
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
DNA Primers
Saccharomyces cerevisiae
Transcription Factors
Regulatory Sequences, Nucleic Acid
Ribosomes
RNA Polymerase II
AT Rich Sequence
Bacteriophage T7
Single-Strand Specific DNA and RNA Endonucleases
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
Nucleotides
5' Untranslated Regions
Peptide Elongation Factors
Deoxyribonucleotides
Taq Polymerase
RNA
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Point Mutation
Sequence Alignment
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.
beta-Galactosidase
Anticodon
DNA-Directed DNA Polymerase
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.
Blotting, Northern
Lac Operon
Suppression, Genetic
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).
Genetic Vectors
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.
DNA, Ribosomal
RNA Phages
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.
Poly U
Repetitive Sequences, Nucleic Acid
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).
RNA, Transfer, Leu
Sequence Homology, Amino Acid
Introns
RNA Polymerase III
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
T-Phages
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.
DNA-Binding Proteins
Transformation, Genetic
DNA, Recombinant
Open Reading Frames
Binding Sites
Chromosome Mapping
DnaB Helicases
Ribosomal Proteins
Chromosomes, Bacterial
Evolution, Molecular
RNA-Binding Proteins
Regulatory Sequences, Ribonucleic Acid
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Oligodeoxyribonucleotides
Peptide Chain Initiation, Translational
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.
RNA Processing, Post-Transcriptional
RNA Cleavage
Polyadenylation
The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here.
Oligonucleotide Probes
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.
Gene Expression Regulation
Exons
Conserved Sequence
Genotype
DNA, Intergenic
Genetic Complementation Test
Blotting, Southern
Recombinant Fusion Proteins
Amino Acyl-tRNA Synthetases
Oligonucleotides
Host Factor 1 Protein
Mutagenesis, Site-Directed
Dideoxynucleosides
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.
Alleles
Endoribonucleases
DNA Transposable Elements
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.
Multigene Family
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)
Escherichia coli K12
Saccharomyces cerevisiae Proteins
Tryptophan
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.
Peptide Termination Factors
Genes, ras
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.
beta-Globins
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.
RNA Stability
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Polyribonucleotide Nucleotidyltransferase
Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)
Transformation, Bacterial
Gene Expression
Riboswitch
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.
Mutagenesis
Genetic Engineering
Gene Expression Regulation, Fungal
Bacillus
Phenotype
DNA Polymerase I
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.
RNA Precursors
RNA transcripts of the DNA that are in some unfinished stage of post-transcriptional processing (RNA PROCESSING, POST-TRANSCRIPTIONAL) required for function. RNA precursors may undergo several steps of RNA SPLICING during which the phosphodiester bonds at exon-intron boundaries are cleaved and the introns are excised. Consequently a new bond is formed between the ends of the exons. Resulting mature RNAs can then be used; for example, mature mRNA (RNA, MESSENGER) is used as a template for protein production.
RNA, Fungal
DNA Helicases
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.
Artificial Gene Fusion
Protein Binding
Amino Acid Substitution
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.
HIV Reverse Transcriptase
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.
3' Untranslated Regions
Gene Expression Regulation, Viral
Archaea
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, Molecular
Bacteria
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.
Polymorphism, Genetic
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, Insertional
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.
Endonucleases
Genes, Reporter
Selection, Genetic
Titrimetry
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, Genetically Modified
RNA, Transfer, Amino Acyl
Consensus Sequence
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.
Substrate Specificity
Cell-Free System
A fractionated cell extract that maintains a biological function. A subcellular fraction isolated by ultracentrifugation or other separation techniques must first be isolated so that a process can be studied free from all of the complex side reactions that occur in a cell. The cell-free system is therefore widely used in cell biology. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p166)
HeLa Cells
RNA, Antisense
RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.
Netropsin
Structure-Activity Relationship
Recombination, Genetic
Computational Biology
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.
Cytidine
Pentosyltransferases
RNA-Directed DNA Polymerase
Transcription Initiation Site
Transfection
Exoribonucleases
Poly A
Vision Disparity
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)
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On the neurobiological redefinition of psychiatric symptoms: elimination, reduction, or what? | SpringerLink
how to stop - Symptoms, Treatments and Resources for how to stop
Fossil: Timeline
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Comparative study of translation termination sites and release factors (RF1 and RF2) in procaryotes<...
Gentamicin-induced readthrough of stop codons in Duchenne muscular dystrophy<...
Inhibition of Translation Termination Mediated by an Interaction of Eukaryotic Release Factor 1 with a Nascent Peptidyl-tRNA |...
Serval - Competition between SsrA tagging and translational termination at weak stop codons in Escherichia coli.
British Library EThOS: Post-transcriptional regulation of gene expression by the (PSI) prion of Saccharomyces cerevisiae
HMRF1L is a human mitochondrial translation release factor involved in the decoding of the termination codons UAA and UAG<...
Recode2 :: Database of translational recoding events
Recode2 :: Database of translational recoding events
Translational control in positive strand RNA plant viruses | Laboratory of W. Allen Miller
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E. coli essential genes (20 sense codon recoding)
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Therapeutic strategies for Huntingtons Disease using stop codon suppression - Available technology for licensing from the...
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Release factor
Scolnick E, Tompkins R, Caskey T, Nirenberg M (October 1968). "Release factors differing in specificity for terminator codons ... A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon ... Although these stop codons are triplets just like ordinary codons, they are not decoded by tRNAs. It was discovered by Mario ... Stop codon recognition activates the RF, sending the GGQ motif to the peptidyl transferase center (PTC) next to the 3′ end of ...
Scarlet fever
A transcriptional terminator is located 69 bases downstream from the translational termination codon. The carboxy terminal ...
Gloria M. Coruzzi
1980) The use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proc. Natl. Acad. Sci. USA 76: 3784-85. ...
Gene structure
Only the region between the start and stop codons encodes the final protein product. The flanking untranslated regions (UTRs) ... The 3' UTR contains a terminator sequence, which marks the endpoint for transcription and releases the RNA polymerase. The 5' ...
Trp operon
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 ...
DUF3577 RNA motif
Many DUF3577 RNAs are located 5′ to Rho-independent transcription terminators, which, in turn, are 5′ to the start codon of the ... These transcription terminators could play a role in the regulatory function of the RNA, although transcription terminators are ...
Functional cloning
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 ...
Gene
... terminator and start and stop codons. In addition, most eukaryotic open reading frames contain untranslated introns which are ... experiment). Additionally, a "start codon", and three "stop codons" indicate the beginning and end of the protein coding region ... There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons) and only 20 ... The correspondence between codons and amino acids is nearly universal among all known living organisms. Transcription produces ...
Attenuator (genetics)
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 ...
List of MeSH codes (D13)
... 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. ...
Index of molecular biology articles
... termination codon - terminator - tertiary structure - tet resistance - thymine - tissue-specific expression - tm - trans - ... start codon - stem-loop - sticky end - stop codon - streptavidin - stringency - structural motif - sub-cloning - substitution ... codon - codon usage bias - competent - complementary - conformational epitope - congenital - consensus sequence - conservative ... nonsense codon - nonsense mutation - nontranslated RNA - Northern blot - NT - nuclear run-on - nuclease - nuclease protection ...
HBAP1
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 ...
Attenuator (genetics)
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. ...
Transcription-translation coupling
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 ...
Terminator (genetics)
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 ...
Stop codon
Genetic code Start codon Terminator gene Griffiths AJF, Miller JH, Suzuki DT, Lewontin RC, Gelbart WM (2000). "Chapter 10 ( ... Stop codon suppression or translational readthrough occurs when in translation a stop codon is interpreted as a sense codon, ... In molecular biology (specifically protein biosynthesis), a stop codon (or termination codon) is a codon (nucleotide triplet ... Codons that can form hidden stops are used in genomes more frequently compared to synonymous codons that would otherwise code ...
Protein metabolism
Amino acids can have multiple codons that correspond to them. Ribosomes do not directly attach amino acids to mRNA codons. They ... Once the RNA reaches a terminator sequence, it dissociates from the DNA template strand and terminates the mRNA sequence as ... Transfer RNAs can bind to amino acids and contain an anticodon which can hydrogen bind to an mRNA codon. The process of bind an ... Ribosomes translate the codons to their respective amino acids. In humans, non-essential amino acids are synthesized from ...
Index of genetics articles
... 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 ...
Nucleic acid sequence
Each group of three bases, called a codon, corresponds to a single amino acid, and there is a specific genetic code by which ... the Kozak consensus sequence and the RNA polymerase III terminator. Peng et al. found the existence of long-range correlations ... form also discounts the difference in acceptance rates between silent mutations that do not alter the meaning of a given codon ...
Stem-loop
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. ...
Northern epilepsy syndrome
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. ...
Phi X 174
"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 ...
Lamivudine
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 ...
Internal ribosome entry site
One can put several genes on one plasmid and just need one promotor and terminator. Within the past decades, IRES sequences ... HCV-like IRESs directly bind the 40S ribosomal subunit to position their initiator codons are located in ribosomal P-site ...
Shine-Dalgarno sequence
The degree of base pairing also plays a role in determining the rate of initiation at different AUG initiator codons. In 1973 ... Dalgarno L, Shine J (1973). "Conserved terminal sequence in 18S rRNA may represent terminator anticodons". Nature. 245 (148): ... Once recruited, tRNA may add amino acids in sequence as dictated by the codons, moving downstream from the translational start ... Since this conserved sequence contained the complement of each of the three eukaryotic termination codons (UAA, UAG and UGA) it ...
Golden Gate Cloning
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 ...
Purine riboswitch
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 ...
Termination factor
... 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". ...
Inverted repeat
However, the replacement also creates a point mutation converting the GCA codon to ACA. If the strand switch event is followed ... The stem-loop on the 3' end is a transcriptional terminator because the sequence immediately following it is a string of ...
Nucleic acid secondary structure
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 ...
RNA world
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] ...
Epigenetics
... 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 ...
Nucleic acid sequence
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 ...
Genomics
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 ...
Protein metabolism
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 ...
DNA
... 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 ...
DNA, ang malayang ensiklopedya
Sa trankripsiyon, ang mga codon ng isang gene ay kinokopya sa mensaherong RNA ng RNA polymerase. Ang kopyang RNA na ito ay dini ... terminator) kung saan ito humihinto at bumabaklas mula sa DNA. Gaya ng sa pantaong nakabatay sa DNA na DNA polymerase, ang RNA ... Ang kodigong henetiko ay binubuo ng talong-letrang mga 'salita' na tinatawag na codon na nabubuo mula sa isang sekwensiya ng ... Dahil sa may mga apat na base sa 3-letrang mga kombinasyon, 64 posibleng mga codon(43 mga kombinasyon). Ang mga ito ay ...
Exon shuffling
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), ...
Exon shuffling
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 ...
Synechocystis sp. PCC 6803
Terminators are the DNA signal which halts transcription. No native Synechocystis terminators have been characterized. ... In Escherichia coli, the beta "clamp" first binds loosely and tightens as the RNAP approaches the start codon (AUG). In ...
Reverse-transcriptase inhibitor
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 ...
BioBrick
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 ...
Artificial gene synthesis
To offer alternative scar sequences that for example give a 6bp scar, or scar sequences that do not contain stop codons, other ... ribosome binding sites or terminator sequences). Flanking the insertion site of the tier 1 destination vectors are a pair of ... as the 6bp scar sequence codes for a tyrosine and a stop codon, causing translation to be terminated after the first domain is ... expressed, while the 8bp scar sequence causes a frameshift, preventing continuous readthrough of the codons. ...
Species (film)
... 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 ...
Codon, Terminator | Harvard Catalyst Profiles | Harvard Catalyst
Terminator" by people in Harvard Catalyst Profiles by year, and whether "Codon, Terminator" was a major or minor topic of these ... "Codon, Terminator" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... Below are the most recent publications written about "Codon, Terminator" by people in Profiles. ... Below are MeSH descriptors whose meaning is more general than "Codon, Terminator". ...
Codon usage influences fitness through RNA toxicity | PNAS
... 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 ...
Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol...
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 ...
Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons
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. ...
IS1675, a Novel Lactococcal Insertion Element, Forms a Transposon-Like Structure Including the Lacticin 481 Lantibiotic Operon ...
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 ...
MEDLINE - Resultado p gina 1
Clinical and genetic characterist... preview & related info | Mendeley
The RNA code: Nature's Rosetta Stone | PNAS
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. ...
Scarlet fever - Wikipedia
Glossary
Codon. Three bases in a DNA or RNA sequence that specify an amino acid or a termination signal (stop codon). See the Figure at ... and a terminator. Similar to operons, however, operons containing multiple promoters and/or terminators correspond to multiple ... Stop Codon. One of three codons that signal that translation of an RNA sequence should cease. ... Termination Codon. One of three codons that signal that translation of an RNA sequence should cease. ...
Ubuntu Manpage:
Bio::Tools::CodonTable - Codon table object
"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 : $ ...
INMT Gene - GeneCards | INMT Protein | INMT Antibody
FKRP Gene - GeneCards | FKRP Protein | FKRP Antibody
Glossary of biotechnology and genetic engineering
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 ...
Brainstorming - 2008.igem.org
Purifying and positive selection in the evolution of stop codons | Scientific Reports
Changes in stop codons are significantly associated with increased substitution frequency immediately downstream of the stop. ... The results indicate that the UAA codons are maintained by purifying selection in all domains of life. In contrast, positive ... Although GC content has a major impact on stop codon frequencies, its contribution to the decreased frequency of UAA differs ... We reconstructed the evolution of stop codons in 40 groups of closely related prokaryotic and eukaryotic genomes. ...
Codon, Nonsense | Harvard Catalyst Profiles | Harvard Catalyst
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 ...
Must the terminator be in frame?: post #1
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. ...
Plus it
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 ...
Gene expression - Conservapedia
... 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. ...
Organization and Expression of a Thermus thermophilusArginine Cluster: Presence of Unidentified Open Reading Frames and Absence...
1). The start codon of argJ overlaps the stop codon of argC. This is also the case for ORF7 and ORF8. A putative rho- ... A putative rho-independent terminator is present between ORF4 and ORF5. The deduced C-terminal amino acid sequence of ORF4 is ... Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471-1480 in 16S ribosomal ... However, downstream from the ATG start codon ofargF and many other Thermus genes (with or without an SD box), sequences were ...
Heterocyst Pattern Formation Controlled by a Diffusible Peptide | Science
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 ...
Release factor - Wikipedia
Scolnick E, Tompkins R, Caskey T, Nirenberg M (October 1968). "Release factors differing in specificity for terminator codons ... A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon ... Although these stop codons are triplets just like ordinary codons, they are not decoded by tRNAs. It was discovered by Mario ... Stop codon recognition activates the RF, sending the GGQ motif to the peptidyl transferase center (PTC) next to the 3′ end of ...
Ratiometric population sensing by a pump-probe signaling system in Bacillus subtilis | Nature Communications
Terminator (genetics) - Wikipedia
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 ...
Bio::PrimarySeqI - search.cpan.org
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 ...
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Team:Harvard/parts - 2010.igem.org
530L notes lecture5 - Lecture 5 IX Protein expression A Strains of bacteria 1 Characteristics of cloning strains Ex DH5alpha...
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 ...
TerminationInitiationTRNASequenceGenesRecognize all three stop codonsRibosomesProteinsDifferent stop codonsStop-codon readthroughMutationRibosomeGeneTranscriptionalDownstreamProteinPromoter and terminatorTranscription terminatorTranslationUpstreamRecognizesTripletsInitiatorTranslational startStartGENETICMeSHSpecificityERF3ComplementaryMammalianAmino acids encodedAnticodonPolymeraseORFsPolypeptideRecognitionMitochondriaMechanismBoundGenomesBacteria
Termination16
- Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). (harvard.edu)
- PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. (harvard.edu)
- Premature termination codon readthrough in Drosophila varies in a developmental and tissue-specific manner. (harvard.edu)
- Although GC content has a major impact on stop codon frequencies, its contribution to the decreased frequency of UAA differs between bacteria and archaea, presumably, due to differences in their translation termination mechanisms. (nature.com)
- A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence. (wikipedia.org)
- 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)
- 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)
- PJS43 had a Tn5 inserted 198 bp from the entB termination codon, and pJS100 had the last 25 codons of entB deleted. (elsevier.com)
- The E. coli rnpb terminator allows efficient transcription termination of the Puro-lowCpG gene. (invivogen.com)
- 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)
- 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)
- 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)
- A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). (genomicglossaries.com)
- 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)
Initiation11
- However, downstream from the ATG start codon of argF and many other Thermus genes (with or without an SD box), sequences were found to be complementary to nucleotides 1392 to 1409 of Thermus 16S rRNA, suggesting that an mRNA-rRNA base pairing in this region is important for correct translation initiation. (asm.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 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)
- Following initiation, a new tRNA-amino acid complex enters the codon next to the AUG codon. (news-medical.net)
- Direct mapping of adeno-associated virus capsid proteins B and C: a possible ACG initiation codon. (semanticscholar.org)
- Initiation codons in mammalian mitochondria: differences in genetic code in the organelle. (mitomap.org)
- The transcriptional initiation site of this gene, mapped using RNA ligase-mediated rapid amplification of cDNA end and primer extension, is located ∼300 bp upstream from the translational start codon. (elsevier.com)
- 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)
- Translation initiation from all 64 codons. (asmblog.org)
- That expression was improved by modifying the 17 bp before the initiation codon in pAB366 to match the sequence of the am gene. (addgene.org)
TRNA18
- 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)
- During translation of mRNA, most codons are recognized by "charged" tRNA molecules, called aminoacyl-tRNAs because they are adhered to specific amino acids corresponding to each tRNA's anticodon. (wikipedia.org)
- It was discovered by Mario Capecchi in 1967 that, instead, tRNAs do not ordinarily recognize stop codons at all, and that what he named "release factor" was not a tRNA molecule but a protein. (wikipedia.org)
- Stop codon recognition activates the RF, sending the GGQ motif to the peptidyl transferase center (PTC) next to the 3′ end of the P-site tRNA. (wikipedia.org)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- [1] High levels of uncharged tRNA promote the anti-terminator sequence leading to increased concentrations of charged tRNA. (wikipedia.org)
- if the ribosome pauses due to insufficient charged tRNA then the anti-terminator structure is favoured. (wikipedia.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)
Sequence11
- 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 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)
- I would like to look at this genes promoter/terminator sequence and need a way to do this. (protocol-online.org)
- 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)
Genes7
- 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)
- Modes of evolution of stop codons in protein-coding genes, especially the conservation of UAA, have been debated for many years. (nature.com)
- In particular, we sought to reveal the connections that might exist between the selection on stops codons and the evolution of the proteins encoded by the respective genes, in an attempt to attain an integrated view of gene evolution. (nature.com)
- The stop codons of the adjacent genes Ca PMU5 and Ca CCR4 are boxed in the promoter and terminator region, respectively. (nih.gov)
- 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)
Recognize all three stop codons1
- a/eRF1 can recognize all three stop codons, while eRF3 (archaea use EF-1α instead) works just like RF3. (wikipedia.org)
Ribosomes5
- 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)
Proteins3
- The sixty-four codons of the genetic code allow the use of twenty different amino acids (the primary amino acids) in the synthesis of proteins. (metacyc.org)
- Terminator proteins present at the stop codon bind to the ribosome and trigger the release of the newly synthesized polypeptide chain. (news-medical.net)
- 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)
Different stop codons2
- These apparent differences in the usage of the stop codons seems to imply that selective factors exist that differentially affect the different stop codons. (nature.com)
- Later, it was demonstrated that different release factors recognize different stop codons. (wikipedia.org)
Stop-codon readthrough3
- Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. (harvard.edu)
- 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)
Mutation2
- 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)
Ribosome6
- RF1 (mitochondrial): MTRF1, MTRF1L, MRPL58 (ICT1), C12orf65 eRF1: ETF1 eRF3: GSPT1, GSPT2 Crystal structures have been solved for bacterial 70S ribosome bound to each of the three release factors, revealing details in codon recognition by RF1/2 and the EF-G-like rotation of RF3. (wikipedia.org)
- This is done by splitting the ribosome with factors like IF1-IF3 or RRF-EF-G. eRF1 can be broken down into four domains: N-terminal (N), Middle (M), C-terminal (C), plus a minidomain: The N domain is responsible for stop codon recognition. (wikipedia.org)
- Upon reaching the stop codon, the ribosome ceases translation and releases the mRNA and newly generated polypeptide. (news-medical.net)
- 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)
- These results suggest that sense codons inhibit conformational changes necessary for RF1 to stably bind to the ribosome and catalyze peptide release. (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)
Gene6
- 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 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)
- Eleven out of 17 Drosophila splice sites map within two codons of splice sites in the human NF1 gene ( 29 ). (sciencemag.org)
- Expression of ble (bleomycin resistance) is regulated by the promoter and terminator regions of the am gene (amination, glutamate dehydrogenase) from N. crassa. (addgene.org)
- Objective 2: Identify and demonstrate the utility of crop-derived gene expression control elements (promoters/enhancers/terminators/insulators) that facilitate trait development in crop plants. (usda.gov)
- Novel transcription terminator sequences will also be isolated from crop plants and fused to a reporter gene. (usda.gov)
Transcriptional1
- 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)
Downstream4
- Changes in stop codons are significantly associated with increased substitution frequency immediately downstream of the stop. (nature.com)
- 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)
- The 3′ end of PfPuf2 is located ∼250 bp downstream from the stop codon. (elsevier.com)
- 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)
Protein6
- Nonetheless, a comparison of in vitro and in vivo data revealed that specific regions exhibited significantly different SHAPE-MaP profiles indicative of structural rearrangements, including rearrangement consistent with binding of the zipcode protein in a region distal to the stop codon. (elsevier.com)
- Exon 18b includes a translational terminator after a single codon, and cDNAs harboring this exon predict a protein ending in PTDKAA. (sciencemag.org)
- Protein-RNA interactions may prevent or stabilize the formation of an anti-terminator structure. (wikipedia.org)
- histidine-rich protein 2 terminator. (nih.gov)
- 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)
- 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)
Promoter and terminator2
- My vector is self-made and the promoter and terminator are specific. (protocol-online.org)
- The functionality of these promoter and terminator testing constructs will be examined in transient expression assays and stably transformed transgenic plants. (usda.gov)
Transcription terminator2
Translation3
- That portion of an mRNA from the 3' end to the position of the last codon used in translation . (metacyc.org)
- 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)
Upstream3
- In the present studies, the position of the upstream terminator codon relative to the preproinsulin restart site has been systematically varied. (asm.org)
- 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)
- Constructs tested all contain 5xEK repeats upstream of the gag stop codon (see Figure 1). (nih.gov)
Recognizes3
- Unlike Bacteria, there are only two release factors in Eukaryotes, eRF1, which is homologous to RF1 and RF2 and recognizes all three stop codons, and eRF3, which is required for eRF1 dissociation 13 . (nature.com)
- Recognizes the appropriate codons on the mRNA and bonds to them with H-bonds. (powershow.com)
- In eukaryotes, a single release factor (eRF1) recognizes all three stop codons ( 4 ). (pubmedcentralcanada.ca)
Triplets3
- Although these stop codons are triplets just like ordinary codons, they are not decoded by tRNAs. (wikipedia.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)
- 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)
Initiator1
- The only differences are in available initiator codons. (ubuntu.com)
Translational start1
- A ) Intron-exon structure and location of translational start (AUG) and in-frame stop (*) codons. (sciencemag.org)
Start6
- As a continuation of our previous work on the evolution of start codons 16 , we were interested in systematically assessing the type of selection pressures that affect evolution of stop codons in different life forms, seeking to identify universal and taxon-specific evolutionary factors. (nature.com)
- 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)
- Numbers refer to the nucleotide positions relative to the ATG start codon. (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)
GENETIC3
- 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)
- 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)
- 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)
MeSH2
- Codon, Terminator" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)
- Codon, Nonsense" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (harvard.edu)
Specificity1
- Release factors differing in specificity for terminator codons. (semanticscholar.org)
ERF31
- Stop codon recognition makes eRF3 hydrolyze the GTP, and the resulting movement puts the GGQ into the PTC to allow for hydrolysis. (wikipedia.org)
Complementary2
- 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)
Mammalian1
- Different pattern of codon recognition by mammalian mitochondrial tRNAs. (mitomap.org)
Amino acids encoded1
- Downward pointing arrows indicate amino acids encoded by the last complete codon in each exon. (sciencemag.org)
Anticodon1
- The 'anticodon tripeptide' motif in RF1 and RF2 interact precisely with the stop codons in the decoding center ( Figure 1 ). (pubmedcentralcanada.ca)
Polymerase1
- 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)
ORFs1
- 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)
Polypeptide1
- Strands of mRNA are made up of codons, each of which signifies a particular amino acid to be added to the polypeptide in a certain order. (news-medical.net)
Recognition2
- Only one residue actually participates in stop codon recognition via hydrogen bonding. (wikipedia.org)
- 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)
Mitochondria1
- However, in 2010 Temperley showed that human mitochondria use only UAA and UAG stop codons. (mitomap.org)
Mechanism1
- 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)
Bound1
- This radioactive complex bound to nitrocellulose membranes creating a simple and rapid means of codon/amino acid assignments. (pnas.org)
Genomes3
- We reconstructed the evolution of stop codons in 40 groups of closely related prokaryotic and eukaryotic genomes. (nature.com)
- To these ends, we calculated the frequencies of stop codon switches in sets of closely related genomes including 36 bacterial, one archaeal, and 3 eukaryotic ones, with varying GC content, and identified stop codon swaps that appear to be affected by purifying selection, whereas others are neutral, or possibly, could be subject to positive selection. (nature.com)
- Two classes of transcription terminators, Rho-dependent and Rho-independent, have been identified throughout prokaryotic genomes. (wikipedia.org)
Bacteria1
- Rho-dependent terminators are found in bacteria and phages. (wikipedia.org)