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.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.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.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.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.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, 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.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.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.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.Argonaute Proteins: A family of RNA-binding proteins that has specificity for MICRORNAS and SMALL INTERFERING RNA molecules. The proteins take part in RNA processing events as core components of RNA-induced silencing complex.RNA, Small Interfering: Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.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.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.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.Proton-Phosphate Symporters: Proteins that cotransport hydrogen ions and phosphate ions across cellular membranes.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.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.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.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.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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.RNA, Antisense: RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. Endogenous antisense RNAs function as regulators of gene expression by a variety of mechanisms. Synthetic antisense RNAs are used to effect the functioning of specific genes for investigative or therapeutic purposes.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.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.Transgenes: Genes that are introduced into an organism using GENE TRANSFER TECHNIQUES.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Plants, Genetically Modified: PLANTS, or their progeny, whose GENOME has been altered by GENETIC ENGINEERING.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.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.RNA, Double-Stranded: RNA consisting of two strands as opposed to the more prevalent single-stranded RNA. Most of the double-stranded segments are formed from transcription of DNA by intramolecular base-pairing of inverted complementary sequences separated by a single-stranded loop. Some double-stranded segments of RNA are normal in all organisms.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.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.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 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.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.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.Tobacco: A plant genus of the family SOLANACEAE. Members contain NICOTINE and other biologically active chemicals; its dried leaves are used for SMOKING.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.Cell Line: Established cell cultures that have the potential to propagate indefinitely.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)Schizosaccharomyces: A genus of ascomycetous fungi of the family Schizosaccharomycetaceae, order Schizosaccharomycetales.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.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.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.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Genes, Plant: The functional hereditary units of PLANTS.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.Green Fluorescent Proteins: Protein analogs and derivatives of the Aequorea victoria green fluorescent protein that emit light (FLUORESCENCE) when excited with ULTRAVIOLET RAYS. They are used in REPORTER GENES in doing GENETIC TECHNIQUES. Numerous mutants have been made to emit other colors or be sensitive to pH.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Cell Line, Tumor: A cell line derived from cultured tumor cells.Lysine: An essential amino acid. It is often added to animal feed.Gene Expression Regulation, Leukemic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in leukemia.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.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.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.Microarray Analysis: The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.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.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.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.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.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.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.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.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.Mice, Inbred C57BLDNA, 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.Real-Time Polymerase Chain Reaction: Methods used for detecting the amplified DNA products from the polymerase chain reaction as they accumulate instead of at the end of the reaction.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.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.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).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).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.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.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.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)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.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.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.Reproducibility of Results: The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.Genetic Vectors: DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Rats, Sprague-Dawley: A strain of albino rat used widely for experimental purposes because of its calmness and ease of handling. It was developed by the Sprague-Dawley Animal Company.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.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.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.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.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.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)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.Bacterial Proteins: Proteins found in any species of bacterium.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.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.Fibroblasts: Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.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.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.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.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.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.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)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.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 18.104.22.168.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.Disease Models, Animal: Naturally occurring or experimentally induced animal diseases with pathological processes sufficiently similar to those of human diseases. They are used as study models for human diseases.Cell Cycle: The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.Epithelial Cells: Cells that line the inner and outer surfaces of the body by forming cellular layers (EPITHELIUM) or masses. Epithelial cells lining the SKIN; the MOUTH; the NOSE; and the ANAL CANAL derive from ectoderm; those lining the RESPIRATORY SYSTEM and the DIGESTIVE SYSTEM derive from endoderm; others (CARDIOVASCULAR SYSTEM and LYMPHATIC SYSTEM) derive from mesoderm. Epithelial cells can be classified mainly by cell shape and function into squamous, glandular and transitional epithelial cells.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.Genes, Immediate-Early: Genes that show rapid and transient expression in the absence of de novo protein synthesis. The term was originally used exclusively for viral genes where immediate-early referred to transcription immediately following virus integration into the host cell. It is also used to describe cellular genes which are expressed immediately after resting cells are stimulated by extracellular signals such as growth factors and neurotransmitters.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Immediate-Early Proteins: Proteins that are coded by immediate-early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals.Neoplasm Proteins: Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.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.Membrane 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.Microdissection: The performance of dissections with the aid of a microscope.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.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.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.RNA, Neoplasm: RNA present in neoplastic tissue.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.Cytokines: Non-antibody proteins secreted by inflammatory leukocytes and some non-leukocytic cells, that act as intercellular mediators. They differ from classical hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. They generally act locally in a paracrine or autocrine rather than endocrine manner.Dose-Response Relationship, Drug: The relationship between the dose of an administered drug and the response of the organism to the drug.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Lac Operon: The genetic unit consisting of three structural genes, an operator and a regulatory gene. The regulatory gene controls the synthesis of the three structural genes: BETA-GALACTOSIDASE and beta-galactoside permease (involved with the metabolism of lactose), and beta-thiogalactoside acetyltransferase.Rats, Wistar: A strain of albino rat developed at the Wistar Institute that has spread widely at other institutions. This has markedly diluted the original strain.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.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.Tumor Necrosis Factor-alpha: Serum glycoprotein produced by activated MACROPHAGES and other mammalian MONONUCLEAR LEUKOCYTES. It has necrotizing activity against tumor cell lines and increases ability to reject tumor transplants. Also known as TNF-alpha, it is only 30% homologous to TNF-beta (LYMPHOTOXIN), but they share TNF RECEPTORS.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Cell Division: The fission of a CELL. It includes CYTOKINESIS, when the CYTOPLASM of a cell is divided, and CELL NUCLEUS DIVISION.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Gene Transfer Techniques: The introduction of functional (usually cloned) GENES into cells. A variety of techniques and naturally occurring processes are used for the gene transfer such as cell hybridization, LIPOSOMES or microcell-mediated gene transfer, ELECTROPORATION, chromosome-mediated gene transfer, TRANSFECTION, and GENETIC TRANSDUCTION. Gene transfer may result in genetically transformed cells and individual organisms.Breast Neoplasms: Tumors or cancer of the human BREAST.Stress, Physiological: The unfavorable effect of environmental factors (stressors) on the physiological functions of an organism. Prolonged unresolved physiological stress can affect HOMEOSTASIS of the organism, and may lead to damaging or pathological conditions.RNA Processing, Post-Transcriptional: Post-transcriptional biological modification of messenger, transfer, or ribosomal RNAs or their precursors. It includes cleavage, methylation, thiolation, isopentenylation, pseudouridine formation, conformational changes, and association with ribosomal protein.Brain: The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM.Drosophila melanogaster: A species of fruit fly much used in genetics because of the large size of its chromosomes.Receptors, Cytoplasmic and Nuclear: Intracellular receptors that can be found in the cytoplasm or in the nucleus. They bind to extracellular signaling molecules that migrate through or are transported across the CELL MEMBRANE. Many members of this class of receptors occur in the cytoplasm and are transported to the CELL NUCLEUS upon ligand-binding where they signal via DNA-binding and transcription regulation. Also included in this category are receptors found on INTRACELLULAR MEMBRANES that act via mechanisms similar to CELL SURFACE RECEPTORS.Proto-Oncogene Proteins: Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Principal Component Analysis: Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.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.Embryo, Nonmammalian: The developmental entity of a fertilized egg (ZYGOTE) in animal species other than MAMMALS. For chickens, use CHICK EMBRYO.Sp1 Transcription Factor: Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Dexamethasone: An anti-inflammatory 9-fluoro-glucocorticoid.Proto-Oncogene Proteins c-fos: Cellular DNA-binding proteins encoded by the c-fos genes (GENES, FOS). They are involved in growth-related transcriptional control. c-fos combines with c-jun (PROTO-ONCOGENE PROTEINS C-JUN) to form a c-fos/c-jun heterodimer (TRANSCRIPTION FACTOR AP-1) that binds to the TRE (TPA-responsive element) in promoters of certain genes.Histone Deacetylases: Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.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.Nerve Tissue ProteinsGenes, Bacterial: The functional hereditary units of BACTERIA.Tissue Distribution: Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.Tumor Markers, Biological: Molecular products metabolized and secreted by neoplastic tissue and characterized biochemically in cells or body fluids. They are indicators of tumor stage and grade as well as useful for monitoring responses to treatment and predicting recurrence. Many chemical groups are represented including hormones, antigens, amino and nucleic acids, enzymes, polyamines, and specific cell membrane proteins and lipids.Muscle, Skeletal: A subtype of striated muscle, attached by TENDONS to the SKELETON. Skeletal muscles are innervated and their movement can be consciously controlled. They are also called voluntary muscles.Inflammation: A pathological process characterized by injury or destruction of tissues caused by a variety of cytologic and chemical reactions. It is usually manifested by typical signs of pain, heat, redness, swelling, and loss of function.Transforming Growth Factor beta: A factor synthesized in a wide variety of tissues. It acts synergistically with TGF-alpha in inducing phenotypic transformation and can also act as a negative autocrine growth factor. TGF-beta has a potential role in embryonal development, cellular differentiation, hormone secretion, and immune function. TGF-beta is found mostly as homodimer forms of separate gene products TGF-beta1, TGF-beta2 or TGF-beta3. Heterodimers composed of TGF-beta1 and 2 (TGF-beta1.2) or of TGF-beta2 and 3 (TGF-beta2.3) have been isolated. The TGF-beta proteins are synthesized as precursor proteins.Gene Knockdown Techniques: The artificial induction of GENE SILENCING by the use of RNA INTERFERENCE to reduce the expression of a specific gene. It includes the use of DOUBLE-STRANDED RNA, such as SMALL INTERFERING RNA and RNA containing HAIRPIN LOOP SEQUENCE, and ANTI-SENSE OLIGONUCLEOTIDES.Kinetics: The rate dynamics in chemical or physical systems.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.Zebrafish: An exotic species of the family CYPRINIDAE, originally from Asia, that has been introduced in North America. They are used in embryological studies and to study the effects of certain chemicals on development.Macrophages: The relatively long-lived phagocytic cell of mammalian tissues that are derived from blood MONOCYTES. Main types are PERITONEAL MACROPHAGES; ALVEOLAR MACROPHAGES; HISTIOCYTES; KUPFFER CELLS of the liver; and OSTEOCLASTS. They may further differentiate within chronic inflammatory lesions to EPITHELIOID CELLS or may fuse to form FOREIGN BODY GIANT CELLS or LANGHANS GIANT CELLS. (from The Dictionary of Cell Biology, Lackie and Dow, 3rd ed.)Pregnancy: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.Genes, Neoplasm: Genes whose abnormal expression, or MUTATION are associated with the development, growth, or progression of NEOPLASMS.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.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.RNA-Binding Proteins: Proteins that bind to RNA molecules. Included here are RIBONUCLEOPROTEINS and other proteins whose function is to bind specifically to RNA.Enzyme Inhibitors: Compounds or agents that combine with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction.Mice, Inbred BALB CViral Proteins: Proteins found in any species of virus.Genes, Insect: The functional hereditary units of INSECTS.Neurons: The basic cellular units of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the NERVOUS SYSTEM.Cell Survival: The span of viability of a cell characterized by the capacity to perform certain functions such as metabolism, growth, reproduction, some form of responsiveness, and adaptability.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.
Bacterial one-hybrid system
Across all living organisms, regulation of gene expression is controlled by interactions between DNA-binding regulatory ... Literature suggests that nearly 8% of human genes encode transcription factors and the functions and specificities of their ... transcription factors fine-tune transcriptional levels by stabilizing/destabilizing binding of RNA polymerase to a gene's ... drives expression of downstream reporter genes. This reporter region facilitates both positive and negative selection by HIS3 ...
... gene. FLC gene in Arabidopsis thaliana encodes for a transcription factor that prevent expression of a range of genes that ... AsRNAs can be involved in this level of gene regulation. For example, in bacterial or eukaryotic cells where complex RNA ... One classic example in human is zinc-finger E-box binding homeobox 2 gene (ZEB2) which encodes E-cadherin, a transcriptional ... Epigenetic regulations such as DNA methylation and histone methylation can repress gene expression by inhibiting initiation of ...
Small non-coding RNAs in the endosymbiotic diazotroph α-proteobacterium Sinorhizobium meliloti
... as major players in post-transcriptional regulation of gene expression in response to environmental stimuli. The α-subdivision ... Two complementary computational screens, eQRNA and RNAz, were used to search for novel sRNA-encoding genes in the intergenic ... Majdalani N, Vanderpool CK, Gottesman S (2005). "Bacterial small RNA regulators". Crit Rev Biochem Mol Biol. 40 (2): 93-113. ... Rhizobial adaptations to soil and plant cell environments require the coordinate expression of complex gene networks in which ...
... transcriptional regulation is also important in antigen switching, since T. brucei has multiple potential expression sites. A ... PfEMP1 is encoded by the diverse family of genes known as the var family of genes (approximately 60 genes in all). The ... Viruses in general have much faster rate of mutation of their genomes than human or bacterial cells. In general viruses with ... Some viruses steal host genes and then incorporate them into their own viral genome, encoding genes that sometimes give them an ...
Study of the control of expression of genes in the lac operon provided the first example of a transcriptional regulation system ... encoded by a regulatory gene, binds to its operator, a specific site on the DNA next to the genes encoding the proteins. (It is ... He theorized on the growth of bacterial cultures and promoted the chemostat theory as a powerful continuous culture system to ... The type of regulation is called negative gene regulation, as the operon is inactivated by a protein complex that is removed in ...
"A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): ... "Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation". ... Winkler, WC; Cohen-Chalamish S; Breaker RR (2002). "An mRNA structure that controls gene expression by binding FMN". Proc Natl ... untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. This ...
... as a critical regulator of capsule expression. Fis is also involved in the regulation of a range of genes in bacterial ... 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 ... suggesting that regulation occurs largely at the transcriptional level. Two RNA polymerase-binding sites and at least six high- ... The fis gene is cotranscribed with the upstream dusB gene encoding a tRNA-modifying enzyme. DusB protein levels are very low ...
Bromo adjacent homology domain containing 1
... is a protein that in humans is encoded by the BAHD1 gene. BAHD1 is involved in heterochromatin formation and transcriptional ... Bierne and colleagues further discovered the function of BAHD1 in the regulation of chromatin structure and gene expression . ... "A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response". Science. 331 (6022): 1319- ... acts as an inhibitor of BAHD1 and activates interferon-stimulated genes . The BAHD1 gene is downregulated in the colon tissue ...
... such as the nod genes). The expression and regulation of nif genes, while sharing common features in all or most of the ... Regulation of the nif genes is at the transcriptional level and is dependent on colonization of the plant host. Nif regulon ( ... The nif genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen into a form of nitrogen available to ... The nif genes can be found on bacterial chromosomes, but in symbiotic bacteria they are often found on plasmids or symbiosis ...
Bacterial small RNAs are involved in post-transcriptional regulation. Using deep sequencing S. coelicolor transcriptome was ... It contains 8,667,507 bp, encoding 7,825 predicted genes, including over 20 gene clusters for the synthesis of known or ... Expression of 11 of them was confirmed by Northern blot. The sRNAs were shown to be only present in Streptomyces species. sRNA ... "Global negative regulation of Streptomyces coelicolor antibiotic synthesis mediated by an absA-encoded putative signal ...
The outcome is an ON or OFF phase of a gene or genes. Transcriptional regulation (bottom portion of figure) occurs in several ... Many bacterial species can utilize inversion to change the expression of certain genes for the benefit of the bacterium during ... is encoded by the Agn43 gene (previously designated as flu) and is important for biofilms and infection. The expression of ... The outcome is the regulation of transcription resulting in switches in gene expression. An outer membrane protein Antigen 43 ( ...
... molecules commonly used as communication signals between bacterial cells in a population to regulate certain gene expression ... was found to contain nine genes homologous to the AiiA gene that encode AHL-inactivating enzymes, with the catalytic zinc- ... This type of gene regulation is known as quorum sensing. Lactonase hydrolyzes the ester bond of the homoserine lactone ring of ... "Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators". Annu. Rev. ...
They negatively regulate the expression of several genes encoding outer membrane proteins, including cirA, CsgD, fecA, fepA and ... Guillier M, Gottesman S (2008). "The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including ... Together with the RNA chaperone Hfq, OmrA-B positively controls bacterial motility and negatively controls the production of ... "Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis". EMBO J. 29 (11): 1840-50. doi:10.1038 ...
The expression of many thousands of genes are regulated by ncRNAs. This regulation can occur in trans or in cis. There is ... This eliminates the ambiguity when addressing a gene "encoding a non-coding" RNA. Extracellular RNA List of RNAs Nucleic acid ... These piRNA complexes (piRCs) have been linked to transcriptional gene silencing of retrotransposons and other genetic elements ... Wadler CS, Vanderpool CK (December 2007). "A dual function for a bacterial small RNA: SgrS performs base pairing-dependent ...
Downes BP, Crowell DN (June 1998). "Cytokinin regulates the expression of a soybean β-expansin gene by a post-transcriptional ... Cho HT, Cosgrove DJ (December 2002). "Regulation of root hair initiation and expansin gene expression in Arabidopsis". Plant ... Turning to the function of bacterial expansins, the bacterial protein named YOAJ or BsEXLX1 binds to plant and bacterial cell ... Laine MJ, Haapalainen M, Wahlroos T, Kankare K, Nissinen R, Kassuwi S, Metzler MC (November 2000). "The cellulase encoded by ...
RsaE and RsaF genes overlap in S.aureus species but appear to have opposite expression patterns. Transcriptional interference ... RsaOG also renamed RsaI is thought to fine-tune the regulation of toxin or invasion mechanisms in S. aureus via trans-acting ... RsaK is found in the leader sequence of glcA mRNA which encodes an enzyme involved in the glucose-specific phosphotransferase ... June 2009). "Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles". Genome ...
... s are essential for the regulation of gene expression and are, as a consequence, found in all living ... Robert O. J. Weinzierl (1999). Mechanisms of Gene Expression: Structure, Function and Evolution of the Basal Transcriptional ... Another example is the transcription factor encoded by the Sex-determining Region Y (SRY) gene, which plays a major role in ... and activate transcription of plant genes that aid in bacterial infection. TAL effectors contain a central repeat region in ...
Locus of enterocyte effacement-encoded regulator
"Transcriptional regulation of type III secretion genes in enteropathogenic Escherichia coli: Ler antagonizes H-NS-dependent ... The locus of enterocyte effacement-encoded regulator (Ler) is a regulatory protein that controls bacterial pathogenicity of ... "A Positive Regulatory Loop Controls Expression of the Locus of Enterocyte Effacement-Encoded Regulators Ler and GrlA". Journal ... The transcript encoding the Ler protein is the open reading frame 1 on the LEE1 operon. The mechanism of Ler regulation ...
284(5412): p. 271-3. Ghosh, S., Regulation of inducible gene expression by the transcription fact or NF-kappaB. Immunol Res, ... Budde, L.M. and S. Ghosh, Cloning and characterisation of the gene encoding mouse IkappaBbeta. Gene, 2000. 247(1-2): p. 279-86 ... 2(2): p. 253-8. Zhong, H., R.E. Voll, and S. Ghosh, Phosphorylation of NF-kappa B p65 by PKA stimula tes transcriptional ... Zhang, G. and S. Ghosh, Molecular mechanisms of NF-kappaB activation induced by bacterial lipopolysaccharide through Toll-like ...
It is an example of repressible negative regulation of gene expression. Within the operon's regulatory sequence, the operator ... 394-402 Yanofsky, C (1981). "Attenuation in the control of expression of bacterial operons". Nature. 289: 751-758. doi:10.1038/ ... which encode tryptophan synthetase. It also contains a repressive regulator gene called trp R. trp R has a promoter where RNA ... The functional importance of the 2nd hairpin for the transcriptional termination is illustrated by the reduced transcription ...
Timeless - The tim gene encodes for the TIM protein that is critical in circadian regulation in Drosophila. Its protein levels ... the leading example of bacterial circadian rhythms. Kai proteins regulate genome wide gene expression. The oscillation of ... The heterodimer enters the nucleus in order to inhibit the CLOCK-CYCLE heterodimer which acts as a transcriptional activator ... Oscillating genes include both core clock component genes and output genes. A core clock component gene is a gene necessary for ...
Robert O. J. Weinzierl (1999). Mechanisms of Gene Expression: Structure, Function and Evolution of the Basal Transcriptional ... which are encoded by homeobox genes, are transcription factors. Homeodomain proteins play critical roles in the regulation of ... and activate transcription of plant genes that aid in bacterial infection. TAL effectors contain a central repeat region in ... gene expression - the process by which information from a gene is used in the synthesis of a functional gene product such as a ...
Amino acid synthesis
Maas WK (1991). "The regulation of arginine biosynthesis: its contribution to understanding the control of gene expression". ... Arginine synthesis also utilizes negative feedback as well as repression through a repressor encoded by the gene argR. The gene ... MetR transcriptional activity is regulated by homocystein, which is the metabolic precursor of methionine. It is also known ... Finally, DAP decarboxylase LysA mediates the last step of the lysine synthesis and is common for all studied bacterial species ...
The transcriptional factor OxyR regulates the expression of OxyR regulon. H2O2 oxidizes the transcriptional factor by forming ... Small changes in cellular oxidant status can be sensed by specific proteins which regulate a set of genes encoding antioxidant ... Regulation of the soxRS regulon occurs by a two-stage process: the SoxR protein is first converted to an oxidized form that ... The complexity in bacterial responses appears to be in the number of proteins induced by oxidative stress. In mammalian cells, ...
The gcvB RNA gene encodes a small non-coding RNA involved in the regulation of a number of amino acid transport systems as well ... Urbanowski ML, Stauffer LT, Stauffer GV (August 2000). "The gcvB gene encodes a small untranslated RNA involved in expression ... Yang, Q; Figueroa-Bossi, N; Bossi, L (Jan 2014). "Translation Enhancing ACA Motifs and Their Silencing by a Bacterial Small ... Coornaert, A; Chiaruttini, C; Springer, M; Guillier, M (Jan 2013). "Post-Transcriptional Control of the Escherichia coli PhoQ- ...
When expression of those transcription factors is altered, transcriptional repressors of E-cadherin were overexpressed in tumor ... In order to study the epigenetic regulation of E-cadherin, M Lombaerts et al. performed a genome wide expression study on 27 ... or uvomorulin is a protein that in humans is encoded by the CDH1 gene. CDH1 has also been designated as CD324 (cluster of ... The ectodomain of this protein mediates bacterial adhesion to mammalian cells, and the cytoplasmic domain is required for ...
Further speculation suggests the simpler RNA thermometer method of gene regulation may have evolved prior to the more complex ... Like other RNA thermometers, FourU is not solely responsible for temperature-dependent expression of its adjacent gene. Instead ... At human body temperature, the thermometer structure opens and to allow transcriptional activator protein ToxT translation, ... Shine, J.; Dalgarno, L. (1975). "Determinant of cistron specificity in bacterial ribosomes". Nature. 254 (5495): 34-8. doi: ...
History of RNA biology
In this way, gene expression can be dramatically regulated at the post-transcriptional level. Another previously unknown ... but still have high biological significance for gene expression and its regulation. Telomerase is an enzyme that is present in ... untranslated region of a vast number of bacterial mRNA molecules, have a profound effect on gene expression through a ... The end result of alternative splicing is that a single gene can encode a number of different protein isoforms that can exhibit ...
AMP deaminase 2
1996). "Cloning, sequence and characterization of the human AMPD2 gene: evidence for transcriptional regulation by two closely ... gene expression reveals alternative transcripts encoding variable N-terminal extensions of isoform L". Biochem. J. 312 (Pt 2): ... Sequence and bacterial expression of human AMPD2 cDNA". J. Biol. Chem. 267 (31): 22407-13. PMID 1429593. Van den Bergh F, ... AMP deaminase 2 is an enzyme that in humans is encoded by the AMPD2 gene. GRCh38: Ensembl release 89: ENSG00000116337 - Ensembl ...
"Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora". Molecular Biology ... Tic56 is also a nuclear encoded protein. The preprotein its gene encodes is 527 amino acids long, weighing close to 62 thousand ... The chloroplast is mostly under nuclear control, though chloroplasts can also give out signals regulating gene expression in ... compact genomes and genes of bacterial origin". BMC Genomics. 16 (1): 204. doi:10.1186/s12864-015-1418-3. PMC 4487195. PMID ...
In mammals, microRNAs (miRNAs) regulate about 60% of the transcriptional activity of protein-encoding genes. Some miRNAs ... Table 1. RAD51 expression in sporadic cancers. Cancer. Over or Under expression. Frequency of altered expression. Evaluation ... a role for p53/activator protein 2 transcriptional regulation". Mol. Cancer Ther. 6 (5): 1650-60. doi:10.1158/1535-7163.MCT-06- ... RAD51 family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51. The protein is highly conserved ...
Ng SY; Chaban B; Jarrell KF (2006). "Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and ... it is estimated to contain only 537 protein-encoding genes. Smaller independent pieces of DNA, called plasmids, are also ... while most genes involved in genome expression are common between Archaea and Eukarya. Within prokaryotes, archaeal cell ... Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are ...
Mutations in maize promoters affect the expression of the promoter genes in a plant-organ-specific manner. A duplication of ... Transcription (Bacterial, Eukaryotic). Transcriptional regulation. prokaryotic. *Operon *lac operon. *trp operon. *gab operon ... MicroRNAs also play a role in replicating viruses such as HIV-1. Novel HIV-1-encoded microRNA have been found to enhance ... Gene transcription by RNA polymerase II depends on the regulation of the core promoter by long-range regulatory elements such ...
Regulation. *Epigenetic *imprinting. *Transcriptional *Gene regulatory network. *cis-regulatory element. *lac operon ... This is the third position of an isoleucine codon: AUU, AUC, or AUA all encode isoleucine, but AUG encodes methionine. In ... Gene expression. Introduction. to genetics. *Genetic code. *Central dogma *DNA → RNA → Protein ... The codons encoding one amino acid may differ in any of their three positions; however, more often than not, this difference is ...
regulation of canonical Wnt signaling pathway. • cellular response to molecule of bacterial origin. • positive regulation of ... Frizzled-5 is a protein that in humans is encoded by the FZD5 gene. ... Katoh Y, Katoh M (2007). "Conserved POU-binding site linked to SP1-binding site within FZD5 promoter: Transcriptional ... More reference expression data. Gene ontology. Molecular function. • amyloid-beta binding. • signal transducer activity. • Wnt- ...
... the regulation of gene expression, and responses to oxidative stress. The importance of proteolytic degradation inside cells ... The genes encoding ubiquitin in eukaryotes are arranged in tandem repeats, possibly due to the heavy transcription demands on ... Some prokaryotes, including many archaea and the bacterial order Actinomycetales, also share homologs of the 20S proteasome, ... "Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators". The EMBO Journal. 24 (10 ...
Morris KL (2008). "Epigenetic Regulation of Gene Expression". RNA and the Regulation of Gene Expression: A Hidden Layer of ... Small interfering RNAs can modulate transcriptional gene expression via epigenetic modulation of targeted promoters. ... "Epigenetic gene regulation in the bacterial world". Microbiol. Mol. Biol. Rev. 70 (3): 830-56. PMC 1594586 . PMID 16959970. doi ... through the transcription factor activity of the proteins they encode. RNA signalling includes differential recruitment of a ...
"Transcriptional regulation of transferrin and albumin genes by retinoic acid in human hepatoma cell line Hep3B". The ... Bowman BH, Yang FM, Adrian GS (1989). "Transferrin: evolution and genetic regulation of expression". Advances in Genetics. ... Human transferrin is encoded by the TF gene. Transferrin glycoproteins bind iron tightly, but reversibly. Although iron ... It is found in the mucosa and binds iron, thus creating an environment low in free iron that impedes bacterial survival in a ...
Several roles in gene expression have been attributed to the untranslated regions, including mRNA stability, mRNA localization ... Katz L, Burge CB (September 2003), "Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes ... Each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. This process of ... Spatial regulation of bold beta-actin translation by Src-dependent phosphorylation of ZBP1 Nature04115. ...
Gene expression in prokaryotes is influenced by an RNA-based system similar in some respects to RNAi. Here, RNA-encoding genes ... SiRNA acts on the post-transcriptional stage of gene expression, so it does not modify or change DNA in a deleterious effect.[ ... of Arabidopsis was shown to be involved in the regulation of several genes that control plant shape. In plants, the ... "Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction" ...
Interferencia de ARN, a enciclopedia libre
"Inhibition of gene expression in plant cells by expression of antisense RNA". Proc Natl Acad Sci USA 83 (15): 5372-5376. PMC ... Guo S, Kemphues K (1995). "par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr ... Hammond S, Bernstein E, Beach D, Hannon G (2000). "An RNA-directed nuclease mediates post-transcriptional gene silencing in ... "Translational repression is sufficient for gene silencing by bacterial small noncoding RNAs in the absence of mRNA destruction" ...
Transcriptional regulation. LDH undergoes transcriptional regulation by PGC-1α. PGC-1α regulates LDH by decreasing LDH A ... The M and H subunits are encoded by two different genes:. *The M subunit is encoded by LDHA, located on chromosome 11p15.4 ( ... Expression of LDH5 and VEGF in tumors and the stroma has been found to be a strong prognostic factor for diffuse or mixed-type ... High levels of lactate dehydrogenase in cerebrospinal fluid are often associated with bacterial meningitis. In the case of ...
When expression of those transcription factors is altered, transcriptional repressors of E-cadherin were overexpressed in tumor ... In order to study the epigenetic regulation of E-cadherin, M Lombaerts et al. performed a genome wide expression study on 27 ... or uvomorulin is a protein that in humans is encoded by the CDH1 gene. CDH1 has also been designated as CD324 (cluster of ... The ectodomain of this protein mediates bacterial adhesion to mammalian cells, and the cytoplasmic domain is required for ...
... is a competitive inhibitor of the HIS3-gene product and may be used to titrate the minimum level of HIS3 expression required ... Bacterial E. coli-based two hybrid methods (abbreviated as B2H) have several characteristics that may make them preferable to ... Lu L, Horstmann H, Ng C, Hong W (December 2001). "Regulation of Golgi structure and function by ARF-like protein 1 (Arl1)". ... In this context, a library may consist of a collection of protein-encoding sequences that represent all the proteins expressed ...
Genes. The polypeptides composing the multi-subunit ACCs of prokaryotes and plants are encoded by distinct genes. In ... controlled by insulin at the transcriptional level, and ChREBP, which increases in expression with high carbohydrates diets.[13 ... Barber MC, Price NT, Travers MT (March 2005). "Structure and regulation of acetyl-CoA carboxylase genes of metazoa". Biochimica ... to take advantage of structural differences between bacterial and human ACCs to create antibiotics specific to the bacterial ...
Iuchi S, Lin EC (1993). "Adaptation of Escherichia coli to redox environments by gene expression". Mol. Microbiol. 9 (1): 9-15 ... Unden G, Bongaerts J (1997). "Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation ... The genes that encode the individual proteins are contained in both the cell nucleus and the mitochondrial genome, as is the ... Dimroth P (1994). "Bacterial sodium ion-coupled energetics". Antonie van Leeuwenhoek. 65 (4): 381-95. doi:10.1007/BF00872221. ...
Emerging New Roles for an Ancient RNA in the Regulation of Gene Expression". Life (Basel). 5: 1638-1651. doi:10.3390/ ... there are 497 nuclear genes encoding cytoplasmic tRNA molecules, and 324 tRNA-derived pseudogenes-tRNA genes thought to be no ... "Tertiary structure of bacterial selenocysteine tRNA". Nucleic Acids Research. 41 (13): 6729-6738. doi:10.1093/nar/gkt321. PMC ... "A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs". Nucleic Acids Research. 42 (11 ...
Tomilin N. V. (2008). "Regulation of mammalian gene expression by retroelements and non-coding tandem repeats". BioEssays. 30 ( ... on the expression of many genes. Length changes in bacterial SSRs can affect fimbriae formation in Haemophilus ... In mammals, 20% to 40% of proteins contain repeating sequences of amino acids encoded by short sequence repeats. Most of ... 2007). "The correlated evolution of Runx2 tandem repeats, transcriptional activity, and facial length in Carnivora". Evol. Dev ...
The vestigial gene acts to regulate the expression of the wing imaginal discs in the embryo and acts with other genes to ... It is caused by mutations in the gene WRN that encodes a protein with essential roles in repair of DNA damage. Mutations in the ... The gene network (transcriptional and protein interactions) governing the early development of the fruit fly embryo is one of ... The transposable P elements, also known as transposons, are segments of bacterial DNA that are transferred into the fly genome ...
T helper cell
Hu, Wanchung (2007). Microarray analysis of PBMC gene expression profiles after Plasmodium falciparum malarial infection (Ph.D ... Richard Armitage at Immunex cloned a cDNA encoding CD154 by screening an expression library with CD40-Ig. Randolph Noelle at ... All of these complications result in an increased susceptibility to aggressive bacterial infections, especially in areas of the ... "GATA3: a master of many trades in immune regulation". Trends in Immunology. 35 (6): 233-42. doi:10.1016/j.it.2014.04.002. PMC ...
Regulation of expression and function of P-gp in cancer cellsEdit. At transcriptional level, the expression of P-gp has been ... P-gp is a glycoprotein that in humans is encoded by the ABCB1 gene. P-gp is a well-characterized ABC-transporter (which ... The structure of mouse P-gp is similar to structures of the bacterial ABC transporter MsbA (3B5W and 3B5X) that adopt an ... regulation of response to osmotic stress. • positive regulation of anion channel activity. • regulation of chloride transport. ...
Vasoactive intestinal peptide
"Structure and expression of the gene encoding the vasoactive intestinal peptide precursor". Proceedings of the National Academy ... negative regulation of smooth muscle cell proliferation. • regulation of sensory perception of pain. • positive regulation of ... expression of the prohormone in bacterial cells". Peptides. 6 Suppl 1 (Suppl 1): 95-102. doi:10.1016/0196-9781(85)90016-6. PMID ... The PKA then activates other intracellular signaling pathways like the phosphorylation of CREB and other transcriptional ...
... which express bacterial salicylate hydroxylase, nahG gene, requires the accumulation of SA for its expression  ... Much work has been done to assign functions to its 27,000 genes and the 35,000 proteins they encode. Post-genomic research ... A. thaliana has been instrumental in dissecting these pathways to better understand the regulation of immune responses, the ... Arabidopsis transcriptional regulatory map. *The Arabidopsis Information Resource (TAIR). *Salk Institute Genomic Analysis ...
Gene expression first involves transcription, in which DNA is used as a template to produce RNA. In the case of genes encoding ... where it forms a transcriptional repressor complex with nuclear proteins to reduce the expression of genes involved in ... implications on cell survival and regulation of lamins A/C expression". The Journal of Cell Biology. 153 (3): 621-6. doi: ... support a bacterial origin for the eukaryotic cell. ... This prevents even low levels of inappropriate gene expression ...
Not listed here are the many kinds of cancers involving aberrant transcriptional regulation owing to creation of chimeric genes ... to drive gene expression in defined brain regions of therapeutic interests.. *ENCODE threads Explorer RNA and chromatin ... Bacterial. In bacteria, the promoter contains two short sequence elements approximately 10 (Pribnow Box) and 35 ... ends of the genes in a bidirectional gene pair. A "bidirectional gene pair" refers to two adjacent genes coded on opposite ...
... which are involved in the regulation of gene expression. ... ENCODE threads explorer ENCODE home page. Nature. *Double Helix ... Myers LC, Kornberg RD (2000). "Mediator of transcriptional regulation". Annual Review of Biochemistry. 69: 729-49. doi:10.1146/ ... "Bacterial gene transfer by natural genetic transformation in the environment". Microbiological Reviews. 58 (3): 563-602. doi: ... In bacteria, this overlap may be involved in the regulation of gene transcription, while in viruses, overlapping genes ...
For nuclear-encoded genes, splicing takes place within the nucleus either during or immediately after transcription. For those ... Differential expression levels across tissues and cell lineages allowed computational approaches to be developed to predict the ... "Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but ... a segment of DNA that is located between two exons of a gene. The term intron refers to both the DNA sequence within a gene and ...
They are involved in a range of processes, like post-transcriptional regulation of gene expression, genomic imprinting, and ... "A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity". Science. 337 (6096): 816-821. doi:10.1126/ ... and inability to distinguish lncRNA function from other confounding factors like cryptically encoded peptides or functional DNA ... effects on gene regulation and chromatin states, as well as specific regulation of certain genes for investigation of gene ...
Multi-Omics Profiling Expression Database: MOPED human and model organism protein/gene knowledge and expression data ... The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In ... Most organisms then process the pre-mRNA (also known as a primary transcript) using various forms of Post-transcriptional ... Samarin S, Nusrat A (2009). "Regulation of epithelial apical junctional complex by Rho family GTPases". Frontiers in Bioscience ...
Protocols and Video Articles Authored by Christopher F. Schuster
Fluorescence Based Primer Extension Technique to Determine Transcriptional Starting Points and Cleavage Sites of RNases In Vivo ... Post-transcriptional Regulation of Gene Expression in Bacterial Pathogens by Toxin-antitoxin Systems Frontiers in Cellular and ... Heterologous expression of the putative toxin-encoding mazF(seq) gene imposed growth cessation but not cell death on ... most of them influence transcriptional and post-transcriptional gene regulation. Antitoxin proteins often act as DNA binding ...
σ54 Enhancer Binding Proteins and Myxococcus xanthus Fruiting Body Development | Journal of Bacteriology
The transcriptional regulation of bacterial gene expression often employs regulatory proteins that act upon RNA polymerase. ... showed increased expression at 12 h of development (Table 1). The level of expression of the dsg gene, which encodes ... Chemosensory regulation of developmental gene expression in Myxococcus xanthus. Proc. Natl. Acad. Sci. USA 100:2008-2013. ... Regulation of expression of the pilA gene in Myxococcus xanthus. J. Bacteriol. 179:7748-7758. ...
Faculty Research Page | Department of Molecular & Cell Biology
Regulation of virulence gene expression. L. monocytogenes lives a biphasic lifestyle that includes growth in the environment, ... Most recently, we identified an 8-gene locus that encodes a flavin-based extracellular electron transport system that makes L. ... Importantly, we have also found these genes in 100s of other bacterial species including members of the intestinal microbiota. ... Most determinants of pathogenesis are controlled by the master virulence transcriptional regulator. We recently found that ...
Characterization and application of endogenous phase-dependent promoters in Bacillus subtilis | SpringerLink
Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol 9(1):395-408Google ... Geissendorfer M, Hillen W (1990) Regulated expression of heterologous genes in Bacillus subtilis using the Tn10 encoded tet ... Yansura DG, Henner DJ (1984) Use of the Escherichia coli lac repressor and operator to control gene expression in Bacillus ... Sierro N, Makita Y, de Hoon M, Nakai K (2008) DBTBS: a database of transcriptional regulation in Bacillus subtilis containing ...
Co-ordinate regulation of Salmonella typhimurium invasion genes by environmental and regulatory factors is mediated by control...
We report here that the expression of six different S. typhimurium invasion genes encoded on SPI1 (Salmonella pathogenicity ... HilA is a transcriptional activator of the OmpR/ToxR family that is also encoded on SPI1. We have found that HilA plays a ... several environmental and regulatory conditions modulate the expression of invasion factors required for bacterial entry into ... Co-ordinate regulation of Salmonella typhimurium invasion genes by environmental and regulatory factors is mediated by control ...
The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium...
... of the regulation of gene expression but will also provide the basis for comprehensive modeling of transcriptional regulatory ... A collection of 127 DNA-binding transcriptional regulators was identified in the C. glutamicum ATCC 13032 genome, whereas 103 ... The common set of DNA-binding transcriptional regulators present in the four corynebacterial genomes consists of 28 proteins ... This work describes characteristic features of a set of conserved DNA-binding transcriptional regulators present within the ...
Coordinate regulation of bacterial virulence genes by a novel adenylate cyclase-dependent signaling pathway. - PubMed - NCBI
The transcriptional response of known TTSS genes indicates a hierarchical pattern of expression in which a set of secretion ... Further analysis of genes coordinately regulated with those encoding the TTSS led to the identification of a signaling pathway ... Coordinate regulation of bacterial virulence genes by a novel adenylate cyclase-dependent signaling pathway.. Wolfgang MC1, Lee ... Type III secretion systems (TTSSs) are utilized by numerous bacterial pathogens to inject effector proteins directly into host ...
Overexpression of the Multidrug Efflux Pumps MexCD-OprJ and MexEF-OprN Is Associated with a Reduction of Type III Secretion in...
Drug Resistance, Multiple, Bacterial. Gene Expression Regulation, Bacterial. Membrane Transport Proteins. Pseudomonas ... a gene encoding a histidine transporter, is associated with a decrease in the expression of the T3S gene exoS (41). The mutant ... To analyze the mutations present in the transcriptional regulators of MDR pumps, the mexR, nfxB, mexT, and mexZ genes were PCR ... and the expression of genes encoding T3S factors was measured by semiquantitative RT-PCR. Expression of rpsL (constitutive ...
Impact of AmpC Derepression on Fitness and Virulence: the Mechanism or the Pathway? | mBio
Multiple genes are involved in the regulation of ampC expression, a process that is intimately linked to peptidoglycan ... Expression of transcriptional regulator AmpR in selected strains determined through RT-PCR, following the protocols described ... Bacterial strains and plasmids.A list and description of the bacterial strains and plasmids used in this work are shown in ... the level of expression of exoS, encoding a key cytotoxin secreted by the TTSS, was 1.9-fold lower in the triple ampD mutant ...
Landscape of Resistance-Nodulation-Cell Division (RND)-Type Efflux Pumps in Enterobacter cloacae Complex | Antimicrobial Agents...
... established that the expression of genes encoding efflux pumps is under tight regulation involving different transcriptional ... Molecular properties of bacterial multidrug transporters. Microbiol Mol Biol Rev 64:672-693. doi:10.1128/MMBR.64.4.672-693.2000 ... All ECC strains naturally possess the cephalosporinase-encoding ampC gene, the expression of which can be induced by some β- ... Expression of homologous RND efflux pump genes is dependent upon AcrB expression: implications for efflux and virulence ...
New levels of sophistication in the transcriptional landscape of bacteria | Genome Biology | Full Text
An extra layer of complexity in the regulation of gene expression in bacteria is now apparent through previously unanticipated ... Most bacterial noncoding RNAs, however, are thought to have roles in the post-transcriptional regulation of gene expression, ... Regulation by antisense RNA (asRNA). (c) Regulation by trans-encoded sRNA. Circled P, promoter; circled S, environmental or ... Winkler WC, Breaker RR: Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol. 2005, 59: 487-517. 10.1146 ...
Dissecting specific and global transcriptional regulation of bacterial gene expression | Molecular Systems Biology
By focusing on one enzyme‐encoding and two TF genes, a recent paper postulates predominance of global regulation in central ... A model for specific and global regulation of bacterial gene expression. Here, we present a model of bacterial gene expression ... Dissecting specific and global transcriptional regulation of bacterial gene expression. Luca Gerosa, Karl Kochanowski, Matthias ... Superimposed to global transcriptional regulation that effects essentially all genes is specific regulation of genes through ...
Frontiers | Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida |...
Relevant targets include genes encoding proteins involved in signal transduction and regulation, metabolism, transport and ... Relevant targets include genes encoding proteins involved in signal transduction and regulation, metabolism, transport and ... It offers a broad overview of the network of processes subjected to this type of regulation and opens the way to define what ... It offers a broad overview of the network of processes subjected to this type of regulation and opens the way to define what ...
Frontiers | Nitric Oxide Mediated Transcriptome Profiling Reveals Activation of Multiple Regulatory Pathways in Arabidopsis...
... with at least 2-folds change in expression after CysNO treatment. Expression patterns of selected genes involved in various ... CysNO infiltration caused differential expression of 6,436 genes (3,448 up-regulated and 2,988 down-regulated) and 6,214 ... CysNO infiltration caused differential expression of 6,436 genes (3,448 up-regulated and 2,988 down-regulated) and 6,214 ... These differentially expressed genes were found to be involved in key physiological processes, including plant defense against ...
Gene Expression Profiling of Helicobacter pylori Reveals a Growth-Phase-Dependent Switch in Virulence Gene Expression |...
In S. enterica serovar Typhimurium, the transcriptional regulation of bacterial flagella has been shown to be composed of an ... genes encoding transport and binding proteins; and genes involved in energy metabolism. The gene showing the greatest reduction ... Operon structure and gene regulation.In most bacteria, the expression of genes carried by multicistronic units is coordinately ... The H. pylori regulatory genes.The apparent coordinated temporal regulation of gene expression found in these TCs suggests that ...
Distribution of Genes Encoding Nucleoid-Associated Protein Homologs in Plasmids
Bacterial nucleoid-associated proteins (NAPs) form nucleoprotein complexes and influence the expression of genes. Recent ... which play important roles in transcriptional regulation networks between plasmids and host chromosomes. In this study, we ... Distribution of Genes Encoding Nucleoid-Associated Protein Homologs in Plasmids. Toshiharu Takeda,1 Choong-Soo Yun,1,2 Masaki ... Plasmids with H-NS gene homologs had less G+C content. It should be noted that plasmids with the NAP gene homolog also carried ...
Genetically engineered light sensors for control of bacterial gene expression
... but with a focus on transcriptional regulation. First, to enable the development and characterization of promoters in different ... Fully genetically encoded light sensors take advantage of the favorable characteristics of light, do not need the ... Herein, we review engineered light-sensor systems with potential for in vivo regulation of gene expression in bacteria, and ... Genetically engineered light sensors for control of bacterial gene expression. Camsund, Daniel Uppsala University, Disciplinary ...
Transcriptional and biochemical regulation of a novel Arabidopsis thaliana bifunctional aspartate kinase-homoserine...
... and biochemical regulation of a novel Arabidopsis thaliana bifunctional aspartate kinase-homoserine dehydrogenase gene isolated ... Cloning and expression of an Arabidopsis thaliana cDNA encoding a monofunctional aspartate kinase homologous to the lysine- ... Concerted regulation of lysine and threonine synthesis in tobacco plants expressing bacter-ial feedback-insensitive aspartate ... Expression of an aspartate kinase homoserine dehydroge-nase gene is subject to specific spatial and temporal regulation in ...
MtrR control of a transcriptional regulatory pathway in Neisseria meningitidis that influences expression of a gene (nadA)...
Gene Expression Regulation, Bacterial* Actions. * Search in PubMed * Search in MeSH * Add to Search ... encoding a vaccine candidate Jason M Cloward et al. PLoS One. 2013. ... Transcriptional regulation of the nadA gene in Neisseria meningitidis impacts the prediction of coverage of a multicomponent ... MtrR control of a transcriptional regulatory pathway in Neisseria meningitidis that influences expression of a gene (nadA) ...
PPT - L1 The lac operon L2 The trp operon L3 Transcriptional regulation by PowerPoint Presentation - ID:6150074
L1 The lac operon L2 The trp operon L3 Transcriptional regulation by alternative σ factors. Molecular Biology. L1:The LAC ... Initially, early genes are expressed by normal bacterial holoenzyme. Among these early genes is the gene encoding σ28, which ... Regulation of Gene Expression - 11. regulation of gene expression. chapter 11 regulation of gene expression. key ... Regulation of gene expression prokaryotes eukaryotes gene activity is regulated - Regulation of gene expression ...
Sankar Adhya, Ph.D. | Center for Cancer Research - National Cancer Institute
Adhya and his team have demonstrated transcriptional regulation both at the level of initiation by activators and repressors ... Transcription is the major target of regulation of gene expression. Our research interest covers modulation of transcription by ... We have demonstrated transcriptional regulation both at the level of initiation by activators and repressors and at the level ... well as to the function of poles in the ability of bacterial cells to communicate with their environment and in gene regulation ...
Abstract 985: BAC Transgenic Analysis of the Smooth Muscle Calponin Gene | Circulation
... of CNN1 is replaced with a bacterial selection gene (galK) reveal complete loss of human CNN1 expression in vascular SMC, with ... and growth regulation. While CNN1s physiology has been studied extensively, its transcriptional regulation has proven to be ... The smooth muscle calponin gene (CNN1) encodes for a multifunctional protein involved in signaling, contractile force ... Regulatory elements controlling gene expression are often found in separate, sometimes remote, regions around gene loci. ...
Selection for in vivo regulators of bacterial virulence | PNAS
RIVET relies on the construction of transcriptional fusions to a promoterless reporter gene, tnpR, encoding a site-specific DNA ... The added regulation afforded by CheZ and VieS may be needed to tightly control the expression of CT with respect to timing and ... Also of the latter class are four genes encoding putative bacterial chemotaxis components, cheA-2 and cheY-3, which encode the ... we recently found that the patterns of transcriptional induction of genes encoding CT and TCP fundamentally differ during in ...
Cyclic Diguanylate Regulates Vibrio cholerae Virulence Gene Expression | Infection and Immunity
Molecular cloning and transcriptional regulation of ompT, a ToxR-repressed gene in Vibrio cholerae. Mol. Microbiol. 35:189-203. ... which encodes a positive regulator that is necessary for vps gene expression (56). This mutation abrogates vps gene expression ... It is possible that regulation of virulence by c-diGMP will become a common theme in pathogenic bacterial species. ... Virulence gene expression in V. cholerae is regulated by a complex cascade of transcriptional activators. Here we show that in ...
Gary Schoolnik | Stanford Medicine Profiles
Gene expression profiling of 15 unique conditions identified differential regulation of 128 of the 169 PE/PPE genes. Expression ... based on fusions to the phoA bacterial reporter gene, was used to identify Mycobacterium tuberculosis genes that encode ... Other genes under sigma(H) control encode transcriptional regulators such as sigB, sigE, and sigH itself. ... Among these, 14 genes may encode novel secreted proteins. Six of the remaining 12 genes were predicted to encode membrane ...
A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution...
... results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression. ... This includes the identification of new layers of transcriptional complexity associated with several key regulators of ... secondary metabolism and morphological development in S. coelicolor and the identification of host-encoded leaderless mRNA and ... A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution ...
Overexpression of Pti5 in Tomato Potentiates Pathogen-Induced Defense Gene Expression and Enhances Disease Resistance to...
The results demonstrate a positive role of Pti5 in defense gene regulation and disease resistance and suggest that a pathogen- ... The tomato Pti5 gene encodes a pathogen-inducible ethylene response element-binding protein-like transcription factor that ... Overexpression of Pti5 or Pti5-VP16, a translational fusion with a constitutive transcriptional activation domain, in tomato ... Additional keywords: bacterial infection, GCC box, general resistance, transgenic plants. Page Content ...
Campylobacter jejuni dsb gene expression is regulated by iron in a Fur-dependent manner and by a translational coupling...
Fur involvement in dsb gene regulation was proven by a reporter gene study in a C. jejuni wild type strain and its isogenic fur ... In the C. jejuni 81-176 genome, the dsb genes of the oxidative pathway are arranged in three transcriptional units: dsbA2-dsbB- ... This protein modification plays an important role in bacterial pathogenesis, and is facilitated by the Dsb (disulfide bond) ... The dba expression is not only essential for the translation of the downstream dsbI gene, but also Dba protein that is produced ...
A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for...
The members of this complex subfamily are possibly involved in the regulation of the expression of proteins taking part in ... Genes encoding MocR proteins were localized in their respective genomes, and the intergenic regions putatively involved in the ... A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for ... R. Münch, K. Hiller, H. Barg et al., "PRODORIC: prokaryotic database of gene regulation," Nucleic Acids Research, vol. 31, no. ...
Bacterial one-hybrid system - Wikipedia
Across all living organisms, regulation of gene expression is controlled by interactions between DNA-binding regulatory ... Literature suggests that nearly 8% of human genes encode transcription factors and the functions and specificities of their ... transcription factors fine-tune transcriptional levels by stabilizing/destabilizing binding of RNA polymerase to a genes ... drives expression of downstream reporter genes. This reporter region facilitates both positive and negative selection by HIS3 ...
GenomeRepressorPathogenesisSalmonellaBiosynthesisMechanismsSpeciesStrainsActivatorRecycling pathwaysPlasmidsVirulence gene expressionGlobal transcriptionalGeneticColonizationInducesEndogenousAntibiotic resistanceVivoRegulates the expressionAnalyzed the transcriptional responseInfectionsBacillusNucleotideRNAsOperonsPlasmidConstitutiveUpstreamPathogenicityMechanismDifferentialDifferentially expressedColiSigmaPatternsResponses
- Upon completion and annotation of the nucleotide sequence of a bacterial genome, a great scientific challenge is to elucidate the regulation of expression of all the predicted genes and to deduce thereof the entirety of regulatory networks present in the respective microorganism. (biomedcentral.com)
- Using a whole-genome microarray, we investigated the conditions and regulatory factors that control the expression of the Pseudomonas aeruginosa TTSS. (nih.gov)
- This low susceptibility is mainly the consequence of the presence of several genes encoding multidrug resistance (MDR) efflux pumps in the genome of this bacterial species. (asm.org)
- the other those encoded in trans from their target gene, which are often located at completely unrelated positions on the genome, such as the canonical small RNAs (sRNA). (biomedcentral.com)
- After it is produced, TnpR functions in trans to permanently excise from the bacterial genome a tetracycline resistance (Tc R ) marker ( tet ) that is flanked by recombinase recognition sequences ( res ). (pnas.org)
- Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. (biomedcentral.com)
- The resulting regulatory network contains ~600 regulated genes per genome that are mostly involved in metabolism of carbohydrates, amino acids, fatty acids, vitamins, metals, and stress responses. (biomedcentral.com)
- We propose that transcriptional overshooting allows genome rebooting after horizontal gene transfer, and might have an adaptive role in overcoming the opposing demands of multilevel selection. (prolekare.cz)
- functions that are encoded in the plasmid genome. (prolekare.cz)
- The chloroplast genome of land plants contains only a single gene for a splicing factor, Maturase K (MatK). (plantphysiol.org)
- Two classes of genes dominate the chloroplast genome of land plants: those coding for components of the photosynthetic apparatus and those encoding components of the chloroplast gene expression system. (plantphysiol.org)
- The transcriptome of PsJN colonizing in vitro potato plants showed a broad array of functionalities encoded in the genome of strain PsJN. (sigmaaldrich.com)
- The genome of M . smegmatis contains a number of genes believed to be involved in nitrogen metabolism, but the real functions of the majority of them are still unknown. (nature.com)
- The heat-shock response of bacteria involves genome-wide changes in gene expression. (nih.gov)
- Expression of Novel Gene Content Drives Adaptation to Low Iron in the Cyanobacterium Acaryochloris Gallagher, Amy L;Miller, Scott R;Gojobori, Takashi 2018-05-29 00:00:00 Variation in genome content is a potent mechanism of microbial adaptation. (deepdyve.com)
- For example, the genome of Acaryochloris strain MBIC11017, which was isolated from an iron-limited environment, is enriched in duplicated and novel genes involved in iron assimilation. (deepdyve.com)
- rather, the maintenance of these duplicates in the MBIC11017 genome is likely due to the sharing of ancestral dosage by expression reduction. (deepdyve.com)
- The study provides insights on the mechanisms of adaptive genome evolution and gene expression in Acaryochloris. (deepdyve.com)
- 2008), temperature stress genome, including gene duplication (Andersson and (Riehle et al. (deepdyve.com)
- 2012). As a result, the relative contributions of the acquisition of novel genes by HGT (i.e., the ﬂexible both duplication and HGT mechanisms within the same genome) for microbial adaptation to environmental genome during adaptation are not clear. (deepdyve.com)
- CT is an adenosine diphosphate-ribosylating toxin encoded in the genome of the filamentous, lysogenic CTXΦ phage. (sciencemag.org)
- This plasticity is a consequence not only of spontaneous mutations or genome rearrangements that can occur during the bacterial life cycle, but also of exogenous gene acquisition through genetic exchange between bacteria and gene capture in integrons. (mdpi.com)
- Still, the transcriptional repressor HrcA (heat regulation at CIRCE [controlling inverted repeat of chaperone expression]) is predicted in the M. genitalium genome as well as three copies of its corresponding regulatory sequence CIRCE. (uthscsa.edu)
- The identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. (osti.gov)
- Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. (osti.gov)
- Next to new genome sequences from projects, surveillance programs in different countries have resulted in public availability of large collections of genome sequences of bacterial pathogens, but many of these genomes are not further analysed for possible virulence markers, antimicrobial resistance genes or possible vaccine candidates for relevant veterinary and zoonotic infections. (surrey.ac.uk)
- HspR acts as a transcriptional repressor for the members of the Hsp70 (DnaK) regulon, and HrcA similarly regulates the Hsp60 (GroE) response. (nih.gov)
- These two specific repressor circuits overlap with broader transcriptional changes mediated by alternative sigma factors during exposure to high temperatures. (nih.gov)
- Here, we describe the in planta function of CBNAC, a calmodulin-regulated NAC transcriptional repressor in Arabidopsis . (pubmedcentralcanada.ca)
- We hypothesize that the complex and co-ordinate regulation of Invasion genes by HilA is an important feature of salmonella pathogenesis and allows salmonellae to enter intestinal epithelial cells. (nih.gov)
- IMPORTANCE Understanding the impact of antibiotic resistance mechanisms on bacterial pathogenesis is critical to curb the spread of antibiotic resistance. (asm.org)
- Thus, the ability of C. jejuni to sense and respond to diverse environmental stimuli and to adapt gene expression to changes in external conditions is crucial for its pathogenesis, commensalism and survival outside the host organism. (biomedcentral.com)
- Our study has shown that IsrM sRNA functions as a pathogenicity island-encoded sRNA directly involved in Salmonella pathogenesis in animals. (prolekare.cz)
- Two hallmarks of Salmonella pathogenesis, i.e. host invasion and intracellular proliferation, correlate with the genes in Salmonella pathogenicity islands (SPIs), which are distinct, relatively large chromosomal regions harboring virulence genes and are commonly found in pathogenic strains , . (prolekare.cz)
- This interdependent relationship has limited our understanding of DksA-mediated functions in bacterial pathogenesis. (asm.org)
- Here, we demonstrate that each of these functions contributes to bacterial pathogenesis. (asm.org)
- Our observations highlight the importance of metabolic adaptation in bacterial pathogenesis and show the mechanism by which DksA orthologues are optimized to sense the levels of oxidative and nitrosative stress encountered in their natural habitats. (asm.org)
- Approximately 10% of the genes that answered these selections encode products that are known or thought to be involved in serovar Typhimurium pathogenesis. (asmscience.org)
- Thus, in vivo pathogenesis from a bacterial perspective is likely more dynamic. (cdc.gov)
- Our research interest is to understand signaling events that occur during bacterial disease pathogenesis. (seattlechildrens.org)
- Co-ordinate regulation of Salmonella typhimurium invasion genes by environmental and regulatory factors is mediated by control of hilA expression. (nih.gov)
- It has been proposed that when Salmonella typhimurium is present in the intestinal lumen, several environmental and regulatory conditions modulate the expression of invasion factors required for bacterial entry into host cells. (nih.gov)
- We report here that the expression of six different S. typhimurium invasion genes encoded on SPI1 (Salmonella pathogenicity island 1) is co-ordinately regulated by oxygen, osmolarity, pH, PhoPQ, and HilA. (nih.gov)
- Fourteen Salmonella typhimurium genes, which were under the control of at least four independent regulatory circuits, were identified to be selectively induced in host macrophages. (sciencemag.org)
- Numerous sRNAs identified in Salmonella are encoded by genes located at Salmonella pathogenicity islands (SPIs) that are commonly found in pathogenic strains. (prolekare.cz)
- In this study, we provide the first direct evidence that a pathogenicity island-encoded sRNA, IsrM, is important for Salmonella invasion of epithelial cells, intracellular replication inside macrophages, and virulence and colonization in mice. (prolekare.cz)
- Consequently, C2 DksA triggers transcriptional responses in Salmonella at levels of oxidative or nitrosative stress normally tolerated by Salmonella expressing C4 orthologues. (asm.org)
- Inappropriate transcriptional regulation by C2 DksA increases the susceptibility of Salmonella to the antimicrobial effects of hydrogen peroxide and nitric oxide, and attenuates virulence in macrophages and mice. (asm.org)
- Por tanto, los reguladores codificados por el hospedador que regulan la transferencia del plásmido de virulencia de Salmonella (pSLT) parecen ejercer funciones análogas en la conjugación mediada por R100. (isciii.es)
- Sequence, regulation, and functions of fis in Salmonella typhimurium. (ebi.ac.uk)
- 2) Humans possess a particular type of T-cell (gamma delta T- cell) that is activated by an intermediate of bacterial isoprenoid biosynthesis. (berkeley.edu)
- By applying our approach to arginine biosynthesis, we obtain a quantitative understanding of both specific and global regulation that allows accurate prediction of the temporal response to simultaneous perturbations in arginine availability and growth rate. (embopress.org)
- An experimental‐computational approach is applied to dissect the contribution of specific transcription factor‐mediated versus global growth‐dependent regulation to bacterial gene expression, and obtain a quantitative understanding of dynamic adaptations in arginine biosynthesis of E. coli . (embopress.org)
- We obtain a quantitative understanding of both specific and global regulation in arginine biosynthesis, as demonstrated by accurate model‐based predictions of complex transient gene‐expression responses to simultaneous perturbation in growth rate and arginine availability. (embopress.org)
- We uncover two principles of joint regulation of the arginine biosynthesis pathway: (i) specific regulation by repression dominates in steady metabolic states and (ii) global regulation sets the maximal expression reachable during transition between steady metabolic states. (embopress.org)
- Strong iron regulation was observed for previously identified genes involved in biosynthesis or uptake of the siderophores pyoverdine and pyochelin, utilization of heterologous siderophores and haem and ferrous iron transport. (nih.gov)
- Cmm infection also induced a subset of host genes involved in ethylene biosynthesis and response. (plantphysiol.org)
- Taken together, our results indicate that the essentiality of Gcp isn't attributable to its negative regulation of ILV biosynthesis in S. aureus. (biomedsearch.com)
- In this work, we review the mechanisms involved in the light-mediated regulation of carotenoid biosynthesis and the effect of light on the levels of expression of carotenogenic genes in higher plants. (scielo.cl)
- The molecular insight gained into the light-regulated expression of carotenoid genes will facilitate our understanding of the regulation of carotenoid biosynthesis. (scielo.cl)
- The RBP is organized in three transcriptional units, the major one containing ribD, ribE, ribA and ribH together with genes involved in functions not directly related to riboflavin biosynthesis such as nrdR and nusB . (biomedcentral.com)
- In addition, operons with RBP genes may also contain genes not directly related to riboflavin biosynthesis. (biomedcentral.com)
- However, little is known about the global mechanisms of gene expression regulation in H. pylori and how this expression is modified to cope with changes in the environment or to facilitate chronic infections in the stomach. (asm.org)
- There is, however, evidence that H. pylori uses other mechanisms of regulation. (asm.org)
- Overall the results illustrate the diversity in mechanisms used by different bacterial groups to facilitate and regulate gene expression. (surrey.ac.uk)
- To study mechanisms by which retroviral transgenes can transcribe to high levels, we used the MS2 system to visualize transcriptional dynamics of high expressing proviral integration sites in embryonic stem (ES) cells. (jove.com)
- The pilin structures and filament models have been instrumental in advancing our understanding of the molecular mechanisms driving pilus assembly and the role of Type IV pili in key bacterial functions such as immune evasion, microcolony formation and DNA uptake. (caister.com)
- However, the mechanisms of plant-endophyte communication and bacterial adaption to the plant environment are still poorly understood. (sigmaaldrich.com)
- Bacterial prokaryotes and eukaryotes employ transcriptional regulatory mechanisms to coordinate expression of genes involved in carbohydrate utilization. (genetics.org)
- To identify new regulatory mechanisms controlling GS activity, we performed a detailed expression analysis of the entire GS gene family of M. truncatula in the major organs of the plant, over a time course of nodule or seed development and during a diurnal cycle. (biomedcentral.com)
- This work provides a comprehensive overview of GS expression and regulation in the model legume M. truncatula , contributing to a better understanding of the specific function of individual isoenzymes and to the identification of novel organ-specific post-translational mechanisms of GS regulation. (biomedcentral.com)
- However, post-transcriptional mechanisms have also been shown ( 15 - 17 ). (aacrjournals.org)
- The regulation of CT and TCP expression has been studied extensively ( 2 ), but the mechanisms by which environmental signals stimulate virulence expression in vivo are not clear. (sciencemag.org)
- In this dissertation, I investigate the regulatory mechanisms used by B. subtilis to control the expression of the pks genes and the production of bacillaene. (tamu.edu)
- The origins of resistance are intensively studied and many mechanisms involved in resistance have been identified, such as exogenous gene acquisition by horizontal gene transfer (HGT), mutations in the targeted functions, and more recently, antibiotic tolerance through persistence. (mdpi.com)
- However, the regulatory mechanisms of plastid gene expression (PGE) are mediated by intricate plastid-nuclear interactions and are still far from being fully understood. (doabooks.org)
- In the introduction to this Theme Issue, we start by defining the general properties of transcriptional enhancers, such as modularity and the coexistence of tight sequence conservation with transcription factor-binding site shuffling as different mechanisms that maintain the enhancer grammar over evolutionary time. (royalsocietypublishing.org)
- The regulatory mechanisms and correlation of the process of regulation of gene expression and flagellum assembly known from the literature are described. (msu.ru)
- Importantly, we have also found these genes in 100s of other bacterial species including members of the intestinal microbiota. (berkeley.edu)
- The cyclic dinucleotide second messenger cyclic diguanylate (c-diGMP) has been implicated in regulation of cell surface properties in several bacterial species, including Vibrio cholerae . (asm.org)
- Cyclic diguanylate (c-diGMP) [bis(3′,5′)-cyclic diguanylic acid] is a prokaryotic cyclic dinucleotide second messenger that has been implicated in controlling properties of the cell surface in diverse bacterial species ( 8 , 23 ). (asm.org)
- Because of their ability to cross inter-species barriers, bacterial plasmids are essential agents for HGT. (prolekare.cz)
- Among them, broad host range (BHR) plasmids of Proteobacteria stand out because of their ability to colonize a wide range of bacterial species. (prolekare.cz)
- Transcripts upregulated in response to plant drought stress were mainly involved in transcriptional regulation, cellular homeostasis, and the detoxification of reactive oxygen species, indicating an oxidative stress response in PsJN. (sigmaaldrich.com)
- apo-Fur regulation has not been definitively shown to occur in any other bacterial species, making the study of Fur regulation of particular interest in H. pylori . (usuhs.edu)
- According to MEROPS peptidase database, Campylobacter species encode 64 predicted peptidases. (westminster.ac.uk)
- The development of antimicrobials has lagged behind the development of antibiotic resistance for many life-threatening bacterial species. (sciencemag.org)
- Bacillaene plays important roles in the fitness of B. subtilis during competition with other bacterial species. (tamu.edu)
- Bacterial Strains and in Vitro Growth Conditions. (pnas.org)
- All of the V. cholerae strains used in this study are isogenic derivatives of El Tor biotype strain, C6709-1, containing the res-tet-res substrate for TnpR resolvase integrated within the endogenous lacZ gene (strain AC-V66) ( 10 ). (pnas.org)
- Host Genetics and Intestinal MicrobiotaAlthough gut microbiota composition shows large inter-individual variability, family members have more similar microbiota than unrelated individuals and, indeed, the same bacterial strains are shared among family members [47,48, (amazonaws.com)
- Using gastric epithelial cells, we analyzed a set of H pylori strains and mutants for their ability to interact with CD46 and/or influence CD46 expression. (diva-portal.org)
- unpublished data), and gene content contrast, experimental evolution studies of microbial on these plasmids varies greatly among strains due to their The Author(s) 2018. (deepdyve.com)
- By comparing maps from different culture conditions and different L. plantarum strains, image analysis revealed 23 spots with altered levels of expression. (mdpi.com)
- The proteomic analysis of L. plantarum WCFS1 and ctsR mutant strains confirms at the translational level the CtsR-mediated regulation of some members of the Clp family, as well as the heat induction of typical stress response genes. (mdpi.com)
- Expression of the transporter is dynamically adjusted in direct response to IL, enabling growth and biofuel production at levels of IL that are toxic to native strains. (nature.com)
- In this thesis the expression and regulation of these important virulence factors as well as the genetic variability among ETEC strains have been studied. (gu.se)
- Using ETEC strains isolated directly from diarrhoeal stool specimens of Bangladeshi patients without sub-culturing the gene expression of the two enterotoxins as well as the two CFs were studied in vivo. (gu.se)
- The bacterial strains and plasmids used in this study are listed in Table 1 . (asm.org)
- The emergence of multi-resistant bacterial strains is a major source of concern and has been correlated with the widespread use of antibiotics. (mdpi.com)
- In general, late genes are downregulated in strains defective in early or middle genes, and neither middle nor late genes are expressed in strains defective in early class genes. (asm.org)
- The Bacillus subtilis araC locus, mapped at about 294 degrees on the genetic map, was defined by mutations conferring an Ara- phenotype to strains bearing the metabolic araA, araB, and araD wild-type alleles (located at about 256 degrees on the genetic map) and by mutants showing constitutive expression of the three genes. (semanticscholar.org)
- The present disclosure provides novel bacterial strains with altered expression or start codon modification of one or more RNA degradation/processing genes. (sumobrain.com)
- HilA is a transcriptional activator of the OmpR/ToxR family that is also encoded on SPI1. (nih.gov)
- ToxT is a cytoplasmic transcriptional activator responsible for directly activating the transcription of the structural genes for CT, TCP, and other virulence factors ( 3 ). (pnas.org)
- In oxygen-limited conditions, DicF enhances global expression of the EHEC type three secretion system, which is a key virulence factor needed for host colonization, through the transcriptional activator PchA. (foodsafetynews.com)
- While this is by far the most common type of Fur regulation, iron-bound Fur has also been shown to function as an activator of some genes. (usuhs.edu)
- Identification of a Transcriptional Activator (ChnR) and a 6-Oxohexanoate Dehydrogenase (ChnE) in the Cyclohexanol Catabolic Pathway in Acinetobacter sp. (asm.org)
- We identified chnR , a gene encoding an AraC-XylS type of transcriptional activator that regulates the expression of chnB , the structural gene for cyclohexanone monooxygenase (CHMO) in Acinetobacter sp. (asm.org)
- Here, we describe the identification of a transcriptional activator, ChnR, which is essential for CHMO expression. (asm.org)
- Accumulation of SA leads to reduction of the oligomeric cytoplasmic form of the transcriptional co-activator NPR1/NIM1 ( nonexpressor of PR genes1 ) to a monomeric form that translocates to the nucleus ( 4-8 ). (pubmedcentralcanada.ca)
- Recent studies have shown that some plasmids carry genes encoding NAP homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. (hindawi.com)
- We found that larger plasmids frequently have NAP gene homologs. (hindawi.com)
- Plasmids with H-NS gene homologs had less G+C content. (hindawi.com)
- It should be noted that plasmids with the NAP gene homolog also carried the relaxase gene involved in the conjugative transfer of plasmids more frequently than did those without the NAP gene homolog, implying that plasmid-encoded NAP homologs positively contribute to transmissible plasmids. (hindawi.com)
- Transformation of a bacterial host with two different plasmids is required. (wikipedia.org)
- We analyzed the transcriptional network of plasmid R388, one of the most promiscuous plasmids in Proteobacteria . (prolekare.cz)
- This ability makes BHR plasmids efficient shuttles for HGT, clearly illustrated in the last decades by their leading role in the spread of antibiotic resistance genes among microbial populations . (prolekare.cz)
- Bacterial plasmids are agents for HGT, but they themselves are genetic replicons with their own, idiosyncratic, evolutionary history , . (prolekare.cz)
- However, since plasmids can only exist inside a bacterial cell, their fitness is also host dependent. (prolekare.cz)
- A ) A library of S. typhimurium-bearing plasmids with random DNA fragments inserted upstream of a promoterless gfp gene ( 39 ) was used to infect a monolayer of RAW 264.7 macrophage-like cells at a multiplicity of infection (MOI) of 5:1. (sciencemag.org)
- The transmission of the ability of bacterial cells of simultaneously resist several antimicrobial drugs is accomplished, in many instances, by plasmids. (ibecbarcelona.eu)
- I. Epidemiology and Ecology of Bacterial Plasmids. (fishpond.com.au)
- Genetic Organization and Expression of Non-Conjugative Plasmids. (fishpond.com.au)
Virulence gene expression4
- Regulation of virulence gene expression. (berkeley.edu)
- Examples are the prfA thermo-sensor of L. monocytogenes [ 10 ], which is involved in controlling virulence genes, or the cyclic-di-GMP-sensing riboswitch of Vibrio cholerae [ 11 ], which controls biofilm formation, cell differentiation, and virulence gene expression. (biomedcentral.com)
- In this chapter, the invasion locus of serovar Typhimurium is used to exemplify several general points about the regulation of virulence gene expression in vivo. (asmscience.org)
- Virulence gene expression in vivo represents a target for antibiotic discovery that has not yet been explored. (sciencemag.org)
- Gerosa L, Kochanowski K, Heinemann M, Sauer U (2013) Dissecting specific and global transcriptional regulation of bacterial gene expression. (springer.com)
- To better understand the basis of this system, spontaneous glycosyl hydrolase mutants were isolated using a genetic screen for mutations, which reduced expression of the lacS gene. (genetics.org)
- During the past decade almost all of the carotenogenic genes have been identified by molecular, genetic and biochemical approaches in the Arabidopsis thaliana model system. (scielo.cl)
- Genetic analysis found a 3-bp deletion in the covR gene of the HH/LC variant. (cdc.gov)
- Genetic and functional analysis of these variants provides insight into the potential contribution of specific bacterial virulence factors to these emerging GBS clinical syndromes. (cdc.gov)
- The genetic basis of the evolved response was examined using microarrays and was characterised by increased expression for many immunity related genes. (beds.ac.uk)
- This suggests oxygen sensing and virulence regulation through DicF provides EHEC with a strategy to amplify virulence within its host colonization niche. (foodsafetynews.com)
- Here we report the identification of a small molecule inhibitor of Vibrio cholerae virulence regulation and demonstrate its ability to inhibit bacterial colonization in an animal model of cholera. (sciencemag.org)
- However, as the present case will illustrate, selective pressures in vivo may cause differential expression of certain GBS surface components during colonization or dissemination. (cdc.gov)
- To assess the functionality of CNN1 CArG elements in vivo , we exploited a 103-kb bacterial artificial chromosome (BAC) containing the human CNN1 locus shown previously to completely recapitulate endogenous mouse CNN1 expression in vivo . (ahajournals.org)
- 2. The genetically engineered host cell of claim 1, wherein the RNA degradation gene is an endogenous gene. (sumobrain.com)
- Understanding the interplay between antibiotic resistance and bacterial fitness and virulence is essential to guide individual treatments and improve global antibiotic policies. (asm.org)
- Understanding the interplay between antibiotic resistance and bacterial fitness and virulence is thus of paramount relevance for guiding individual treatments and global antibiotic policies. (asm.org)
- Likewise, reduced fitness is expected to directly impair bacterial virulence, but the interplay between virulence and antibiotic resistance is far more complex, including regulatory circuits controlling both traits ( 4 , 5 ). (asm.org)
- In this review, we focus on factors leading to integron rearrangements and gene capture facilitating antibiotic resistance acquisition, maintenance and spread. (mdpi.com)
- While CNN1's physiology has been studied extensively, its transcriptional regulation has proven to be intractable to conventional in vivo assays. (ahajournals.org)
- Transgenic mice carrying the 38-kb BAC with point mutations in all four intronic CArG elements show similar findings suggesting that SRF directly mediates in vivo expression of CNN1 primarily through intronic CArG elements. (ahajournals.org)
- We propose that full in vivo CNN1 gene expression requires multiple elements, including five CArG boxes, spread over 14-kb of genomic sequence. (ahajournals.org)
- Therefore, the true nature of the in vivo regulation of these virulence factors within a host remains unclear. (pnas.org)
- Furthermore, IsrM is found to be differentially expressed in vivo , with higher expression in the ileum than in the spleen. (prolekare.cz)
- Our results also suggest that sRNAs may represent a distinct class of virulence factors that are important for bacterial infection in vivo . (prolekare.cz)
- When administered in vivo , LiCl increased hepatic β-catenin level in a dose-dependent manner with simultaneous increase in NOS2 expression. (aacrjournals.org)
- The chapter also includes a brief description of in vivo expression technology (IVET), designed to select for bacterial genes that are transcriptionally induced in the host. (asmscience.org)
Analyzed the transcriptional response1
- Continuously increasing antimicrobial resistance, added to the limited development of new antibiotics, is of growing concern since it severely compromises our therapeutic arsenal to fight life-threatening bacterial infections ( 1 ). (asm.org)
- Plus, they are popularly used to prevent and cure Candidiasis yeast infection and vaginal bacterial infections, which are quite common in women. (amazonaws.com)
- We are entering a challenging era where microbial resistance to antibiotics will complicate the treatment of nearly all common bacterial infections. (sciencemag.org)
- A main concern with bacterial infections is the selection of isolates that are resistant to several antimicrobial drugs. (ibecbarcelona.eu)
- Geissendorfer M, Hillen W (1990) Regulated expression of heterologous genes in Bacillus subtilis using the Tn10 encoded tet regulatory elements. (springer.com)
- The pks genes are the largest antibiotic- encoding gene cluster in Bacillus subtilis and encode the Pks enzymatic complex that produces bacillaene. (tamu.edu)
- Bacillus subtilis GntR regulation modified to devise artificial transient induction systems. (semanticscholar.org)
- Characterization of abn2 (yxiA), encoding a Bacillus subtilis GH43 arabinanase, Abn2, and its role in arabino-polysaccharide degradation. (semanticscholar.org)
- Regulation of Plasmid Specified MLS-Resistance in Bacillus Subtilis by Conformational Alteration of RNA Structure. (fishpond.com.au)
- In this way, researches can gauge how strongly bait binds its prey (correlated with the level of expression of HIS3) and thus determines which nucleotide binding-sites have strong or weak preferences for a given base. (wikipedia.org)
- Here we identify sites involved in RNA processing and degradation as well as transcription within a nucleotide-resolution map of the transcriptional landscape. (surrey.ac.uk)
- Nucleotide sequence and transcriptional regulation of the yeast recombinational repair gene RAD51. (asm.org)
- Goodman HJK, Woods DR: Cloning and nucleotide sequence of the Butyrivibrio fibrisolvens gene encoding a type III glutamine synthetase. (springer.com)
- Two recent papers from Pascale Cossart and colleagues [ 6 , 7 ] present a comprehensive microarray analysis of the trans-criptome of Listeria monocytogenes in different conditions, uncovering an unsuspected variety of regulatory roles for noncoding RNAs in controlling changes in gene expression that characterize the transition from saprophytic to pathogenic lifestyle. (biomedcentral.com)
- Therefore, we set out to perform a comprehensive expression analysis of MatK and its target RNAs in order to assess possible checkpoints within this small gene expression network. (plantphysiol.org)
- In order to identify specific substrates of each pump, we individually expressed in trans all operons containing an RND pump-encoding gene into the Δ acrB hypersusceptible strain. (asm.org)
- An important finding was that the regulation of expression of these virulence factors does not seem to occur at the transcriptional level of the virulence operons. (gu.se)
- Also, a genomic database search found a negative correlation between the presence of nrdR and nusB and the FMN riboswitch in bacterial RBP operons. (biomedcentral.com)
- The other plasmid contains a region of randomized sequence representing potential binding sites (prey) which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes. (wikipedia.org)
- Computational simulations and theoretical analysis indicated that this architecture would show a transcriptional burst after plasmid conjugation, linking the magnitude of the feedback gain with the intensity of the transcriptional burst. (prolekare.cz)
- Experimental analysis showed that transcriptional overshooting occurred when the plasmid invaded a new population of susceptible cells. (prolekare.cz)
- The DNA sequence in the region of the fusion between bla and tRNAArg5 genes is displayed above the plasmid map. (nih.gov)
- To distinguish between the hypotheses described above we constructed a transcriptional fusion between the bla gene and a sequence encoding a tRNA (tRNAArg5) such that both genes become expressed as one single transcript from plasmid pRL11 (Fig. 3). (nih.gov)
- Plasmid Mini-F Encoded Functions Involved in Replication and Incompatibility. (fishpond.com.au)
- Construction and Properties of Plasmid Vectors Containing the trp Regulatory Region Suitable for Expressing Foreign Genes. (fishpond.com.au)
- A Mutational and Transcriptional Analysis of a Tumor Inducing Plasmid of Agrobacterium Tumefaciens. (fishpond.com.au)
- Transfer, Maintenance and Expression of Genes Introduced into Plant Cells Via the Tl Plasmid. (fishpond.com.au)
- A failure to see improvements in constitutive expression of the cellular genes suggests either that increases might come at too great a cost or that patterns of expression in adults are decoupled from the larval phase where increases would be most effective. (beds.ac.uk)
- Increasing the constitutive expression of these humoral genes, though more costly, could also be beneficial. (beds.ac.uk)
- This is the first global study assessing the role of all RND efflux pumps chromosomally encoded by the ECC, which confirms the major role of AcrB in both pathogenicity and resistance and the potential involvement of other RND-type members in acquired resistance. (asm.org)
- A number of factors known to be involved in virulence, such as the cag pathogenicity island ( cag PAI), motility, and the urease enzyme, have been extensively studied, and significant advances regarding the regulation of expression of these factors have been made ( 1 , 31 ). (asm.org)
- A soluble form of CD46 bound to H pylori and inhibited growth, in a dose- and time-dependent manner, by interacting with urease and alkyl hydroperoxide reductase, which are essential bacterial pathogenicity-associated factors. (diva-portal.org)
- Virulence factors such as the cable pilus and Cenocepacia Pathogenicity Island were unaltered in expression. (biomedcentral.com)
- Bacterial Pathogenicity, An Overview. (fishpond.com.au)
- 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)
- Although the mechanism has not yet been elucidated, increased concentration of the c-diGMP second messenger activates vps gene expression. (asm.org)
- Fine-tuned regulation of gene expression in response to extracellular and intracellular signals is a key mechanism for successful adaptation of microorganisms to changing environmental conditions. (biomedcentral.com)
- Differential effects on the expression of the three transcription factor B ( tfb ) genes hint at a mechanism for the modulation of transcriptional patterns in response to DNA damage. (biomedcentral.com)
- Here we identify an IL-resistance mechanism consisting of two adjacent genes from Enterobacter lignolyticus , a rain forest soil bacterium that is tolerant to an imidazolium-based IL. (nature.com)
- To cover a potentially complex IL-tolerance mechanism with many genes involved, we used relatively large DNA fragments (30-50 kb) to construct a fosmid library for screening in E. coli . (nature.com)
- To understand the mechanism of transcriptional induction, we isolated altered tryptophan regulation ( atr ) mutants in Arabidopsis thaliana with activated transcription of tryptophan genes. (genetics.org)
- This text then examines the molecular mechanism by which steroid hormones regulate specific gene expression. (elsevier.com)
- The similarity in fold change increase across all immunity genes may suggest a shared mechanism for the evolution of increased transcription in small, discrete units such as duplication of cis -regulatory elements. (beds.ac.uk)
- CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. (frontiersin.org)
- We have developed a selection methodology, on the basis of differential fluorescence induction (DFI) ( 7 ), for the rapid identification of bacterial genes induced upon association with host cells that would work independently of drug susceptibility and nutritional requirements. (sciencemag.org)
- Using RNA-sequencing transcriptomics, we determined that E. lignolyticus responds to [C 2 mim]Cl exposure by the differential expression of 688 genes, resulting in a complex response with numerous phenotypic changes 15 . (nature.com)
- We investigated the transcriptional response of M. genitalium to elevated temperatures and detected the differential induction of four hsp genes. (uthscsa.edu)
- These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. (frontiersin.org)
- Of the 9,254 tomato genes represented on the array, 122 were differentially expressed in Cmm -infected plants, compared with mock-inoculated plants. (plantphysiol.org)
- E. coli has a small form of RNA that activates particular genes when oxygen levels are low enough, according to the study. (foodsafetynews.com)
- Commensal E. coli encode one dicF gene but EHEC acquired three additional dicF copies during its evolution. (foodsafetynews.com)
- Taken together, the results that we present expand our knowledge about a regulatory network for different adhesin gene systems in uropathogenic E. coli and suggest a hierarchy for expression of the fimbrial adhesins. (diva-portal.org)
- The culture of the recombinant (pCom8-GPo1 alkB/E. coli DH5α) with the oil biodegradation bacterial consortium increased the degradation ratio of diesel oil at 24 h from 31% to 50%, and the facilitation rates were increased as the proportion of pCom8-GPo1 alkB / E. coli DH5α to the consortium increased. (scielo.br)
- The results suggested that the expression of the GPo1 gene in E. coli DH5α could enhance the function of diesel oil degradation by the bacterial consortium. (scielo.br)
- We transfer these genes to an engineered E. coli host, and demonstrate enhanced production of a terpene-based biofuel in the presence of this IL. (nature.com)
- Recently, by hybridizing an E. coli K-12 gene array with cDNA synthesized from RNA extracted from EHEC strain 86-24 and its isogenic luxS mutant, we observed that other potential virulence-associated factors, such as genes encoding the expression and assembly of flagella, motility and chemotaxis, were also activated by quorum sensing. (utmb.edu)
- Genes with modulated expression included genes for extracytoplasmatic function (ECF) group IV sigma factors. (sigmaaldrich.com)
- Six ECF sigma factor genes were expressed in PsJN colonizing potato plants. (sigmaaldrich.com)
- The expression of one ECF sigma factor was upregulated whereas that of another one was downregulated in a plant genotype-specific manner when the plants were stressed. (sigmaaldrich.com)
- As its name indicates, all subunits of the PEP, except its sigma factor subunit, are products of chloroplast genes. (royalsocietypublishing.org)
- The sigF gene encodes an alternate sigma factor found in Mycobacterium tuberculosis and related pathogenic mycobacteria. (asm.org)
- Departing from discovery and intuitive reasoning, the current focus is on understanding the quantitative and dynamic responses of transcriptional circuits to perturbations, for example to uncover DNA repair dynamics ( Ronen et al , 2002 ) or to design de novo synthetic circuits ( Cox et al , 2007 ). (embopress.org)
- To investigate plant responses activated during this compatible interaction, we used microarray analysis to monitor changes in host gene expression during disease development. (plantphysiol.org)
- Therefore, negative regulation of defense responses is very important. (pubmedcentralcanada.ca)
- 14-16 NFκB is known to play a central role in immune and inflammatory responses and is involved in transcriptional regulation of many cytokine genes, including TNF. (bmj.com)