Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.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.DNA-Binding Proteins: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.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.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).Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.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.Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.MicroRNAs: Small double-stranded, non-protein coding RNAs, 21-25 nucleotides in length generated from single-stranded microRNA gene transcripts by the same RIBONUCLEASE III, Dicer, that produces small interfering RNAs (RNA, SMALL INTERFERING). They become part of the RNA-INDUCED SILENCING COMPLEX and repress the translation (TRANSLATION, GENETIC) of target RNA by binding to homologous 3'UTR region as an imperfect match. The small temporal RNAs (stRNAs), let-7 and lin-4, from C. elegans, are the first 2 miRNAs discovered, and are from a class of miRNAs involved in developmental timing.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.RNA, Untranslated: RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.DNA, Single-Stranded: A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Bacterial Proteins: Proteins found in any species of bacterium.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.Gene Expression Regulation, Archaeal: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.Electrophoretic Mobility Shift Assay: An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Signal Transduction: The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.Gram-Negative Bacteria: Bacteria which lose crystal violet stain but are stained pink when treated by Gram's method.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Cloning, Molecular: 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.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Gram-Positive Bacteria: Bacteria which retain the crystal violet stain when treated by Gram's method.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Poly(A)-Binding Proteins: Proteins that bind to the 3' polyadenylated region of MRNA. When complexed with RNA the proteins serve an array of functions such as stabilizing the 3' end of RNA, promoting poly(A) synthesis and stimulating mRNA translation.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.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)Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.RNA Stability: The extent to which an RNA molecule retains its structural integrity and resists degradation by RNASE, and base-catalyzed HYDROLYSIS, under changing in vivo or in vitro conditions.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.DNA Replication: The process by which a DNA molecule is duplicated.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Viral Proteins: Proteins found in any species of virus.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Up-Regulation: A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Bacteria, AnaerobicSequence 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.Zinc Fingers: Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.Cell Line, Tumor: A cell line derived from cultured tumor cells.Hypertrophy: General increase in bulk of a part or organ due to CELL ENLARGEMENT and accumulation of FLUIDS AND SECRETIONS, not due to tumor formation, nor to an increase in the number of cells (HYPERPLASIA).Oligodeoxyribonucleotides: 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.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Kinetics: The rate dynamics in chemical or physical systems.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Genes, Reporter: 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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.3' Untranslated Regions: The sequence at the 3' end of messenger RNA that does not code for product. This region contains transcription and translation regulating sequences.Gene Regulatory Networks: Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Replication Protein A: A single-stranded DNA-binding protein that is found in EUKARYOTIC CELLS. It is required for DNA REPLICATION; DNA REPAIR; and GENETIC RECOMBINATION.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.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.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.5' Untranslated Regions: The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Epigenesis, Genetic: A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Genes, Bacterial: The functional hereditary units of BACTERIA.CCAAT-Enhancer-Binding Proteins: A class of proteins that were originally identified by their ability to bind the DNA sequence CCAAT. The typical CCAAT-enhancer binding protein forms dimers and consists of an activation domain, a DNA-binding basic region, and a leucine-rich dimerization domain (LEUCINE ZIPPERS). CCAAT-BINDING FACTOR is structurally distinct type of CCAAT-enhancer binding protein consisting of a trimer of three different subunits.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Tacrolimus Binding Proteins: A family of immunophilin proteins that bind to the immunosuppressive drugs TACROLIMUS (also known as FK506) and SIROLIMUS. EC 5.2.1.-Poly T: A group of thymine nucleotides in which the phosphate residues of each thymine nucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Bacteria, AerobicMolecular Weight: The sum of the weight of all the atoms in a molecule.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.DNA Footprinting: A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)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.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Fungal Proteins: Proteins found in any species of fungus.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.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.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.NFI Transcription Factors: Transcription factors that were originally identified as site-specific DNA-binding proteins essential for DNA REPLICATION by ADENOVIRUSES. They play important roles in MAMMARY GLAND function and development.Poly(A)-Binding Protein I: A poly(A) binding protein that has a variety of functions such as mRNA stabilization and protection of RNA from nuclease activity. Although poly(A) binding protein I is considered a major cytoplasmic RNA-binding protein it is also found in the CELL NUCLEUS and may be involved in transport of mRNP particles.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.Binding, Competitive: The interaction of two or more substrates or ligands with the same binding site. The displacement of one by the other is used in quantitative and selective affinity measurements.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Leucine Zippers: DNA-binding motifs formed from two alpha-helixes which intertwine for about eight turns into a coiled coil and then bifurcate to form Y shaped structures. Leucines occurring in heptad repeats end up on the same sides of the helixes and are adjacent to each other in the stem of the Y (the "zipper" region). The DNA-binding residues are located in the bifurcated region of the Y.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.Y-Box-Binding Protein 1: Y-box-binding protein 1 was originally identified as a DNA-binding protein that interacts with Y-box PROMOTER REGIONS of MHC CLASS II GENES. It is a highly conserved transcription factor that regulates expression of a wide variety of GENES.Helix-Turn-Helix Motifs: The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)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)Cyclic AMP Response Element-Binding Protein: A protein that has been shown to function as a calcium-regulated transcription factor as well as a substrate for depolarization-activated CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES. This protein functions to integrate both calcium and cAMP signals.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Response Elements: Nucleotide sequences, usually upstream, which are recognized by specific regulatory transcription factors, thereby causing gene response to various regulatory agents. These elements may be found in both promoter and enhancer regions.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Insulin-Like Growth Factor Binding Proteins: A family of soluble proteins that bind insulin-like growth factors and modulate their biological actions at the cellular level. (Int J Gynaecol Obstet 1992;39(1):3-9)Oligonucleotides: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Chromatin Immunoprecipitation: A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.Chromatography, Affinity: A chromatographic technique that utilizes the ability of biological molecules to bind to certain ligands specifically and reversibly. It is used in protein biochemistry. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.Ultraviolet Rays: That portion of the electromagnetic spectrum immediately below the visible range and extending into the x-ray frequencies. The longer wavelengths (near-UV or biotic or vital rays) are necessary for the endogenous synthesis of vitamin D and are also called antirachitic rays; the shorter, ionizing wavelengths (far-UV or abiotic or extravital rays) are viricidal, bactericidal, mutagenic, and carcinogenic and are used as disinfectants.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Deoxyribonuclease I: An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.Mice, Inbred C57BLMembrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Basic-Leucine Zipper Transcription Factors: A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Helix-Loop-Helix Motifs: Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. They are found in many sequence-specific DNA-BINDING PROTEINS and in CALCIUM-BINDING PROTEINS.Fatty Acid-Binding Proteins: Intracellular proteins that reversibly bind hydrophobic ligands including: saturated and unsaturated FATTY ACIDS; EICOSANOIDS; and RETINOIDS. They are considered a highly conserved and ubiquitously expressed family of proteins that may play a role in the metabolism of LIPIDS.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Heterogeneous-Nuclear Ribonucleoproteins: A family of ribonucleoproteins that were originally found as proteins bound to nascent RNA transcripts in the form of ribonucleoprotein particles. Although considered ribonucleoproteins they are primarily classified by their protein component. They are involved in a variety of processes such as packaging of RNA and RNA TRANSPORT within the nucleus. A subset of heterogeneous-nuclear ribonucleoproteins are involved in additional functions such as nucleocytoplasmic transport (ACTIVE TRANSPORT, CELL NUCLEUS) of RNA and mRNA stability in the CYTOPLASM.Transcription Factor AP-1: A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA 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 DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.beta-Galactosidase: 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.Octamer Transcription Factor-1: A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.Genetic Complementation Test: 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.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.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.Bacillus subtilis: A species of gram-positive bacteria that is a common soil and water saprophyte.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Culture Media: Any liquid or solid preparation made specifically for the growth, storage, or transport of microorganisms or other types of cells. The variety of media that exist allow for the culturing of specific microorganisms and cell types, such as differential media, selective media, test media, and defined media. Solid media consist of liquid media that have been solidified with an agent such as AGAR or GELATIN.Recombination, Genetic: 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.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).DNA Primase: A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.Pseudomonas Phages: Viruses whose host is Pseudomonas. A frequently encountered Pseudomonas phage is BACTERIOPHAGE PHI 6.Anti-Bacterial Agents: Substances that reduce the growth or reproduction of BACTERIA.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Adenosine Triphosphatases: A group of enzymes which catalyze the hydrolysis of ATP. The hydrolysis reaction is usually coupled with another function such as transporting Ca(2+) across a membrane. These enzymes may be dependent on Ca(2+), Mg(2+), anions, H+, or DNA.DNA Damage: Injuries to DNA that introduce deviations from its normal, intact structure and which may, if left unrepaired, result in a MUTATION or a block of DNA REPLICATION. These deviations may be caused by physical or chemical agents and occur by natural or unnatural, introduced circumstances. They include the introduction of illegitimate bases during replication or by deamination or other modification of bases; the loss of a base from the DNA backbone leaving an abasic site; single-strand breaks; double strand breaks; and intrastrand (PYRIMIDINE DIMERS) or interstrand crosslinking. Damage can often be repaired (DNA REPAIR). If the damage is extensive, it can induce APOPTOSIS.Operon: 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.Polydeoxyribonucleotides: A group of 13 or more deoxyribonucleotides in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.Chloramphenicol O-Acetyltransferase: An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 2.3.1.28.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.DNA Repair: The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.Host Cell Factor C1: A cellular transcriptional coactivator that was originally identified by its requirement for the stable assembly IMMEDIATE-EARLY PROTEINS of the HERPES SIMPLEX VIRUS. It is a nuclear protein that is a transcriptional coactivator for a number of transcription factors including VP16 PROTEIN; GA-BINDING PROTEIN; EARLY GROWTH RESPONSE PROTEIN 2; and E2F4 TRANSCRIPTION FACTOR. It also interacts with and stabilizes HERPES SIMPLEX VIRUS PROTEIN VMW65 and helps regulate GENETIC TRANSCRIPTION of IMMEDIATE-EARLY GENES in HERPES SIMPLEX VIRUS.
... - a protein that binds to DNA and regulates gene expression by promoting or suppressing transcription ... Mitchell PJ, Tjian R (July 1989). "Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins". ... bind plant promoter sequences, and activate transcription of plant genes that aid in bacterial infection.[33] TAL effectors ... secreted by Xanthomonas bacteria. When injected into plants, these proteins can enter the nucleus of the plant cell, ...
... is also a DNA-binding protein that participates in mtDNA maintenance and gene expression regulation. LONP1 degrades ... Lon protease (LONP1) is a conserved serine peptidase identified from bacteria to eukaryotic cells. In mitochondrial matrix, a ... "A human mitochondrial ATP-dependent protease that is highly homologous to bacterial Lon protease". Proceedings of the National ... coli regulates gene expression by targeting specific regulatory proteins for degradation. Lon protease binds a specific ...
Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation ... B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4. Multiple ligand-binding ... when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria: ... involved in expression of late-expressing competence genes) 2. Regulators which are activated, or in very rare cases repressed ...
... encoded by a regulatory gene, binds to its operator, a specific site on the DNA next to the genes encoding the proteins. (It is ... Study of the control of expression of genes in the lac operon provided the first example of a transcriptional regulation system ... He coined the term diauxie to denote the frequent observations of two distinct growth phases of bacteria grown on two sugars. ... He theorized on the growth of bacterial cultures and promoted the chemostat theory as a powerful continuous culture system to ...
... regulation of gene expression is controlled by interactions between DNA-binding regulatory proteins (transcription factors) and ... It ultimately arose as a variation of the bacteria two-hybrid system, conceived in 2000, which itself was inspired by the yeast ... DNA sequences in or around genes that act as target sites for DNA-binding proteins. By binding to cis-regulatory sequences and ... Transformation of a bacterial host with two different plasmids is required. One is designed to express a DNA-binding protein-of ...
Identification of a regulatory protein required for pressure-responsive gene expression in the deep-sea bacterium ... ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae, where it regulates a considerable number of ... abundance and activity of this protein is influenced by hydrostatic pressure and its role is related to the regulation of genes ... nov., a new, moderately barophilic bacterial species isolated from a deep-sea sediment. Extremophiles, 1998. 2(1): p. 1-7. ...
Many bacterial species can utilize inversion to change the expression of certain genes for the benefit of the bacterium during ... DNA-binding proteins and the presence or absence of DNA binding sites) and a site-specific recombinase. There is a change in ... The outcome is the regulation of transcription resulting in switches in gene expression. An outer membrane protein Antigen 43 ( ... The expression of Agn43 is dependent on the binding of the regulator protein OxyR. When OxyR is bound to the regulatory region ...
LuxQ activates LuxU, which then acts on LuxO, a DNA-binding protein which represses HapR gene expression. HapR is thought to ... All characterized bacterial-targeting T6SS proteins act as toxins, either by killing or preventing the growth of target cells. ... This level of regulation has also been observed in P. fluorescens and P. syringae There are various examples in which quorum ... Although the ancestral function of the T6SS appears to be targeting of bacteria, a handful of systems have been identified that ...
... nonspecific DNA binding protein) and oxyS (a small regulatory RNA). Reduced OxyR provides autorepression by binding only to the ... Oxidized SoxR then induces the expression of SoxS protein, which in turn activates the transcription of structural genes of the ... antioxidant defense system for proteins. The complexity in bacterial responses appears to be in the number of proteins induced ... Regulation of the soxRS regulon occurs by a two-stage process: the SoxR protein is first converted to an oxidized form that ...
... as a critical regulator of capsule expression. Fis is also involved in the regulation of a range of genes in bacterial ... It also regulates its own expression (autoregulation). Fis is one of the most abundant DNA binding proteins in Escherichia coli ... Besides modulating chromatin architecture, it is known to influence numerous promoters of E. coli and several other bacteria. ... fis is the E. coli gene encoding FIS protein. The regulation of this gene is more complex than most other genes in the E. coli ...
... protein contains no signal peptide, no DNA/RNA binding sites, no mitochondrial targeting motifs and no peroxisomal ... RUN and FYVE domain containing 2 (RUFY2) is a protein that in humans is encoded by the RUFY2 gene. The RUFY2 gene is named for ... RUFY2 protein has been shown to mainly be expressed in the brain, lung, and testes while microarray expression shows RUFY2 ... and FYVE domain-containing protein RUFY1. A possible role of ETK in regulation of vesicle trafficking". J. Biol. Chem. 277 (33 ...
Binding of this protein to the consensus sequence represents gene expression by reducing transcription. It is not known what ... "Repressor binding to a regulatory site in the DNA coding sequence is sufficient to confer transcriptional regulation of the vir ... being a normal product of the breakdown of the bacterial cell wall. Other bacteria recycle this molecule back into the ... most notably the flagellin gene flaA. The regulation of Bvg repressed genes is mediated by the product of a 624-bp open reading ...
Gene regulation - some toxins act as a means of general repression of gene expression while others are more specific. Growth ... CcdB protein, for example, affects DNA gyrase by poisoning DNA topoisomerase II whereas MazF protein is a toxic ... "Bacterial Programmed Cell Death and Multicellular Behavior in Bacteria". PLoS Genet. 2 (10): e135. doi:10.1371/journal.pgen. ... The protein toxin in a type II system is inhibited post-translationally by the binding of another protein antitoxin. A single ...
Other transcription factors differentially regulate the expression of various genes by binding to enhancer regions of DNA ... Mitchell PJ, Tjian R (July 1989). "Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins". ... secreted by Xanthomonas bacteria. When injected into plants, these proteins can enter the nucleus of the plant cell, bind plant ... and activate transcription of plant genes that aid in bacterial infection. TAL effectors contain a central repeat region in ...
Many proteins involved in the regulation of gene expression contain DNA-binding domains. For example, proteins that regulate ... "DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats". Nucleic Acids Research. 43 ... which form a DNA-binding pseudobarrel protein fold. TAL effectors are found in bacterial plant pathogens of the genus ... OB-folds bind single-stranded DNA, and hence are single-stranded binding proteins. OB-fold proteins have been identified as ...
Two DesR-P proteins will dimerize and bind to the DNA promoters of the des gene and recruit RNA polymerase to begin ... Regulation This pathway undergoes transcriptional regulation by FadR and FabR. FadR is the more extensively studied protein and ... "Complex binding of the FabR repressor of bacterial unsaturated fatty acid biosynthesis to its cognate promoters." Molecular ... This second pathway is regulated by repressor protein DesT. DesT is also a repressor of fabAB expression for anaerobic ...
... and was an important discovery towards understanding gene expression and regulation. Shine undertook post doctoral research at ... studies he discovered the RNA sequence necessary for ribosome binding and the initiation of protein synthesis in the bacterium ... He also founded the Centre for Recombinant DNA Research at ANU. In 1982 he was awarded that Gottschalk Medal by the Australian ... Shine, J.; Dalgarno, L. (6 March 1975). "Determinant of cistron specificity in bacterial ribosomes". Nature. 254 (5495): 34-38 ...
A major difference between human and mouse SAA genes is the expression of the mouse Saa3 gene for a functional protein, ... "Serum amyloid A protein binds to outer membrane protein A of gram-negative bacteria". The Journal of Biological Chemistry. 280 ... Jensen LE, Whitehead AS (Sep 1998). "Regulation of serum amyloid A protein expression during the acute-phase response". The ... "Serum amyloid A is a retinol binding protein that transports retinol during bacterial infection". eLife. 3: e03206. doi:10.7554 ...
... and a conserved DNA binding protein that acts as a ratchet to reel DNA into the cytoplasm. Vibrio cholerae bacteria Diagram of ... That means that the genes of a virus were integrated into the bacterial genome and made the bacteria pathogenic. The molecular ... The larger first chromosome contains the crucial genes for toxicity, regulation of toxicity, and important cellular functions, ... R. obeum autoinducer represses the expression of several V. cholerae virulence factors. This inhibitory mechanism is likely to ...
These alterations can change gene function or regulation of gene expression and possibly contribute to progression to cancer. ... They bind to DNA damaged sites and activate Chk1, Chk2, and, in animal cells, p53. Together, these proteins make up the DNA ... Genes homologous to RecA and to other central genes in the SOS response pathway are found in almost all the bacterial genomes ... For example, in bacteria, a regulatory network aimed at repairing DNA damages (called the SOS response in Escherichia coli) has ...
Epigenetic regulations such as DNA methylation and histone methylation can repress gene expression by inhibiting initiation of ... hemoglobin alpha1 gene (HBA1) is downregulated by a abnormal transcript of putative RNA-binding protein Luc7-like (LUC71) that ... AsRNAs can be involved in this level of gene regulation. For example, in bacterial or eukaryotic cells where complex RNA ... The initial asRNAs discovered were in prokaryotes including plasmids, bacteriophage and bacteria. For example, in plasmid ColE1 ...
Gene expression. Introduction. to genetics. *Genetic code. *Central dogma *DNA → RNA → Protein ... In bacteria, there is one general RNA transcription factor: sigma. RNA polymerase core enzyme binds to the bacterial general ... Main article: Regulation of transcription in cancer. In vertebrates, the majority of gene promoters contain a CpG island with ... which inhibits Bacterial transcription of DNA into mRNA by inhibiting DNA-dependent RNA polymerase by binding its beta-subunit ...
... the protein preferably binds to double-stranded DNA rather than single-stranded DNA. The ability of lactoferrin to bind DNA is ... Lactoferrin binds to lipopolysaccharide of bacterial walls, and the oxidized iron part of the lactoferrin oxidizes bacteria via ... Reghunathan R, Jayapal M, Hsu LY, Chng HH, Tai D, Leung BP, Melendez AJ (2005). "Expression profile of immune response genes in ... but also in the regulation of their intake. Presence of loose ions of zinc and copper does not affect the iron binding ability ...
Ma, X.Y., et al., The interferon-inducible p202a protein modulates NF-kappaB activity by inhibiting the binding to DNA of p50/ ... 284(5412): p. 271-3. Ghosh, S., Regulation of inducible gene expression by the transcription fact or NF-kappaB. Immunol Res, ... Genes Dev, 2004. 18(18): p. 2195-224. Zhang, D., et al., A toll-like receptor that prevents infection by uropathogenic bacteria ... Gene, 2000. 247(1-2): p. 279-86. Zhang, G. and S. Ghosh, Molecular mechanisms of NF-kappaB activation induced by bacterial ...
... a DNA-binding protein, which binds to a specific DNA binding site, the promoter, immediately upstream of the genes. Binding of ... result in a decreased level of expression in the presence of IPTG and even in strains of the bacterium lacking the repressor or ... Joung J, Ramm E, Pabo C (2000). "A bacterial two-hybrid selection system for studying protein-DNA and protein-protein ... The protein that is formed by the lacI gene is known as the lac repressor. The type of regulation that the lac operon undergoes ...
The DNA sequence that a transcription factor binds to is called a transcription factor-binding site or response element.[55]. Transcription factors interact with their binding sites using a combination of electrostatic (of which hydrogen bonds are a special case) and Van der Waals forces. Due to the nature of these chemical interactions, most transcription factors bind DNA in a sequence specific manner. However, not all bases in the transcription factor-binding site may actually interact with the transcription factor. In addition, some of these interactions may be weaker than others. Thus, transcription factors do not bind just one sequence but are capable of binding a subset of closely related sequences, each with a different strength of interaction. For example, although the consensus binding site for the TATA-binding protein (TBP) is ...
Cancer is a disease characterized by uncontrolled cell growth and proliferation. For cancer to develop, genes regulating cell growth and differentiation must be altered; these mutations are then maintained through subsequent cell divisions and are thus present in all cancerous cells. Gene expression profiling is a technique used in molecular biology to query the expression of thousands of genes simultaneously. In the context of cancer, gene expression profiling has been used to more accurately classify tumors. The information derived from gene expression profiling often helps in predicting the patient's clinical outcome. Oncogenesis is the process by which normal cells acquire the properties of cancer cells leading to the formation of a cancer or tumor (see: tumorigenesis). It is characterized by a molecular reprogramming of ...
CCAAT/enhancer-binding protein beta is a protein that in humans is encoded by the CEBPB gene. The protein encoded by this intronless gene is a bZIP transcription factor that can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related proteins CEBP-alpha, CEBP-delta, and CEBP-gamma. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses and has been shown to bind to the IL-1 response element in the IL-6 gene, as well as to regulatory regions of several acute-phase and cytokine genes. In addition, the encoded protein can bind the promoter and upstream element and stimulate the expression of the collagen type I gene. CEBP-beta is critical for normal macrophage functioning, an important immune cell sub-type; mice ...
... refers to the practice of altering the expression of a gene at one of various stages, with a view to alleviate some form of ailment. It differs from gene therapy in that gene modulation seeks to alter the expression of an endogenous gene (perhaps through the introduction of a gene encoding a novel modulatory protein) whereas gene therapy concerns the introduction of a gene whose product aids the recipient directly. Modulation of gene expression can be mediated at the level of transcription by DNA-binding agents (which may be artificial transcription factors), small molecules, or synthetic oligonucleotides. It may also be mediated post-transcriptionally through RNA interference. An approach to therapeutic modulation utilizes agents that modulate endogenous transcription ...
In mammalian biology, insulated neighborhoods are chromosomal loop structures formed by the physical interaction of two DNA loci bound by the transcription factor CTCF and co-occupied by cohesin. Insulated neighborhoods are thought to be structural and functional units of gene control because their integrity is important for normal gene regulation. Current evidence suggests that these structures form the mechanistic underpinnings of higher-order chromosome structures, including topologically associating domains (TADs). Insulated neighborhoods are functionally important in understanding gene regulation in normal cells and dysregulated gene expression in disease. Mammalian gene transcription is generally controlled by enhancers. Enhancers can regulate transcription of genes at large distances by looping to ...
In molecular biology miR-203 is a short non-coding RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms, such as translational repression and Argonaute-catalyzed messenger RNA cleavage. miR-203 has been identified as a skin-specific microRNA, and it forms an expression gradient that defines the boundary between proliferative epidermal basal progenitors and terminally differentiating suprabasal cells. It has also been found upregulated in psoriasis and differentially expressed in some types of cancer. MicroRNAs are short (20-22nt), non-coding RNA molecules involved in the regulation of messenger RNAs (mRNAs) by pairing with their 3' UTR and affecting their stability or directing their silencing or degradation. MicroRNAs are likely to play roles in most cellular processes, including proliferation, development, differentiation and apoptosis. They are located in intergenic and intragenic ...
Data analysis of microarrays has become an area of intense research.[11] Simply stating that a group of genes were regulated by at least twofold, once a common practice, lacks a solid statistical footing. With five or fewer replicates in each group, typical for microarrays, a single outlier observation can create an apparent difference greater than two-fold. In addition, arbitrarily setting the bar at two-fold is not biologically sound, as it eliminates from consideration many genes with obvious biological significance. Rather than identify differentially expressed genes using a fold change cutoff, one can use a variety of statistical tests or omnibus tests such as ANOVA, all of which consider both fold change and variability to create a p-value, an estimate of how often we would observe the data by chance alone. Applying p-values to microarrays is complicated by the large number of multiple comparisons (genes) involved. For example, a ...
Bidirectional promoters are short (,1 kbp) intergenic regions of DNA between the 5' ends of the genes in a bidirectional gene pair.[14] A "bidirectional gene pair" refers to two adjacent genes coded on opposite strands, with their 5' ends oriented toward one another.[15] The two genes are often functionally related, and modification of their shared promoter region allows them to be co-regulated and thus co-expressed.[16] Bidirectional promoters are a common feature of mammalian genomes.[17] About 11% of human genes are bidirectionally paired.[14]. Bidirectionally paired genes in the Gene Ontology database shared at least one database-assigned functional category with their partners 47% of the time.[18] Microarray analysis has shown bidirectionally paired genes to be co-expressed to a higher degree than random ...
... is the activation of genes within specific tissues of an organism at specific times during development. Gene activation patterns vary widely in complexity. Some are straightforward and static, such as the pattern of tubulin, which is expressed in all cells at all times in life. Some, on the other hand, are extraordinarily intricate and difficult to predict and model, with expression fluctuating wildly from minute to minute or from cell to cell. Spatiotemporal variation plays a key role in generating the diversity of cell types found in developed organisms; since the identity of a cell is specified by the collection of genes actively expressed within that cell, if gene expression was uniform spatially and temporally, there could be at most one kind of cell. Consider the gene wingless, a member of the wnt family of genes. In the early embryonic ...
மரபணு வெளிப்பாடு (Gene expression) என்பது மரபணுவில் இருக்கும் தகவல்கள், தொழிற்படக்கூடிய மரபணு உற்பத்திப்பொருளாக (gene product) மாற்றப்படும் செயல்முறையாகும். மரபணுவிலிருக்கும் மரபணுக் குறியீட்டுப்பகுதியில் (coding region) இருந்து இவ்வகையான மரபணு உற்பத்திப்பொருட்கள் உருவாகின்றன. மரபணு உற்பத்திப்பொருட்கள் உயிர்வேதியியல் பொருட்களாகும். பொதுவாக இந்த மரபணு உற்பத்திப் பொருட்கள் தொழிற்படும் ...
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Van Holde, K., J. Zlatanova, G. Arents, and E. Moudrianakis. 1995. Elements of chromatin structure: histones, nucleosomes, and fibres, p. 1-26. In S. C. R. Elgin (ed.), Chromatin structure and gene expression. IRL Press at Oxford University Press, Oxford ...
বংশাণু সাধারণতঃ প্রোটিন তৈরির মাধ্যমে তাদের প্রকাশ ঘটায়, যেটি কিনা কোষের সবচেয়ে জটিল কাজগূলো সম্পাদনকারী অণু। প্রোটিন হল এমিনো এসিডের চেইন, আর বংশাণুর ডিএনএ ক্রম (আরএনএ অন্তবর্তীর মাধ্যমে) সুনির্দিষ্ট প্রোটিন ক্রম তৈরির জন্যে ব্যবহৃত হয়। এই প্রক্রিয়াটি বংশাণুর ডিএনএ ক্রমের সাথে মিল থাকা আরএনএ অণু তৈরির মাধ্যমে আরম্ভ হয়, যে প্রক্রিয়াটি প্রতিলিপিকরণ (transcription) নামে পরিচিত। ...
The enteric pathogen Salmonella typhimurium co-ordinates the expression of virulence determinants in response to environmental ... DNA-Binding Proteins * PhoQ protein, Bacteria * Phosphates * RNA, Bacterial * Recombinant Fusion Proteins ... Environmental regulation of Salmonella pathogenicity island 2 gene expression Mol Microbiol. 1999 Mar;31(6):1759-73. doi: ... to SPI2 genes to analyse expression and used antibodies against recombinant SPI2 proteins to monitor levels of SPI2 proteins ...
... their role in bacterial physiology remains largely unknown. The two-dimensional protein patterns were compared and expression ... Despite many years of intense work investigating the function of nucleoid-associated proteins in prokaryotes, ... Bacterial Proteins * DNA Primers * DNA-Binding Proteins * H-NS protein, bacteria * RNA, Messenger ... Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS Mol ...
Eukaryotic DNA and the Regulation of Gene Expression. Regulatory Sequences in DNA. Regulatory Proteins. Post-Transcriptional ... The Operator and the Repressor-An Introduction to DNA-Binding Proteins.Box 14.1: Gene Transfer in Bacteria.Box 14.2: Negative ... Gene Regulation and the Green Revolution.16. Genomes. An Introduction to Whole-Genome Sequencing. Bacterial and Archaeal ... Control of Gene Expression in Bacteria. Gene Regulation and Information Flow. Identifying the Genes Involved in Lactose ...
... and sequence-independent DNA-binding capacity, the nucleoid-associated protein HU has long been characterized as the bacterial ... Bacteria can switch their gene-expression program rapidly and precisely in response to environmental changes. We propose that ... the ostensible lack of influence of chromosome organization over global gene regulation is surprising. ... gene expression is believed to be regulated by operon-specific factors, adjacent DNA control elements and local DNA ...
... with an allosteric mechanism of signal transmission in the regulation of DNA binding and thus virulence gene expression. ... 2008) in Chemical Communication Among Bacteria, LuxR-type proteins in Pseudomonas aeruginosa quorum sensing: Distinct ... 2002) Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA. Nature 417:971-974. ... where each subunit binds to one half of the palindromic 18-bp binding site. Despite the dyad symmetry of the DNA, TraR binds as ...
Trigger enzymes may have a second activity as a direct regulatory protein that can bind specific DNA or RNA targets under ... Enzymes that have a second (so-called moonlighting) function in the regulation of gene expression are collectively referred to ... It is thus not surprising that bacteria have evolved a variety of strategies to employ this information in the control of gene ... provide an overview on these mechanisms and discuss the relevance of trigger enzymes for virulence gene expression in bacterial ...
Anaplasma phagocytophilum AnkA binds to granulocyte DNA and nuclear proteins. Cell Microbiol. 2004;6:743-51. DOIPubMed ... be altered by infection compels further investigation of a direct pathogenetic role in regulation of eukaryotic gene expression ... phagocytophilum known to be secreted by the bacterium, that passes through the bacterial and vacuolar membrane (presumably by ... Within the nucleus of infected neutrophils or HL-60 cells, AnkA binds nuclear proteins and complexes to AT-rich nuclear DNA ...
... abundant DNA architectural proteins of the bacterial chromoid binding multiple low affinity sites and thus modulating the ... In E. coli the transcriptional regulation of gene expression involves both dedicated regulators binding specific DNA sites with ... Abstract: In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be ... in the presence of global DNA architectural proteins regulation is mostly of the analog type, coupling spatially neighboring ...
The transcriptional regulation of bacterial gene expression often employs regulatory proteins that act upon RNA polymerase. ... many EBPs have a C-terminal DNA binding domain thought to allow the protein to bind its specific DNA enhancer sequence. All ... the expression of potential EBP genes by comparing total RNA samples from vegetatively growing cells with those from bacteria ... The single largest family of DNA binding regulatory proteins identified so far in M. xanthus are its EBPs. Thirty-seven genes ...
This approach is implemented for pleiotropic bacterial regulators, including σ70 (bacterial housekeeping σ factor) target ... This approach is implemented for pleiotropic bacterial regulators, including σ70 (bacterial housekeeping σ factor) target ... These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which ... These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which ...
The emerging picture is that bacterial chromosomes are structured at multiple length-scales by various DNA-binding proteins and ... 3) Chromosomal domains/supercoiling domains and their influence on gene expression and regulation ... has begun to reveal the general principles of chromosome organization in bacteria. ... including DNA replication, DNA segregation, DNA repair, homologous recombination, and horizontal gene transfer. Recent work, ...
... are important elements in the regulation of gene expression for bacteria. Hfq is a bacterial RNA-binding protein that ... RNA based regulation of gene expression. RNA-protein interaction. Thermodynamics of DNA and RNA structural motifs ... Current research is directed at understanding the interaction of the RNA-binding protein Hfq with short regulatory RNAs and its ... Hfq is highly conserved in bacterial phyla and has been shown to be a virulence factor in several bacterial species. The ...
DNA-Binding Proteins / genetics * Escherichia coli Proteins* * Fimbriae, Bacterial * Gene Expression Regulation, Bacterial ... agfD protein, Salmonella typhimurium * sigma factor KatF protein, Bacteria * UhpA protein, Bacteria ... Promoter and expression analysis revealed that the genes downstream of agfD agfEFG most likely did not contribute to the ... transmembrane protein with a C-terminal GGDEF domain of unknown function although it is present in over 50 bacterial proteins. ...
... suggesting that modification of these sites might modulate the DNA binding capacity of HupB and thereby alter gene expression. ... Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol. 8, 185-195 (2010).. ... such as DNA methylation and positive feedback loops, typically involve regulation of only one or a few genes (38-40). Our ... DNA methylation in bacteria: From the methyl group to the methylome. Curr. Opin. Microbiol. 25, 9-16 (2015).. ...
The potential DNA binding sites of these two proteins, which include a pho box and -10 and -35 elements, are proposed. ... These three proteins form a signal transduction pathway known as PUMA3, which controls expression of P. aeruginosa virulence ... Intriguingly, the genes of the VreI regulon are also expressed in low Pi despite the fact that the VreI repressor, the anti ... Next to the primary  factor, most bacteria contain a variable number of alternative  factors of which the extracytoplasmic ...
... protein across eubacteria is necessary for maintaining the nucleoid organization and global regulation of gene expression. ... A number of small histone-like DNA binding proteins now known as nucleoid-associated proteins (NAP) organize the bacterial ... These results provide first insights into the modulation of the nucleoid structure by lysine acetylation in bacteria. ... Lysine acetylation of theMycobacterium tuberculosisHU protein modulates its DNA binding and genome organization. ...
Bacterial Proteins/physiology*. *DNA-Binding Proteins/physiology*. *Gene Expression Regulation, Bacterial*. *Gram-Positive ... Many Gram-positive bacteria encode a homolog of Bacillus subtilis CodY, a protein that controls more than a hundred genes that ... In at least some pathogenic Gram-positive bacteria, major virulence factor genes are among the targets of CodY. ... CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria.. Sonenshein AL1. ...
Fis, a DNA nucleoid-associated protein, is involved in Salmonella typhimurium SPI-1 invasion gene expression. Mol. Microbiol. ... HilD binding sequences appear to be important for chromosomal hilA expression.. It is unclear why plasmid hilA regulation does ... The bacterial strains and plasmids used in the present study are shown in Table 1. Bacteria were routinely grown in Luria broth ... DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture. Genes Dev. 10:16-26. ...
... availability of bacterial genomes allows massive comparisons of DNA sequences that can be the target of regulatory proteins. In ... Although this chapter deals primarily with negative regulation by iron, it should be noted that several Escherichia coli genes ... including acnA, bfr, ftnA, fumA, fumB, sdhCDAB, and sodB) and other bacteria are positively controlled by FeFur. While some of ... Regardless of the specific mechanism by which Fur binds its target DNA, it is possible to describe Fur sites in a genome as an ...
A method of killing bacteria before disease is caused in a mammal by applying a panel of bacteriophages on the mammal, wherein ... Upon binding to the bacteria, the DNA gains entry into the bacterial host where it is transcribed and translated into various ... Theoretically a vir mutant may arise due to a dominant negative mutation in the repressor protein gene. The repressor protein ... The prophage directs the synthesis of a repressor which blocks the expression of its own genes and also those of any closely- ...
... at the Wyss Institute for Biologically Inspired Engineering explain how you can use truncated gRNAs to regulate gene expression ... These fusion proteins retain the ability to recognize and bind to DNA; when complexed with a gRNA that directs them to the ... "Orthogonal Cas9 proteins for RNA-guided gene regulation and editing." Nature methods 10.11 (2013): 1116-1121. PubMed PMID: ... Cas9 proteins derived from different bacterial species, each of which interacts with a distinct gRNA that allows users to ...
Study Bacterial Genetic Variation (complete) flashcards from Eooooo m ... Bacteria can increase/decrease transcription based on the new environments. - Done by DNA-binding proteins (interact with ... Repressor protein* maintains lysogenic stage, which blocks gene expression necessary for viral DNA replications/lytic ... 1) Regulation of transcription. 2) Control of transcription by DNA rearrangement 2 ...
Bacteria Transcription And Regulation flashcards from Charli Ward ... An example of bacterial gene expression regulation. Its ... How does the repressor (regulatory protein) work? By binding to operator (specific DNA sequence) in operon ... Bacteria Transcription And Regulation Flashcards Preview Molecular Biology , L3: Operons, Bacteria Transcription And Regulation ... Clusters of bacterial genes with related functions and whose products are needed under the same conditions. Genes in operons ...
... two molecules form a tandem dimer upon binding to adjacent sites on DNA. The protein:protein and protein:DNA interfaces ... We therefore tested whether uncoupling autolysin gene expression from WalKR-dependent regulation could compensate for its ... This is the first example of an ftsH gene controlled by the CtsR repressor, and the first of the low-G+C gram-positive bacteria ... A bacterial two-hybrid approach, designed to identify interactions between the GraXSR and VraFG proteins, was carried out in ...
LONP1 is also a DNA-binding protein that participates in mtDNA maintenance and gene expression regulation. LONP1 degrades ... Lon protease (LONP1) is a conserved serine peptidase identified from bacteria to eukaryotic cells. In mitochondrial matrix, a ... "A human mitochondrial ATP-dependent protease that is highly homologous to bacterial Lon protease". Proceedings of the National ... coli regulates gene expression by targeting specific regulatory proteins for degradation. Lon protease binds a specific ...
  • The enteric pathogen Salmonella typhimurium co-ordinates the expression of virulence determinants in response to environmental cues from the host organism. (nih.gov)
  • Crystal structures of TraR from the plant pathogen Agrobacterium tumefaciens bound to the cognate AHL 3-oxo-octanoyl-homoserine lactone (3OC8-HSL) and DNA-binding site ( 14 , 15 ), as well as CviR from a human pathogen Chromobacterium violaceum bound to antagonist have been reported ( 16 ). (pnas.org)
  • Such knowledge is in turn crucial for both biotechnology applications and fundamental understanding of how bacteria respond to changing environment (e.g., during host pathogen interactions). (frontiersin.org)
  • 30. The method of claim 29, wherein each of the first and second strains of bacteria is a human, animal, or plant pathogen. (freepatentsonline.com)
  • We extended the use of Drosophila beyond being a model for signaling pathways required for pattern recognition immune signaling and show that the fly can be used to identify genes required for pathogenesis and host-pathogen interactions. (genetics.org)
  • The use of microarrays to analyze the kinetics of the transcriptional response of a bacterial pathogen to a changing environment has enabled the discovery of previously unappreciated relationships between genes by elucidation of coordinated gene expression profiles. (asm.org)
  • However, understanding how bacterial transcriptional regulatory networks function during host-pathogen interaction is limited. (prolekare.cz)
  • Transcriptional repression of pathogen defense-related genes is essential for plant growth and development. (pubmedcentralcanada.ca)
  • A T-DNA insertional mutant ( cbnac1 ) displayed enhanced resistance to a virulent strain of the bacterial pathogen Pseudomonas syringae DC3000 ( Pst DC3000), whereas resistance was reduced in transgenic CBNAC overexpression lines. (pubmedcentralcanada.ca)
  • Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an opportunistic human pathogen, showing great adaptability and metabolic versatility ( 17 , 36 , 46 ). (asm.org)
  • Here, we present a study where manipulation of cultural growth conditions and in planta experiments have been used to validate the expression stability of reference gene candidates for the plant pathogen Pectobacterium atrosepticum , belonging to the family Enterobacteriaceae . (biomedcentral.com)
  • However, the study of pathogen gene expression inside infected host tissue poses some problems, as there is no straightforward way of measuring the total pathogen RNA concentration. (biomedcentral.com)
  • An increase in target transcript at different time points after infection could either come from an up-regulation of transcription or merely from an increase in the pathogen population inside the host tissue, or both. (biomedcentral.com)
  • Pectobacterium atrosepticum (formerly known as Erwinia carotovora subspecies atroseptica [ 10 , 11 ]) is an important bacterial pathogen of potato in temperate regions, where it causes blackleg of plants and soft rot of tubers by the utilization of a huge machinery of plant cell wall degrading exoenzymes mainly encompassing pectinases, cellulases and proteases. (biomedcentral.com)
  • In particular, infections caused by the bacterial pathogen Staphylococcus aureus are becoming increasingly difficult to treat due to the rising incidence of multidrug-resistant isolates. (asm.org)
  • We are studying how actinomycete bacteria, such as the dreaded human pathogen Mycobacterium tuberculosis , employ a primitive form of the eukaryotic ubiquitin-proteasome system to survive under conditions of nutrient and oxidative stress. (washington.edu)
  • The First Living Entity.Box 3.1: How Do Biologists Define Life?Box 3.2: Gel Electrophoresis and Autoradiography.Box 3.3: How Proteins Catalyze Reactions.Box 3.4: Models in Biology: The Double Helix.Essay: Molecular Handedness and the Thalidomide Tragedy.4. (bookdepository.com)
  • In 1994, through application of broad range molecular amplification and DNA sequencing, the causative agent was recognized as distinct from E . chaffeensis . (cdc.gov)
  • The fifth edition of this highly successful book provides students with an essential introduction to the molecular genetics of bacteria covering the basic concepts and the latest developments. (nhbs.com)
  • Molecular Biology cAMP receptor protein The Plac promoter is not a strong promoter. (slideserve.com)
  • In molecular biology, the LuxR-type DNA-binding HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids. (wikipedia.org)
  • GO enrichment analysis of molecular function and biological process were performed as well as Interpro protein functional domains and pBLAST analyses. (biomedcentral.com)
  • Proteins constitute the main molecular workers in the cell, whose roles include sensing signals from the environment, carrying out enzymatic reactions, and performing transcription and translation. (illinois.edu)
  • We employ simple bacterial and bacteriophage model systems, because these systems can be defined in detail biochemically and investigated at a molecular level. (nih.gov)
  • Using molecular modeling, we have demonstrated how this is possible: they are located like spokes on a wheel around the DNA double-helix. (nih.gov)
  • As the synthesis and delivery of these molecules entail considerable costs for the producers, their expression is tightly regulated, often by molecular systems detecting physiological stresses or environment-specific cues. (usda.gov)
  • High-resolution molecular structures are normally determined in vitro, but Brian was part of the team that solved the first structure of a protein inside living cells. (gla.ac.uk)
  • We collaborate widely with other biologists and chemists and currently have particular interests in the biophysics and application of natural surfactant proteins, in fatty acid binding proteins from nematode parasites, in the structural basis of epigenetic gene regulation, in the regulation of viral life cycles, in the molecular basis of endotoxin sensing, and in ultraviolet light perception by plants. (gla.ac.uk)
  • Molecular signals including DNA methylation and modification of histone tails are key to these processes. (gla.ac.uk)
  • By combining the powerful techniques of synthetic organic chemistry, molecular biology and protein semisynthesis, we produce chemically modified proteins. (washington.edu)
  • The structures of TraR bound to 3OC8-HSL ( 14 , 15 ) confirmed the view from genetic dissection that LuxR homologs are homodimers of two-domain polypeptides with N-terminal ligand-binding domains (LBDs) and a C-terminal DNA-binding domain (DBD) ( 19 , 20 ). (pnas.org)
  • Cas9 is a DNA binding protein that can be directed to virtually any genetic locus when complexed with an appropriately designed small RNA, or guide RNA (gRNA). (addgene.org)
  • Consider, for instance, the challenge of attempting to simultaneously and selectively induce both cutting and regulation of expression at different genetic loci within a single cell. (addgene.org)
  • Consequently, fewer genetic tools for targeted transcriptional and epigenetic regulation have been validated with these proteins. (addgene.org)
  • To overcome these limitations, we performed a forward genetic screen in whole Drosophila to identify host genes required to survive infections. (genetics.org)
  • Further understanding of this QS genetic mechanism may potentially be used for inhibiting bacterial proliferation and infection, modifying the natural genetic system to elicit alternate desired responses, or extracted and applied to a highly customizable and sensitive in vitro biosensor. (umd.edu)
  • Transformation is the process by which a foreign chromosome fragment (plasmid) is incorporated into the bacterial chromosome via recombination, creating new inheritable genetic combination. (wikibooks.org)
  • These virions may infect other bacteria and introduce new genetic arrangements through recombination with the new host cell's DNA. (wikibooks.org)
  • This was the first study of metabolic regulation based on genetic analysis of the lac system. (golifescience.com)
  • Twenty-six strains representing these three genetic configurations were selected to investigate the transcription and expression levels of scpB and lmb genes. (pubmedcentralcanada.ca)
  • The basic unit of genetic information is called a gene, which is a region of the DNA that contains the instructions to produce messenger RNAs (mRNAs). (illinois.edu)
  • also known as TnSeq) is a potent approach commonly used to comprehensively define the genetic loci that contribute to bacterial fitness in diverse environments. (harvard.edu)
  • Acquired resistance develops with gene mutations or via external genetic acquisition from nearby resistant organisms, through horizontal gene transfer (HGT). (asm.org)
  • Cytoplasmic FMR1-Interacting Protein 2 Is a Major Genetic Factor Underlying Binge Eating. (kumarlab.org)
  • Bacterial plasmids are agents for HGT, but they themselves are genetic replicons with their own, idiosyncratic, evolutionary history , . (prolekare.cz)
  • Genetic and biochemical evidence obtained in animal, fungal, and bacterial model systems have suggested that light resets the clock through changes in the phase of negative components that ultimately define the phase of the oscillator so that clock-controlled processes are appropriately phased ( Devlin and Kay, 2001 ). (plantcell.org)
  • Using a gain-of-function HUα mutant, we demonstrate that nucleoid structural reorganization in bacteria can directly induce a radical change in the gene-expression profile, resulting in dramatic changes in cellular morphology and physiology. (pnas.org)
  • Generally, the AHL receptors are members of a family of related transcription factors, and although they have been targets for development of antivirulence therapeutics there is very little structural information about this class of bacterial receptors. (pnas.org)
  • UV absorbance monitored transitions and temperature gradient gel electrophoresis are being employed to determine the stability and conformational switching of structural motifs in RNA and DNA. (gatech.edu)
  • Bacterial structural genes are mostly organized as clusters, consisting of genes coding for proteins whose functions are related. (golifescience.com)
  • Pentapeptide repeat proteins include a number of examples which are thought to function as structural mimics of DNA and act to competitively bind to the type II topoisomerase DNA gyrase, an important antibacterial target. (springer.com)
  • Ligand recognition is achieved by the aptamer domain, and ligand‐dependent structural changes of the expression platform then usually mediate termination of transcription or translational initiation. (deepdyve.com)
  • A plasmid bearing the blaU structural gene and the blaA-blaB regulatory region was constructed and shown to confer on an S. lividans host the capacity to produce inducible beta-lactamase. (ac.be)
  • In unicellular organisms such as bacteria the same acquired mutations beneficial in one environment can be restrictive in another. (arxiv.org)
  • Tumor Suppressor: Mutations in the protein p53 are strongly correlated with the transformation of a healthy cell into a cancerous cell. (uci.edu)
  • Many cancers can be traced to a set of several individual point mutations in this protein that result in destabilization of the structure and thus inactivation of the protein. (uci.edu)
  • Infection is initiated by entry of the bacteria into intestinal epithelial cells and is mediated by a type III secretion system that is encoded by genes in Salmonella pathogenicity island 1. (asm.org)
  • Salmonella infections are caused by the ingestion of contaminated food or water, after which the bacteria are able to colonize the small intestine and invade intestinal enterocytes and M cells of the follicle-associated epithelium of Peyer's patches ( 9 , 30 , 41 ). (asm.org)
  • Salmonella has evolved a highly complex regulatory scheme to control the expression of invasion genes. (asm.org)
  • A DNA microarray was constructed from the M1genome that includes those homologs and 318 other M. xanthus genes for comparison. (asm.org)
  • Genomic binding and DNA microarray analyses are conducted and three novel sites putatively regulated by LsrR, yegE-udk, mppA and yihF, are revealed. (umd.edu)
  • The global pattern of growth-phase-dependent gene expression of Helicobacter pylori during in vitro culture was analyzed by using a high-density DNA microarray. (asm.org)
  • Using an oligonucleotide-based microarray, we normalized the transcriptomic data by genomic DNA signals in order to have access to inter-gene comparison data. (biomedcentral.com)
  • Thus, we used the microarray technology to study the effects of subinhibitory concentrations of a β-lactam antibiotic, imipenem, on gene expression in biofilm populations. (asm.org)
  • We have developed a series of activity-based probes to investigate the functions and substrate-scope of enzymes associated with the prokaryotic ubiquitin-like protein (Pup). (washington.edu)
  • The expression of approximately 5% of the genes and/or the accumulation of their protein was directly or indirectly altered in the hns mutant strain. (nih.gov)
  • The increased expression of several genes in the mutant resulted in a better ability of this strain to survive at low pH and high osmolarity than the wild-type strain. (nih.gov)
  • The mutant protein transformed the loosely packed nucleoid into a densely condensed structure. (pnas.org)
  • Many constitutive housekeeping genes involved in nutrient utilization were repressed, whereas many quiescent genes associated with virulence were activated in the mutant. (pnas.org)
  • Although the spectinomycin-resistance marker, on its own, did not show any of the phenotypes displayed by HUα E38K,V42L , there was a sharp reduction in the mutant HUα expression when some other selective markers were used as substitutes, the basis of which is not known. (pnas.org)
  • Predictions about signal binding and dimerization contacts were supported by studies of mutant QscR proteins in vivo. (pnas.org)
  • The interactions of wild type and mutant Hfq proteins with specific RNAs are being examined. (gatech.edu)
  • AdrA mutant cells, which still formed thin aggregative fimbriae with all binding characteristics, exhibited community behaviour but, unlike the wild type, lacked long-range intercellular adhesion. (nih.gov)
  • Basal resistance to Pst DC3000 and derepression of PR1 expression was greater in the cbnac1 sni1 double mutant than in either cbnac1 or sni1 mutants. (pubmedcentralcanada.ca)
  • Usf1 , a suppressor of the circadian clock mutant, reveals the nature of the DNA-binding of the CLOCK:BMAL1 complex in mice. (kumarlab.org)
  • Our results show that TOC1 RNA interference and toc1-2 mutant plants displayed an important reduction in sensitivity to red and far-red light in the control of hypocotyl elongation, whereas increments in TOC1 gene dosage clearly enhanced light sensitivity. (plantcell.org)
  • Furthermore, the red light-mediated induction of CCA1/LHY expression was decreased in TOC1 RNA interference and toc1-2 mutant plants, indicating a role for TOC1 in the phytochrome regulation of circadian gene expression. (plantcell.org)
  • Compared to the wild type strain, expression of rtx genes deceased in the hlyU mutant while expression of vah1 and plp was not affected in the hlyU mutant. (uri.edu)
  • Further, expression of rtxA , rtxH , rtxB , vah1 and plp increased in the hns mutant, and decreased in the complemented hns mutant strain when compared to the wild type strain. (uri.edu)
  • This effect is not unique to tt19 and extends to at least one other anthocyanin pathway gene mutant. (scoop.it)
  • Since the presence of microorganisms (bacteria and yeasts) can modulate not only the lifespan of the fly, but also serve as source of nutrients we are investigating how exposure to microbes differentially affects gene expression in wild type and mutant flies under different dietary regiments, as well as how these manipulations affect the ability of microbes to colonize their fruit fly hosts. (liu.edu)
  • These include slipped-strand mispairing within genes ( 28 ) and in putative promoter regions ( 4 ) and methylation by its nine type II methyltransferases ( 37 , 54 ). (asm.org)
  • The proximal promoter regions of both Rho (-225 to +70 base pairs relative to the transcription start site) [ 11 - 13 ] and IRBP (-123 to +18 bp) [ 6 , 14 ] are sufficient to drive photoreceptor-specific expression of reporter genes in transgenic mice. (biomedcentral.com)
  • ATP binding to the AAA module of the Lon complex results in a change in Lon conformation into a proteolytically active state. (wikipedia.org)
  • These regions can be presented to Lon protease when proteins are damaged and lost their conformation integrity. (wikipedia.org)
  • Using NMR spectroscopy, we will probe the conformation of the protein in solution to determine if the closed state is the most populated or merely one of the existing conformations trapped by the crystallization process. (uci.edu)
  • The peaks arising from the amide NH of each amino acid residue are seen to jump from one position to another as oleate is titrated into the protein indicating that it can bind multiple ligands, adopting a distinct conformation in each case. (gla.ac.uk)
  • FUNCTION: Binds to DNA and alters its conformation. (univ-lyon1.fr)
  • Our data are consistent with an allosteric mechanism of signal transmission in the regulation of DNA binding and thus virulence gene expression. (pnas.org)
  • An important consequence of this regulatory mechanism is that transcription of a gene can be turned off completely, a distinct advantage for developmental genes. (asm.org)
  • The term `quorum sensing' (QS) is used to define a population density based communication mechanism which uses chemical signal molecules called autoinducers to trigger unique and varied changes in gene expression. (umd.edu)
  • In mitochondrial matrix, a majority of damaged proteins is removed via proteolysis led by Lon protease, which is an essential mechanism for mitochondrial protein quality control (PQC). (wikipedia.org)
  • The basic mechanism for the control of gene expression was discovered in 1961 by Francois Jacob and Jacques Monod at the Pasteur Institute in Paris. (golifescience.com)
  • Our study highlights a novel mechanism to induce B7H6 expression and suggests a pharmacological approach to improve B7H6-directed immunotherapy. (weizmann.ac.il)
  • Pentapeptide repeat proteins are therefore of wide interest not only because of their unusual structure, function, and potential as an antibacterial target, but also because knowledge of their mechanism of action may lead to both a greater understanding of the details of DNA gyrase function as well as being a useful template for the design of new DNA gyrase inhibitors. (springer.com)
  • The group are trying to understand the mechanism of UV perception and the conformational changes in the protein that effect downstream signalling. (gla.ac.uk)
  • In chapter two, we characterized the mechanism by which F. novicida CRISPR-Cas9 (FnoCas9) represses the expression of bacterial lipoproteins (BLPs), allowing evasion of the host immune system. (hu-berlin.de)
  • In this newly-described mechanism, the non-canonical RNA duplex tracrRNA:scaRNA guides FnoCas9 to the DNA target located downstream of the promoter of the BLP-coding genes, causing transcriptional interference. (hu-berlin.de)
  • One transcriptional regulatory mechanism involves a regulatory protein, FlgM, that escapes from the cell (and thus can no longer act) through a complete flagellum and is held inside when the structure has not reached a later stage of completion. (asm.org)
  • Alarmingly, a plasmid-mediated colistin resistance mechanism ( mcr-1 gene) has been reported in over 30 countries across five continents since it was first identified in 2015, raising major public health concern ( 7 ⇓ - 9 ). (mcponline.org)
  • Reversible protein phosphorylation is a well-established mechanism of regulating gene expression in response to a variety of environmental stress factors ( 13 ) and in recent years, growing evidence has linked two-component systems as well as serine/threonine/tyrosine kinase signaling to AMR ( 13 ⇓ - 15 ). (mcponline.org)
  • Bacterial cells in a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity. (nature.com)
  • However, existing SMRT sequencing-based methods for studying bacterial methylomes rely on a population-level consensus that lacks the single-cell resolution required to observe epigenetic heterogeneity. (nature.com)
  • SMALR is a powerful new tool that enables de novo detection of epigenetic heterogeneity and empowers investigation of its functions in bacterial populations. (nature.com)
  • It has been postulated that epigenetic control of gene expression mediated by phase variation (epigenetic control of a single gene) or phasevarions (multiple genes regulated simultaneously) allows an essentially clonal population to adopt multiple distinct phenotypes 26 . (nature.com)
  • Modified cytosine variants 5-methylcytosine (5mC) and the recently discovered 5-hydroxymethylcytosine (5hmC) are involved in the epigenetic regulation of gene expression in humans. (vu.lt)
  • It is becoming increasingly evident that longer forms of non-protein-coding RNAs (ncRNAs) are involved directly in regulating gene expression and epigenetic states. (keystonesymposia.org)
  • In the crystal lattice, two molecules form a tandem dimer upon binding to adjacent sites on DNA. (jove.com)
  • The information that instructs cells on how to create the molecules that perform cellular functions resides within the DNA. (illinois.edu)
  • The over-expression of OmpX can balance the decreased expression of non-specific porins, OmpF and OmpC, for the exclusion of small harmful molecules. (biomedcentral.com)
  • OmpR-P binds to four (F4, F1, F2, and F3 from the 5' to 3' direction) and three (C1, C2, and C3) sites within the upstream regions of ompF and ompC , respectively, with each containing two tandem 10 bp subsites ('a' and 'b') bound by two OmpR-P molecules. (biomedcentral.com)
  • While some of the minor divergences between the different models could be attributed to peculiarities of the Fur proteins from different origins, the ultimate understanding of the Fur-DNA interactions requires accessing the cocrystal of Fur bound to its canonical 19-bp consensus target. (asmscience.org)
  • Overall, these findings propose a novel concept establishing the role of carbohydrate-protein interactions to provide efficient food particle sorting, and establish a new dimension for the role of evolutionarily conserved mannose/glucose-binding proteins in metazoans. (biologists.org)
  • The luciferase protein fragment complementation assay is a powerful tool for studying protein-protein interactions. (harvard.edu)
  • Last, we highlight several recent studies examining microbe/protist interactions that postulate an answer to the outstanding question of why microbes might harbor and express Shiga toxin genes in the environment. (mdpi.com)
  • The modern era of biology began when, together, a biologist and a physicist uncovered the nature of the interactions holding together the strands of DNA in the famous double helix. (nap.edu)
  • The relatively simple interactions between different pairs of nucleotides immediately revealed the nearly infinite information storage capacity of the DNA heteropolymer and defined, for the first time, the intimate connection between interaction and information that makes up the fabric of living matter. (nap.edu)
  • Indeed, characterization of such interaction profiles allows an understanding of interactions at the level of the whole organism and bioinformatic approaches are now extensively used for identifying regulatory targets of transcription factors-proteins that control gene expression. (nap.edu)
  • We have employed a strategy utilizing differential fluorescence induction (DFI) in an effort to identify Staphylococcus aureus genes whose products can be targeted for antimicrobial drug development. (asm.org)
  • This approach is implemented for pleiotropic bacterial regulators, including σ 70 (bacterial housekeeping σ factor) target predictions, which is a classical bioinformatics problem characterized by low specificity. (frontiersin.org)
  • Locke and Morozov, 2015 ), but in either case the inferred DNA binding specificity is represented in a form of a matrix, often called position specific weight matrix (PSWM). (frontiersin.org)
  • To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. (cnrs.fr)
  • DNA gyrase-targeting pentapeptide repeat proteins can both inhibit DNA gyrase-a potentially useful therapeutic property-and contribute to resistance to quinolone antibacterials (by acting to prevent them forming a lethal complex with the DNA and enzyme). (springer.com)
  • Antibiotics kill bacteria or inhibit their growth by blocking key cellular pathways. (asm.org)
  • CNS Regeneration: Nogo is a membrane protein known to inhibit axonal growth within the central nervous system (CNS). (uci.edu)
  • Each amino acid has its own aminoacyl-tRNA synthetase, which has an active site that binds to both the amino acid and its corresponding tRNA, catalyzing their attachment to form an aminoacyl-tRNA complex. (wikibooks.org)
  • If the bacterium does not get the amino acid tryptophan from the host's food, it activates a pathway to make its own tryptophan (as it needs this amino acid in order to survive) from another compound. (golifescience.com)