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Transcription, GeneticTranscription FactorsPromoter Regions, GeneticMolecular Sequence DataBase SequenceGene Expression RegulationAmino Acid SequenceBinding SitesDNA-Binding ProteinsRNA, MessengerProtein BindingTranscription Initiation SiteTranscriptional ActivationRepressor ProteinsGene Expression Regulation, BacterialNuclear ProteinsDNAMutationRNA Polymerase IIChromatinCell LineTrans-ActivatorsChromatin ImmunoprecipitationGene Expression Regulation, FungalGene Expression ProfilingCloning, MolecularSp1 Transcription FactorRegulatory Sequences, Nucleic AcidTranscription Initiation, GeneticHeLa CellsHistonesCell NucleusGenes, ReporterDNA-Directed RNA PolymerasesBacterial ProteinsSaccharomyces cerevisiaeSignal TransductionPlasmidsOligonucleotide Array Sequence AnalysisModels, GeneticSaccharomyces cerevisiae ProteinsEscherichia coliTransfectionReverse Transcriptase Polymerase Chain ReactionGene Expression Regulation, ArchaealProtein Structure, TertiaryGene Expression Regulation, DevelopmentalEnhancer Elements, GeneticSequence AlignmentConserved SequenceTATA BoxViridiplantaeDNA FootprintingSequence Analysis, DNASequence Homology, Amino AcidGene ExpressionHomeodomain ProteinsSequence Homology, Nucleic AcidModels, BiologicalCells, CulturedRecombinant Fusion ProteinsGene Regulatory NetworksRegulatory Elements, TranscriptionalOperonBlotting, NorthernLuciferasesNucleic Acid ConformationCarrier ProteinsDNA, ComplementaryCell Line, TumorGene Expression Regulation, ViralMultigene FamilyTranscription Factor AP-1Drosophila ProteinsSTAT3 Transcription FactorGene Expression Regulation, PlantCell DifferentiationFungal ProteinsConsensus SequenceGenesRibosomal ProteinsGene DeletionTranscription Factor TFIIDBasic Helix-Loop-Helix Transcription FactorsTwo-Hybrid System TechniquesChromatin Assembly and DisassemblyTranscription Factors, TFIIAcetylationBlotting, WesternPhylogenyRNA, RibosomalNucleosomesEscherichia coli ProteinsComputational BiologyGene Expression Regulation, EnzymologicRestriction MappingDNA, BacterialGene Expression Regulation, NeoplasticDrosophila melanogasterDown-Regulation
BacteriaBiosynthesisGenomesVirulencePathogenBiofilmsRegulateExpressionOperonsPolymeraseRegulatory genesTranscriptional regulationMechanismsGeneticDifferentially expressedFluorescent ProteinsMembraneEnzymesEffectorPathogensEscherichiaCellularSignal transductionMechanismBiofilm formationPolymerasesInhibit the transcriptionEncodePromotersRepressionSubsetInteractions2023StrainsFactorsTarget genesChromatinChemotaxisUpstreamStructuralPathwaysLociPolysaccharidesInteractionDefectsColiChloroplastPhysiologyPathwayReplicationMutationsRepressorKinaseVirulentCaenorhabditisFunctionQuantitativeRecombinationSubstrateMotility
Bacteria13
  • In order to react effectively to changes in the surroundings, bacteria must be able to quickly turn specific genes on or off. (sciencedaily.com)
  • Each repressor targets a specific co-regulated group of genes by recognizing a specific sequence of DNA, called the operator in bacteria . (proteopedia.org)
  • Given the high number of virulence factors present in these bacteria, and the niche-specific role many of them play during different stages of the infectious process, gene expression must be finely tuned in order to efficiently coordinate their expression, and also continue to preserve energy pools. (biomedcentral.com)
  • An important factor of bacterial virulence is the formation of biofilms which are aggregates of microorganisms incorporated into an extracellular matrix that protects bacteria from hostile environments. (usp.br)
  • Flagellum-mediated bacterial motility is important for bacteria to take up nutrients, adapt to environmental changes, and establish infection. (bvsalud.org)
  • We study the functional interplay of pausing, termination and continued transcription, which constitutes a pervasive gene regulatory principle in bacteria. (fu-berlin.de)
  • This study also identified 43 growth-impairing inserts carrying multiple loci targeting 105 genes, of which 25 have homologs reported as essential in other bacteria. (biomedcentral.com)
  • Well-known examples are the eukaryotic and archaeal histones that wrap DNA and the nucleoid-associated proteins in bacteria and archaea that bend and bridge DNA. (universiteitleiden.nl)
  • It is remodeled actively in eukaryotes by motor enzymes that can move or displace nucleosomes, in addition to remodeling mechanisms more ubiquitous in bacteria and archaea that are based on the interplay between multiple architectural proteins. (universiteitleiden.nl)
  • Models suggest that in bacteria and archaea there are direct effects of physicochemical factors such as osmolarity, temperature and pH on the action of chromatin proteins, in addition to indirect effects by modulating the expression ratios of different types of chromatin proteins. (universiteitleiden.nl)
  • Biofilms form when groups of bacteria cover themselves in a sticky mixture of sugars, protein, and DNA. (the-scientist.com)
  • Bacteria sense these microenvironments and adapt by up or down regulating the expression of certain genes to influence different cell processes. (the-scientist.com)
  • In bacteria and archaea , structural proteins with related functions are usually encoded together within the genome in a block called an operon and are transcribed together under the control of a single promoter , resulting in the formation of a polycistronic transcript ( Figure 12.30 ). (pressbooks.pub)
Biosynthesis4
Genomes4
  • A comparison of the TF repertoire of S. aureus against 1209 sequenced bacterial genomes was carried out allowing us to identify a core set of orthologous TFs for the Staphylococacceae , and also allowing us to assign potential functions to previously uncharacterized TFs. (biomedcentral.com)
  • We have evaluated the orthologous distribution of these elements in other sequenced bacterial genomes using the repertoire of TFs identified in USA300, and identified a core set of regulators for both the Firmicutes phylum, and the Staphylococacceae group. (biomedcentral.com)
  • Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)
  • Independent of these cytological differences, all genomes are shaped by the action of abundant proteins with architectural function. (universiteitleiden.nl)
Virulence5
  • Finally, we examine the conservation of 135 USA300 TFs amongst 11 other S. aureus strains, identifying a key group of regulators that display a high degree of conservation, including many that have previously been demonstrated to play a role in virulence gene regulation. (biomedcentral.com)
  • Most of this regulation is carried out directly by transcription factors that modulate the activity of promoters aimed at expressing virulence factors. (usp.br)
  • Gene regulatory network inference and gene module regulating virulence in Fusarium oxysporum. (openwetware.org)
  • Thus, the pyrD gene appears to be essential for several cellular processes involved in AIEC virulence. (rossimicrolab.com)
  • Altogether, our results suggest that the crucial role played by the pyrD gene in AIEC virulence, and the presence of structural differences between E. coli and human DHOD allowing for the design of specific inhibitors, make E. coli DHOD a promising target for therapeutical strategies aiming at counteracting chronic inflammation in CD by acting selectively on its bacterial triggers. (rossimicrolab.com)
Pathogen7
  • The bacterial pathogen Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20 - 30 seconds. (aiche.org)
  • A deletion allele of egl-5 was isolated in a screen for animals which fail to develop swollen tails when exposed to the bacterial pathogen Microbacterium nematophilum. (ox.ac.uk)
  • The correlations proposed provide a guide for further experimentation leading to a better understanding of MDR EP gene expression in this important pathogen. (manchester.ac.uk)
  • A virulent pathogen, successfully recognized by the action of disease resistance (R) gene products in plant, elicit a biphasic ROS accumulation that act as direct reactive substrates to kill pathogens, and to strengthen plant cell walls by via cross-linking of glycoproteins to obstruct further extension of the pathogen [20]. (austinpublishinggroup.com)
  • Understanding the interaction between the gene expression of a pathogen and that of its human host is important for the understanding of a particular infectious disease. (pressbooks.pub)
  • Borrelia burgdorferi , an emerging bacterial pathogen, is maintained in nature by transmission from one vertebrate host to another by ticks. (cdc.gov)
  • By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. (cdc.gov)
Biofilms4
  • Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins. (ox.ac.uk)
  • Interestingly, FLU-exposed biofilms showed no significant changes in gene expression over the course of the experiment. (who.int)
  • In AMB-exposed biofilms, 2.7% of the genes showed altered expression, while in CAS-exposed biofilms, 13.0% of the genes had their expression modified. (who.int)
  • There was little overlap between AMB- or CAS-responsive genes in biofilms and those that have been identified as AMB, FLU, or CAS responsive in C. albicans planktonic cultures. (who.int)
Regulate6
  • We propose a model in which TFs act on a spectrum from specific local control of gene expression to widespread binding with little or no direct impact on proximal genes, and suggest that many prokaryotic TFs bind DNA prolifically yet still home to and directly regulate a limited number of targets. (aiche.org)
  • Like RafK, the presence of DLDH also activated the expression of raf operon genes, as DLDH-negative pneumococci showed a significantly decreased expression of aga and rafEFG, but DLDH did not regulate rafK or the putative regulatory genes rafR and rafS. (lu.se)
  • Researchers can now provide a picture of how proteins regulate genetic expression at the atomic level. (sciencedaily.com)
  • Additionally, TcERF15, which played the positive role to regulate tasy gene, was up-regulated by TcMYC2a. (frontiersin.org)
  • Our interest lies in understanding how architectural proteins act on DNA and how they regulate transcription. (universiteitleiden.nl)
  • Genomic DNA contains both structural gene s, which encode products that serve as cellular structures or enzymes, and regulatory gene s, which encode products that regulate gene expression. (pressbooks.pub)
Expression38
  • To understand the dynamics of bacterial growth physiology and size control in dynamic nutrient environments, we have developed a coarse-grained proteome sector model which connects gene expression to growth rate and division control, and accurately predicts the cell-level E. coli response to nutrient perturbations in both exponential and stationary phase seen in experimental data 5 , 25 . (nature.com)
  • We developed a high-throughput system based on ChIP-Seq for mapping transcription factor (TF) binding, and assayed genome-wide expression following induction of each TF. (aiche.org)
  • Pneumococci lacking RafK showed a 50- to 80-fold reduction in expression of the raf operon genes aga (alpha-galactosidase) and rafEFG (raffinose substrate binding and permease genes), and both glucose and sucrose inhibited raffinose uptake through inducer exclusion. (lu.se)
  • The lactose ("lac") repressor controls the expression of bacterial enzymes involved in the metabolism of of the sugar lactose. (proteopedia.org)
  • Bacterial intercellular communication provides a mechanism for signal-dependent regulation of gene expression to promote coordinated population behavior. (mcmaster.ca)
  • Here we report that luxS expression is constitutive but that the transcription of pfs is tightly correlated to AI-2 production in Salmonella serovar Typhimurium 14028. (mcmaster.ca)
  • The expression of retS over time was also evaluated by western blot when co-cultivated with Staphylococcus aureus and Candida albicans in artificial sputum media and we noticed that there was no change in the expression of this gene when compared to the axenically cultured PAO1. (usp.br)
  • Quantitative reverse transcription-PCR data revealed that the regulons of the Rcs system displayed differential expression in the tat mutant, indicating that the Rcs signaling was activated. (bvsalud.org)
  • Construction and Analysis of Gene Co-Expression Network in the Pathogenic Fungus Ustilago maydis. (openwetware.org)
  • 22.Control of gene expression. (unizg.hr)
  • Numerous fundamental cellular processes, including virtually every aspect of gene expression and regulation, depend on the cooperation of RNAs and proteins. (fu-berlin.de)
  • Specific RNAs and proteins associate to build up some of the most complex macromolecular machineries of living cells, such as ribosomes and spliceosomes, which mediate particular steps of gene expression. (fu-berlin.de)
  • RNP-based processive anti-termination underlies the switching from immediate-early to delayed-early gene expression in other lambdoid phages as well as ribosomal RNA synthesis in Escherichia coli . (fu-berlin.de)
  • Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. (ox.ac.uk)
  • We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots. (ox.ac.uk)
  • The association between the expression of immune-process DEGs and abundance of immune infiltrates from gene signatures in normal colorectal tissues was estimated from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) project. (biomedcentral.com)
  • The analysis revealed a 25-gene signature of immune-associated DEGs and their expression profile was positively correlated with naïve T-cell, effector memory T-cell, central memory T-cell, resident memory T-cell, exhausted T-cell, resting Treg T-cell, effector Treg T-cell and Th1-like colorectal gene signatures. (biomedcentral.com)
  • We screened the literature from inception until January 2022 by querying the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) using the search terms: (microbiome OR microbial OR microbiota OR microflora OR dysbiosis). (biomedcentral.com)
  • The geminivirus transient expression system allows rapid analysis of RNAs transcribed from foreign genes and can serve as a preliminary screen in the construction of transgenic plants. (ncsu.edu)
  • Chromatin structure and expression of plant ribosomal RNA genes. (ncsu.edu)
  • We find that this allele carries an inserted repeat element approximately 13.8 kb upstream of the egl-5 open reading frame, which specifically disrupts the cell-specific expression of this gene in HSN egg-laying neurons. (ox.ac.uk)
  • Together these findings extend the complexity of regulation and function of Hox genes in C. elegans and demonstrate the importance of their tissue-specific expression for correct development and response to infection. (ox.ac.uk)
  • Microbiological, quantitative gene expression, mRNA half-life and genome data for 11 strains of S. aureus combined with bioinformatic analyses were used to identify correlates of increased MDR EP gene expression. (manchester.ac.uk)
  • The presence of qacA/B and/or increased expression of one to two MDR EP genes were identified in eight strains. (manchester.ac.uk)
  • Microbiological and gene expression data correlated in four instances, existing knowledge of the substrate specificity of NorC resulted in correlation in two others, and a transcriptional/translational disconnect is possible for the remaining two. (manchester.ac.uk)
  • To also target low expressed essential genes, we included some variant steps that were expected to overcome the non-stringent regulation of the promoter carried by the expression vector used for the shotgun antisense libraries. (biomedcentral.com)
  • For the first time in P. aeruginosa , we applied regulated antisense RNA expression and showed the feasibility of this technology for the identification of novel essential genes. (biomedcentral.com)
  • This article reviews the current knowledge and experimental research about the mechanisms by which fatty acids and their derivatives control specific gene expression involved during carcinogenesis. (springer.com)
  • Knowledge of the mechanisms by which fatty acids control specific gene expression may identify important risk factors for cancer and provide insight into the development of new therapeutic strategies for a better management of whole body lipid metabolism. (springer.com)
  • Effect of dietary fatty acids on inflammatory gene expression in healthy humans. (springer.com)
  • TcMYC2a was able to affect the expression of GUS reporter gene by binding with the T/G-box, G-box, and E-box, which were the key cis -elements of TASY and TcERF12/15 promoter. (frontiersin.org)
  • TcMYC2a overexpression also led to significantly increased expression of TASY , tat , dbtnbt, t13h , and t5h genes. (frontiersin.org)
  • The expression of a gene is a highly regulated process. (pressbooks.pub)
  • Whereas regulating gene expression in multicellular organisms allows for cellular differentiation, in single-celled organisms like prokaryotes, it primarily ensures that a cell's resources are not wasted making proteins that the cell does not need at that time. (pressbooks.pub)
  • Elucidating the mechanisms controlling gene expression is important to the understanding of human health. (pressbooks.pub)
  • These interactions lead to the expression of some genes and the suppression of others, depending on circumstances. (pressbooks.pub)
  • however, gene expression in eukaryotes is more complicated because of the temporal and spatial separation between the processes of transcription and translation. (pressbooks.pub)
  • Thus, although most regulation of gene expression occurs through transcriptional control in prokaryotes, regulation of gene expression in eukaryotes occurs at the transcriptional level and post-transcriptionally (after the primary transcript has been made). (pressbooks.pub)
Operons2
  • Operons regulation by repressor. (unizg.hr)
  • As transcription of many genes and operons responds to environmental changes and as these are often mediated by chromatin proteins, it is expected that 1) the architectural interplay of such proteins and/or 2) their direct response to physicochemical changes determines loop formation and dissolution leading to altered transcription levels. (universiteitleiden.nl)
Polymerase3
  • This gene was tagged by insertion of the Tc1 transposon, and the wild-type gene was cloned by chromosomal walking 11 kb from ama-1, a cloned gene encoding the large subunit of RNA polymerase II. (ncsu.edu)
  • The enzyme responsible for the synthesis of protein-coding mRNA is termed RNA polymerase II . (chemeurope.com)
  • a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. (frontiersin.org)
Regulatory genes1
Transcriptional regulation6
  • Mapping transcriptional regulation of biofilm-related genes promoters in Pseudomonas. (usp.br)
  • RNAs and proteins can also engage in more transient interactions, for example during co-transcriptional regulation of RNA polymerases or during post-transcriptional regulation of (pre-)mRNA life cycles. (fu-berlin.de)
  • Transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which is virtually universal in microorganisms. (lu.se)
  • With a minimalist model of metabolism, cell growth and transcriptional regulation in a microorganism, we explore how the interaction between environmental conditions and gene regulation set the growth rate of cells in the phase of exponential growth. (lu.se)
  • Citation: Troein C, Ahre´n D, Krogh M, Peterson C (2007) Is Transcriptional Regulation of Metabolic Pathways an Optimal Strategy for Fitness? (lu.se)
  • INTRODUCTION broken, which in realistic situations can severly constrain the Transcriptional regulation of effector genes is a highly successful regulatory options. (lu.se)
Mechanisms7
  • Although the overall mechanisms behind gene regulation have long been known, the fine details have eluded scientists for decades. (sciencedaily.com)
  • We investigate the molecular mechanisms, by which RNAs and proteins cooperate to bring about the biological functions of selected RNPs involved in transcription and pre-mRNA splicing. (fu-berlin.de)
  • Regulatory mechanisms for chromosomal genes encoding multidrug resistance (MDR) efflux pumps (EPs) in Staphylococcus aureus are poorly defined. (manchester.ac.uk)
  • The discovery of novel essential genes or pathways that have not yet been targeted by clinical antibiotics can underlie the development of alternative effective antibacterials to overcome existing mechanisms of resistance. (biomedcentral.com)
  • Architectural proteins, although minimally conserved in terms of structure and sequence among kingdoms, act upon DNA using conserved mechanisms (Luijsterburg et al. (universiteitleiden.nl)
  • Roger Kornberg and his research group have made several fundamental discoveries concerning the mechanisms and regulation of eukaryotic transcription. (chemeurope.com)
  • After recognition, plant's constitutive basal defense mechanisms [12] initiates a diverse set of downstream signaling events, leading to an activation of complex signaling cascades such as rapid microbursts of Reactive Oxygen Species (ROS), callose deposition to strengthen the cell wall, ion channels and MAP kinase cascades, phytohormones like Salicylic Acid (SA), Jasmonic Acid (JA), Ethylene (ET) and transcriptional induction of defense related genes [18,19]. (austinpublishinggroup.com)
Genetic3
  • Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. (biomedcentral.com)
  • Kornberg was awarded the Nobel Prize in Chemistry in 2006 "for his studies of the molecular basis of eukaryotic transcription " which explains the process by which genetic information from DNA is copied to RNA . (chemeurope.com)
  • With the advances in BMT and gene therapy, patients now have a better likelihood of developing a functional immune system in a previously lethal genetic disease. (medscape.com)
Differentially expressed4
  • In this study, a comparative transcriptomics analysis was performed with extraintestinal pathogenic Escherichia coli (ExPEC), which identified a considerable number of genes differentially expressed when the Tat system was disrupted. (bvsalud.org)
  • We investigated publicly available transcriptomic gut profiles of young germ-free mouse hosts transplanted with old donor gut microbiota to identify immune-associated differentially expressed genes (DEGs). (biomedcentral.com)
  • A total of 112 differentially expressed genes (DEGs) were identified and used to construct a gut network of encoded proteins, in which DEGs were functionally annotated as being involved in an immune process based on gene ontology. (biomedcentral.com)
  • We additionally searched the National Library of Medicine (NLM) PubMed using the additional terms: (differentially expressed genes OR DEGs). (biomedcentral.com)
Fluorescent Proteins1
  • This is a false colored mesoscopic image of two strains of E. coli expressing different fluorescent proteins. (the-scientist.com)
Membrane4
  • Monoclonal antibody identification of a 100-kDa membrane protein in HeLa cells and human spinal cord involved in poliovirus attachment. (ncsu.edu)
  • Membrane proteins implicated in long-chain fatty acid uptake by mammalian cells: CD36, FATP and FABPm. (springer.com)
  • Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes. (springer.com)
  • Dietary fatty acids and membrane protein function. (springer.com)
Enzymes4
  • We also study selected RNP-remodeling enzymes as drivers of molecular RNP machineries and as mediators of co- and post-transcriptional gene regulation. (fu-berlin.de)
  • In this way, regulation of the transcription of all of the structural genes encoding the enzymes that catalyze the many steps in a single biochemical pathway can be controlled simultaneously, because they will either all be needed at the same time, or none will be needed. (pressbooks.pub)
  • For example, in E. coli , all of the structural genes that encode enzymes needed to use lactose as an energy source lie next to each other in the lactose (or lac ) operon under the control of a single promoter, the lac promoter. (pressbooks.pub)
  • A very natural place to study gene detecting and metabolizing lactose, it is known that the overall regulation is in the metabolism of the cell, and then specifically in effect of expressing the lac genes in vain is a drop in the growth rate the regulation of genes that code for enzymes and transporter of as much as 5% [1,6]. (lu.se)
Effector2
  • In Bacillus subtilis, RbsR was shown to interact with Histidine-containing protein (HPr), an allosteric effector of the related LacI/GalR protein Catabolite Control Protein A (CcpA). (wikipedia.org)
  • However virulent pathogens, escape PTI-based surveillance by transporting small effector proteins in the plant cells, which in turn cause effector triggered plant susceptibility. (austinpublishinggroup.com)
Pathogens2
  • It is the body's first-line defense against many bacterial pathogens. (medscape.com)
  • Targeting of novel essential pathways is expected to play an important role in the discovery of new antibacterial agents against bacterial pathogens, such as Pseudomonas aeruginosa , that are difficult to control because of their ability to develop resistance, often multiple, to all current classes of clinical antibiotics. (biomedcentral.com)
Escherichia2
  • In Escherichia coli, RbsR is responsible for regulation of genes involved in D-ribose metabolism. (wikipedia.org)
  • In this study, we combine transcriptomics analysis and bacterial genetics, which reveal that transcription regulation plays an important role in mediating the motility defects of the tat mutant of extraintestinal pathogenic Escherichia coli. (bvsalud.org)
Cellular3
  • Furthermore, it is unclear if bacterial size modulation is simply a byproduct of the complex cellular response to changing environmental conditions, or if it serves as an adaptive mechanism employed by the cell to improve fitness in time-varying environments. (nature.com)
  • As bioactive molecule, ceramide is involved in the regulation of many cellular processes. (elifesciences.org)
  • In most cases, proteins perform a cellular function specified by the gene. (chemeurope.com)
Signal transduction2
Mechanism2
  • who also correctly proposed the general mechanism of regulation by the lac repressor. (proteopedia.org)
  • In these processes, transcript-borne regulatory RNAs alone or in conjunction with protein factors assemble on the surface of RNAP and accompany the enzyme during further transcription by an RNA looping mechanism, rendering the elongation complex resistant to pause and/or termination signals downstream of the original modification site. (fu-berlin.de)
Biofilm formation2
  • In addition, pyrD inactivation reduced flagellar motility and strongly affected biofilm formation by downregulating transcription of both type 1 fimbriae and curli subunit genes. (rossimicrolab.com)
  • In particular, exposure to CAS resulted in the upregulation of hypha-specific genes known to play a role in biofilm formation, such as ALS3 and HWP1. (who.int)
Polymerases3
  • Eukaryotic transcription three types of RNA polymerases. (unizg.hr)
  • In contrast to bacterial RNA polymerases, eukaryotic RNA polymerases are alone incapable of gene transcription, and require a complex assembly of accessory proteins to accomplish this task in an accurate and efficient manner. (chemeurope.com)
  • The PEP enzyme recognizes the -10 and -35 cis -elements, similar to those found in bacterial promoters whereas the NEP enzyme recognizes the YRTA-motif, which can also be found upstream of several genes with PEP promoters indicating that these genes can be transcribed by both polymerases ( Pfannschmidt and Liere, 2005 ). (frontiersin.org)
Inhibit the transcription1
Encode2
  • The DNA sequence reveals that dpy-13 is a member of the collagen multi-gene family, and it could encode a polypeptide of 302 amino acids. (ncsu.edu)
  • Members of the Hox gene family encode transcription factors that specify positional identity along the anterior-posterior axis of nearly all metazoans. (ox.ac.uk)
Promoters2
  • In this sense, we aim to characterize the behaviour of different promoters of genes involved in biofilm regulation under different conditions and to search for possible new DNAbinding proteins associated with their promoter regions. (usp.br)
  • PraR bound to the promoters of several of these genes indicating direct repression. (ox.ac.uk)
Repression1
Subset3
  • RafK carries a C-terminal regulatory domain present in a subset of ATP-binding proteins that has been involved in both direct regulation of transporter activity (inducer exclusion) and transcription of transporter genes. (lu.se)
  • Only a subset of proteins in a cell at a given time is expressed. (pressbooks.pub)
  • Somatic mutations at the phosphotyrosine-binding pocket of the C-terminal SH2 domain of GTPase-activating protein RASA1 have been found in a subset of Basal-cell carcinoma (BCC) [Friedman, 1995]. (lu.se)
Interactions1
  • Gene regulation involves a complex web of interactions within a given cell among signals from the cell's environment, signalling molecules within the cell, and the cell's DNA. (pressbooks.pub)
20233
  • 2023. Editorial: Role of Transcription Factors and Sigma Factors in Bacterial Stress. (openwetware.org)
  • 2023. Comparative genomics sheds light on transcription factor-mediated regulation in the extreme acidophilic Acidithiobacillia representatives. (openwetware.org)
  • 2023. The gene regulatory network of Staphylococcus aureus ST239-SCCmecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds. (openwetware.org)
Strains2
  • Even though diverse strains of S. aureus have been extensively studied, and subjected to genome sequencing, the function of a large proportion of their genes remains unidentified. (biomedcentral.com)
  • Over time, OspC genes were transferred between strains through recombinations involving the whole or parts of the gene and one or both flanks. (cdc.gov)
Factors9
  • This is done through regulation of the activity of proteins that already exist in the cell, but also by the binding of special proteins-transcription factors-to specific sites on the DNA, turning certain genes on or off, which in turn regulates the cell's production of various proteins. (sciencedaily.com)
  • Roughly 40 years ago it was observed that these transcription factors find their binding sites on DNA much more quickly that free diffusion in three dimensions would allow. (sciencedaily.com)
  • Theoretical and empirical studies have shown that it is likely that the transcription factors bind to a chromosome wherever they encounter one and then glide along the DNA in search of their binding sites. (sciencedaily.com)
  • In this context, DNA-binding transcription factors (TFs) play an important regulatory role by either repressing or activating genes in response to environmental and physiological conditions. (biomedcentral.com)
  • Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms. (openwetware.org)
  • The α 2 ββ'ω core enzyme cooperates with transcription factors and responds to signals on DNA templates and nascent RNAs to achieve full functionality in vivo . (fu-berlin.de)
  • Their regulation may be carried out either through direct binding to DNA as peroxisome proliferator-activated receptors or via modulation in an indirect manner of signaling pathway molecules (e.g., protein kinase C) and other transcription factors (nuclear factor kappa B and sterol regulatory element binding protein). (springer.com)
  • Among all JA downstream transcription factors, MYC2 is considered as the fatal point of the entire JA signaling pathway ( Kazan and Manners, 2013 ). (frontiersin.org)
  • Published September 5, 2007 transcription factors and replicating extra DNA, rather than going directly into growth of the cell. (lu.se)
Target genes1
  • Database analyses retrieved 40 active ingredients and 47 target genes in SHD. (hindawi.com)
Chromatin5
  • This folded structure including the associated architectural proteins is referred to as chromatin. (universiteitleiden.nl)
  • Remodeling of chromatin is also mediated by chemical modifications of the DNA, the architectural proteins that shape it or physicochemical cues. (universiteitleiden.nl)
  • Also, my group is investigating the (architectural) interplay between different types of chromatin proteins in vitro (Laurens et al. (universiteitleiden.nl)
  • In addition to dissecting these mechanistic aspects of gene regulation, we are interested in the roles and physiological consequences of the products of genes regulated by chromatin proteins. (universiteitleiden.nl)
  • While a postdoctoral fellow working with Aaron Klug and Francis Crick at the MRC in the 1970s, Kornberg discovered the nucleosome as the basic protein complex packaging chromosomal DNA in the nucleus of eukaryotic cells (chromosomal DNA is often termed "chromatin" to reflect this protein packaging). (chemeurope.com)
Chemotaxis2
  • [ 1 ] Neutrophils move to the site of invasion by means of chemotaxis, which occurs in response to microbial products, activated complement proteins, and cytokines. (medscape.com)
  • Chemotaxis of neutrophils involves movement of pseudopodia and polymerization of cytoskeletal proteins or actin. (medscape.com)
Upstream3
  • For this, the upstream regions of the gacA, gacS, ladS, retS, rsmA, rsmZ and PA1611 genes were cloned separately into a miniTn7 vector and inserted into the PAO1 chromosome. (usp.br)
  • Para isso, as regiões upstream dos genes gacA, gacS, ladS, retS, rsmA, rsmZ e PA1611 foram clonadas separadamente em um vetor repórter miniTn7 e inseridas no cromossomo de PAO1. (usp.br)
  • One CCGG site 164 base-pairs upstream from the start of transcription is preferentially unmethylated in some genes. (ncsu.edu)
Structural3
  • 7.Membranes structural components: lipids and proteins. (unizg.hr)
  • Huang YH, Said N, Loll B, Wahl MC (2019) Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis. (fu-berlin.de)
  • Krupp F, Said N, Huang YH, Loll B, Bürger J, Mielke T, Spahn CMT, Wahl MC (2019) Structural basis for the action of an all-purpose transcription anti-termination factor. (fu-berlin.de)
Pathways2
  • A rat MCAO model was established to evaluate the pharmacodynamics of SHD in the treatment of IS, and Western blot analysis assessed the level of proteins in the related pathways. (hindawi.com)
  • A number of studies have explored how regulation of generally, and at least to a first approximation, it is obvious that metabolic pathways affects the growth rate of microorganisms, gene regulation only is useful if the environmental conditions vary both in the steady state and in response to changes in the local with time. (lu.se)
Loci3
  • The methylation pattern within a specific multigene locus is influenced by the number and type of rRNA genes in other rDNA loci in the cell. (ncsu.edu)
  • Dominant, very active loci have a higher proportion of rRNA genes with unmethylated cytosine residues in comparison with recessive and inactive loci. (ncsu.edu)
  • Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. (cdc.gov)
Polysaccharides1
  • Some individuals focus on reproduction to expand the colony, while others specialize in construction, oozing polysaccharides and proteins that make up the extracellular matrix. (the-scientist.com)
Interaction1
  • The study, to be published in a coming issue of Proceedings of the National Academy of Sciences (PNAS), compares the energy required to break off the interaction with DNA with the energy needed to glide along the DNA and how many times a protein binds back to the same DNA strand before it starts to look elsewhere. (sciencedaily.com)
Defects2
  • The Tat substrate proteins responsible for the motility defects are identified. (bvsalud.org)
  • The prin2.2 and csp41b-2 single mutants displayed pale phenotypes, abnormal chloroplasts with reduced transcript levels of photosynthesis genes and defects in embryo development. (frontiersin.org)
Coli2
  • In the case of the lac operon of E. coli, a well-studied system for whether a gene is regulated. (lu.se)
  • In unicellular organisms like E. coli and yeast, the benefits of between potential cost and benefit, regulation can make the most a well-adapted regulatory system are readily quantified, as the difference to the long-term growth rate if the resource in question fitness of an individual can be estimated by its growth rate in is only available a similarly small fraction of the time. (lu.se)
Chloroplast2
  • Transcription of the wheat chloroplast gene that encodes the 32 kd polypeptide. (ncsu.edu)
  • We show here that PLASTID REDOX INSENSITIVE 2 (PRIN2) and CHLOROPLAST STEM-LOOP BINDING PROTEIN 41 kDa (CSP41b), two proteins identified in plastid nucleoid preparations, are essential for proper plant embryo development. (frontiersin.org)
Physiology4
  • While previous studies have characterized bacterial growth physiology at steady-state, a quantitative understanding of bacterial physiology in time-varying environments is lacking. (nature.com)
  • The twin-arginine translocation system (Tat) is an important protein export system, playing a critical role in bacterial physiology and pathogenesis. (bvsalud.org)
  • IMPORTANCE The Tat system is an important protein export system critical for bacterial physiology and pathogenesis. (bvsalud.org)
  • Identifying gene makers of immune dysregulation during gut microbiota ageing may contribute to mechanistic insights in preventing age-related alterations of intestinal physiology and associated disease. (biomedcentral.com)
Pathway4
  • To further investigate regulation of AI-2 production in Salmonella , we constructed pfs and luxS promoter fusions to a luxCDABE reporter in a low-copy-number vector, allowing an examination of transcription of the genes in the pathway for signal synthesis. (mcmaster.ca)
  • We show that, in the AIEC strain LF82, inactivation of the pyrD gene, encoding dihydroorotate dehydrogenase (DHOD), an enzyme of the de novo pyrimidine biosynthetic pathway, completely abolished its ability of to grow in a macrophage environment-mimicking culture medium. (rossimicrolab.com)
  • Present study reviews rice defense signaling pathway in disease resistance against blast, bacterial blight, BPH and Asian rice gall midge. (austinpublishinggroup.com)
  • STAT5B acts as a part of the growth hormone signalling pathway leading to stimulation of insulin-like growth factor I (IGF-I) gene transcription [Woelfle et al. (lu.se)
Replication2
  • Introduction into replication, transcription and translation. (unizg.hr)
  • Synthesis of AR1 RNA was dependent on T-DNA transfer and TGMV DNA replication, demonstrating that it is a plant transcription product. (ncsu.edu)
Mutations9
  • Mutations in the Caenorhabditis elegans dpy-13 (dumpy) gene result in a short, chunky body shape. (ncsu.edu)
  • Mutations in the 5'-untranslated and/or coding regions were identified that may affect transcription efficiency. (manchester.ac.uk)
  • Similarly, all cells in two pure bacterial cultures inoculated from the same starting colony contain the same DNA, with the exception of changes that arise from spontaneous mutations. (pressbooks.pub)
  • SCID results from mutations in any of more than 15 known genes. (medscape.com)
  • X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's tyrosine kinase (BTK) [Väliaho et al. (lu.se)
  • ZAP-70 deficiency is a rare autosomal recessive form of severe combined immunodeficiency (SCID) caused by mutations in the gene coding for T cell receptor z-chain associated protein kinase [ Chan et al. (lu.se)
  • Noonan syndrome (NS) is caused by mutations in PTPN11 , a gene encoding the nonreceptor protein tyrosine phosphatase SHP2. (lu.se)
  • Mutations in the PIK3R1 gene encoding phosphatidylinositol 3-kinase (PI3-kinase) have been found to cause severe insulin resistance [Baynes et al. (lu.se)
  • 1997]. Mutations in the STAT1 gene cause complete STAT1 deficiency. (lu.se)
Repressor3
  • The Ribose repressor (RbsR) is a bacterial DNA-binding transcription repressor protein and a member of the LacI/GalR protein family. (wikipedia.org)
  • The lac repressor, and the group of genes it controls, which is called an operon , were the first such gene regulatory system to be discovered. (proteopedia.org)
  • What percentage of time this DNA sequence spends in a kinked state, in the absence of bound lac repressor protein, is not known, but it may be a significant percentage (see next section below). (proteopedia.org)
Kinase2
  • We show that compromised rectal development, which occurs as a result of loss of egl-5 function, results in a failure of rectal epithelial cells to express the ERK MAP kinase mpk-1, which was previously shown to mediate tail-swelling in response to bacterial infection. (ox.ac.uk)
  • Majority of R genes cloned so far belong to the Nucleotide-Binding Site Leucine-Rich Repeat (NBS-LRR) or LRR Kinase super-families [7]. (austinpublishinggroup.com)
Virulent1
  • In this study, we constructed a transposon (Tn) mutagenesis library covering Tn insertion in over 72% of the chromosome-encoded genes of a virulent and multi-drug resistant porcine ExPEC strain PCN033. (bvsalud.org)
Caenorhabditis1
  • One among the Caenorhabditis elegans Hox genes is egl-5. (ox.ac.uk)
Function2
  • For example, even if comprehensive insertion libraries are produced, it is inevitable that some genes, especially the shortest ones, could elude insertion and be spuriously annotated as essential, while transposon insertions that occur at gene ends and do not fully inactivate the function could lead to genes being incorrectly classified as non-essential. (biomedcentral.com)
  • Here, the function of regulation is quite clear: expressing energy and carbon, that a number around 0.2% would be the right genes at the right time will enable the cell to make the expected, and that the difference is more or less specific to the lac most of the resources within its reach, by maximizing the uptake operon [7]. (lu.se)
Quantitative1
  • Here we develop a quantitative theory connecting bacterial growth and division rates to proteome allocation in time-varying nutrient environments. (nature.com)
Recombination1
  • Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. (cdc.gov)
Substrate1
Motility2
  • It has been observed for a long time that the Tat system is critical for bacterial motility. (bvsalud.org)
  • We for the first time reveal the link between the Tat system and bacterial motility, which is important for understanding the physiological functions of the Tat system. (bvsalud.org)