Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks.

No abstract is available for this paper.

• Publication year

  2010

• Venue

  FEMS Microbiology Reviews

• Publication date

  2010-09-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1111/j.1574-6976.2010.00227.xPMID 20491932
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Transcriptome analysis.

  2012cited by this paper
• Erratum: Structure of the CAP-DNA complex at 2.5 Å resolution: A complete picture of the protein-DNA Interface (Journal of Molecular Biology (1996) 260:3 (395-408))

  2011cited by this paper
• A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions

  2010cited by this paper
• Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors.

  2010cited by this paper
• Involvement of the Leucine Response Transcription Factor LeuO in Regulation of the Genes for Sulfa Drug Efflux

  2009cited by this paper
• THE TURKISH ECONOMY AFTER THE CRISIS

  2009cited by this paper
• Participation of Regulator AscG of the β-Glucoside Utilization Operon in Regulation of the Propionate Catabolism Operon

  2009cited by this paper
• Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

  2009cited by this paper
• Genome‐wide responses to carbonyl electrophiles in Bacillus subtilis: control of the thiol‐dependent formaldehyde dehydrogenase AdhA and cysteine proteinase YraA by the MerR‐family regulator YraB (AdhR)

  2009cited by this paper
• The Nucleoid: an Overview

  2009cited by this paper
• Transcriptional Regulatory Networks in Saccharomyces cerevisiae

  2009cited by this paper
• Identifying promoter features of co-regulated genes with similar network motifs

  2009cited by this paper
• The Uncharacterized Transcription Factor YdhM Is the Regulator of the nemA Gene, Encoding N-Ethylmaleimide Reductase

  2008influential reference
• University of Birmingham The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

  2008cited by this paper
• Global phenotypic characterization of bacteria

  2008cited by this paper
• The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

  2008cited by this paper
• Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli

  2008cited by this paper
• Anaerobic Regulation of Citrate Fermentation by CitAB in Escherichia coli

  2008cited by this paper
• Escherichia coli NsrR Regulates a Pathway for the Oxidation of 3-Nitrotyramine to 4-Hydroxy-3-Nitrophenylacetate

  2008cited by this paper
• Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.

  2008cited by this paper
• The transcription regulator AllR senses both allantoin and glyoxylate and controls a set of genes for degradation and reutilization of purines.

  2008influential reference
• The molecular basis of selective promoter activation by the σS subunit of RNA polymerase

  2007cited by this paper
• RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

  2007cited by this paper
• PdhR (Pyruvate Dehydrogenase Complex Regulator) Controls the Respiratory Electron Transport System in Escherichia coli

  2007cited by this paper
• Enhancement of the Synthesis of RpoN, Cra, and H-NS by Polyamines at the Level of Translation in Escherichia coli Cultured with Glucose and Glutamate

  2007cited by this paper
• RutR is the uracil/thymine‐sensing master regulator of a set of genes for synthesis and degradation of pyrimidines

  2007cited by this paper
• CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

  2007cited by this paper
• Structure-based analysis of HU-DNA binding.

  2007cited by this paper
• Genomic SELEX Search for Target Promoters under the Control of the PhoQP-RstBA Signal Relay Cascade

  2007cited by this paper
• Effects of Fis on Escherichia coli gene expression during different growth stages.

  2007cited by this paper
• 22 Phylogenetic Footprinting

  2007cited by this paper
• folA, a New Member of the TyrR Regulon in Escherichia coli K-12

  2007cited by this paper
• Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology.

  2006cited by this paper
• DNA microarray technologies for measuring protein-DNA interactions.

  2006cited by this paper
• Stepwise binding and bending of DNA by Escherichia coli integration host factor

  2006cited by this paper
• DksA Is Required for Growth Phase-Dependent Regulation, Growth Rate-Dependent Control, and Stringent Control of fis Expression in Escherichia coli

  2006cited by this paper
• Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome

  2006cited by this paper
• Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110

  2006cited by this paper
• A previously undescribed pathway for pyrimidine catabolism.

  2006cited by this paper
• Escherichia coli K-12: a cooperatively developed annotation snapshot—2005

  2006cited by this paper
• The yjeB (nsrR) Gene of Escherichia coli Encodes a Nitric Oxide-Sensitive Transcriptional Regulator

  2006cited by this paper
• A Reassessment of the FNR Regulon and Transcriptomic Analysis of the Effects of Nitrate, Nitrite, NarXL, and NarQP as Escherichia coli K12 Adapts from Aerobic to Anaerobic Growth*

  2006cited by this paper
• Global gene expression analysis revealed an unsuspected deo operon under the control of molybdate sensor, ModE protein, in Escherichia coli

  2005cited by this paper
• Genome-Wide Transcriptional Response of Chemostat-Cultured Escherichia coli to Zinc

  2005cited by this paper
• Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome.

  2005cited by this paper
• Systematic search for the Cra‐binding promoters using genomic SELEX system

  2005cited by this paper
• Immobilization of Escherichia coli RNA Polymerase and Location of Binding Sites by Use of Chromatin Immunoprecipitation and Microarrays

  2005cited by this paper
• Functional Characterization in Vitro of All Two-component Signal Transduction Systems from Escherichia coli*

  2005influential reference
• RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

  2005cited by this paper
• A Global Regulatory Role of Gluconeogenic Genes in Escherichia coli Revealed by Transcriptome Network Analysis*

  2005cited by this paper
• Making connections between novel transcription factors and their DNA motifs.

  2005cited by this paper
• Charting gene regulatory networks: strategies, challenges and perspectives.

  2004cited by this paper
• Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes.

  2004cited by this paper
• Dps Protects Cells against Multiple Stresses during Stationary Phase

  2004cited by this paper
• The Escherichia coli fis Promoter Is Regulated by Changes in the Levels of Its Transcription Initiation Nucleotide CTP*

  2004cited by this paper
• RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12

  2004cited by this paper
• Transcriptional regulatory code of a eukaryotic genome

  2004cited by this paper
• Expression profiling using a hexamer-based universal microarray

  2004cited by this paper
• Identification of the CRP regulon using in vitro and in vivo transcriptional profiling.

  2004influential reference
• Maximizing the potential of functional genomics

  2004cited by this paper
• Network biology: understanding the cell's functional organization

  2004cited by this paper
• Probing the ArcA-P Modulon of Escherichia coli by Whole Genome Transcriptional Analysis and Sequence Recognition Profiling*

  2004cited by this paper
• Structure and evolution of transcriptional regulatory networks.

  2004cited by this paper
• Genome-Wide Transcriptional Analysis of the Cold Shock Response in Wild-Type and Cold-Sensitive, Quadruple-csp-Deletion Strains of Escherichia coli

  2004cited by this paper
• Gene expression in Escherichia coli biofilms

  2004cited by this paper
• Classification and Strength Measurement of Stationary-Phase Promoters by Use of a Newly Developed Promoter Cloning Vector

  2004cited by this paper
• Evolution of transcription factors and the gene regulatory network in Escherichia coli.

  2003cited by this paper
• The σ70 family of sigma factors

  2003cited by this paper
• Regulatory network of Escherichia coli: consistency between literature knowledge and microarray profiles.

  2003cited by this paper
• The role of Fe-S proteins in sensing and regulation in bacteria.

  2003cited by this paper
• Determinants of DNA bending in the DNA-cyclic AMP receptor protein complexes in Escherichia coli.

  2003cited by this paper
• Regulatory network of acid resistance genes in Escherichia coli

  2003cited by this paper
• Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites

  2003cited by this paper
• Transcriptional regulation of drug efflux genes by EvgAS, a two-component system in Escherichia coli.

  2003cited by this paper
• Global Gene Expression Profiling in Escherichia coli K12

  2003cited by this paper
• Identifying global regulators in transcriptional regulatory networks in bacteria.

  2003cited by this paper
• Entropic nature of the interaction between promoter bound CRP mutants and RNA polymerase.

  2003cited by this paper
• Multiple sigma subunits and the partitioning of bacterial transcription space.

  2003cited by this paper
• The sigma70 family of sigma factors.

  2003cited by this paper
• The role of dimerization in noise reduction of simple genetic networks.

  2003cited by this paper
• Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein.

  2002cited by this paper
• Two different modes of transcription repression of the Escherichia coli acetate operon by IclR

  2002cited by this paper
• Global Expression Profiling of Acetate-grown Escherichia coli *

  2002cited by this paper
• Transcriptional Regulatory Networks in Saccharomyces cerevisiae

  2002cited by this paper
• Network motifs in the transcriptional regulation network of Escherichia coli

  2002cited by this paper
• Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics

  2002cited by this paper
• Transcriptome analysis of all two‐component regulatory system mutants of Escherichia coli K‐12

  2002cited by this paper
• DNA microarray analysis of fim mutations in Escherichia coli

  2002cited by this paper
• Pseudomonas aeruginosa Displays Multiple Phenotypes during Development as a Biofilm

  2002cited by this paper
• LrhA as a new transcriptional key regulator of flagella, motility and chemotaxis genes in Escherichia coli

  2002cited by this paper
• Factors influencing the identification of transcription factor binding sites by cross-species comparison.

  2002cited by this paper
• Escherichia coli Gene Expression Responsive to Levels of the Response Regulator EvgA

  2002cited by this paper
• Conservation of gene co-regulation in prokaryotes and eukaryotes.

  2002cited by this paper
• Collaborative Regulation of Escherichia coli Glutamate-Dependent Acid Resistance by Two AraC-Like Regulators, GadX and GadW (YhiW)

  2002cited by this paper
• Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data

  2002cited by this paper
• DNA supercoiling and transcription in Escherichia coli: The FIS connection.

  2001cited by this paper
• DNA Microarray-Mediated Transcriptional Profiling of the Escherichia coli Response to Hydrogen Peroxide

  2001cited by this paper
• Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.

  2001cited by this paper
• A comparative genomics approach to prediction of new members of regulons.

  2001cited by this paper
• Global Impact of sdiA Amplification Revealed by Comprehensive Gene Expression Profiling of Escherichia coli

  2001cited by this paper

• Using Network Models to Understand Biological Signaling Architecture

  2026cites this paper
• Transcription Factor HusR (YnfL) Is a Novel Regulator for Hydroxyurea Sensitivity in Escherichia coli K-12

  2026cites this paper
• A Chemical Epigenetic Probe to Capture the Site-Specific DNA-Binding Protein Complex

  2025cites this paper
• The pheS5-fit95 interface is essential for eliciting hallmark phenotype of fitA76 in Escherichia coli

  2025cites this paper
• Exploring the concept of bacterial memory

  2025cites this paper
• The role of YbdO in regulating acid resistance and biofilm formation in avian pathogenic Escherichia coli

  2025cites this paper
• Escherichia coli is poised to grow using 5′-deoxynucleosides via MtnR and CRP regulation of DHAP shunt gene expression

  2025cites this paper
• Analyzing Wet-Neuromorphic Computing Using Bacterial Gene Regulatory Neural Networks

  2025cites this paper
• RetS-mediated environmental sensing coordinates TetR-dependent regulation of type III secretion system and virulence in Pseudomonas syringae pv. actinidiae

  2025cites this paper
• A chemical epigenetic tool to probe site-specific DNA-binding protein complexes.

  2025cites this paper
• Comparative Genomic Analysis of 66 Bacteriophages Infecting Morganella morganii Strains

  2025cites this paper
• RcsB and H-NS Both Contribute to the Repression the Expression of the csgDEFG Operon

  2025cites this paper
• pheST operon dynamics and pheS gene duplication mediated genome stability and evolution in E. coli: evidence that fitC4 is an allele of pheS

  2025cites this paper
• Novel Regulators of the flhDC Gene Encoding the Flagella Master Regulator in Escherichia Coli K-12

  2025cites this paper
• The CitAB two-component system is involved in pathogenesis regulation in Avian pathogenic Escherichia coli

  2025cites this paper
• Genetic and molecular characterization of fit95 mutation of Escherichia coli: evidence that fit95 is an allele of pheT

  2024cites this paper
• TetR family transcriptional regulators: Lipid metabolism and drug resistance in mycobacteria

  2024cites this paper
• The MarR family regulator RmaH mediates acid tolerance of Lactococcus lactis through regulating peptidoglycan modification genes.

  2024cites this paper
• Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?

  2024cites this paper
• Identification of a novel alternate promoter element in the pheST operon of Escherichia coli

  2024cites this paper
• The mechanisms of environmental stress tolerance in Gluconobacter oxydans: progress and perspectives

  2024cites this paper
• The Trimeric Autotransporter Adhesin EmaA and Infective Endocarditis

  2024cites this paper
• MSMEG_5850, a global TetR family member supports Mycobacterium smegmatis to survive environmental stress

  2024cites this paper
• Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis

  2024cites this paper
• Environment signal dependent biocontainment systems for engineered organisms: Leveraging triggered responses and combinatorial systems

  2024cites this paper
• Protein‐metabolite Interactions Based on Chemical Targeting Methods

  2024cites this paper
• Advances in succinic acid production: the enhancement of CO2 fixation for the carbon sequestration benefits

  2024cites this paper
• Genetic and molecular studies of fitC4 and its suppressors fitA76* and fit95 in Escherichia coli

  2024cites this paper
• Genomic SELEX Screening of Regulatory Targets of Transcription Factors.

  2024cites this paper
• Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis

  2023cites this paper
• Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis

  2023cites this paper
• Revealing gene regulation-based neural network computing in bacteria

  2023cites this paper
• Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance

  2023cites this paper
• Small RNAs, Large Networks: Posttranscriptional Regulons in Gram-Negative Bacteria.

  2023cites this paper
• Regulation of adhesin synthesis in aggregatibacter actinomycetemcomitans.

  2023cites this paper
• Genomic SELEX Reveals Pervasive Role of the Flagella Master Regulator FlhDC in Carbon Metabolism

  2023cites this paper
• The Knowns and Unknowns in Protein–Metabolite Interactions

  2023cites this paper
• Sulisobenzone is a potent inhibitor of the global transcription factor Cra.

  2023cites this paper
• Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis

  2023cites this paper
• Regulation by cyclic di-GMP attenuates dynamics and enhances robustness of bimodal curli gene activation in Escherichia coli

  2023cites this paper
• Metal-Responsive Transcription Factors Co-Regulate Anti-Sigma Factor (Rsd) and Ribosome Dimerization Factor Expression

  2023cites this paper
• Generating information-dense promoter sequences with optimal string packing

  2023cites this paper
• Expression of tardigrade disordered proteins impacts the tolerance to biofuels in a model cyanobacterium Synechocystis sp. PCC 6803

  2023cites this paper
• CRISPR Interference (CRISPRi) Mediated Suppression of OmpR Gene in E. coli: An Alternative Approach to Inhibit Biofilm

  2022cites this paper
• Biosynthetic Pathway and Metabolic Engineering of Succinic Acid

  2022cites this paper
• De novo design of the global transcriptional factor Cra‐regulated promoters enables highly sensitive glycolysis flux biosensor for dynamic metabolic control

  2022cites this paper
• Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage

  2022cites this paper
• SigH stress response mediates killing of Mycobacterium tuberculosis by activating nitronaphthofuran prodrugs via induction of Mrx2 expression

  2022cites this paper
• Transcription Factor SrsR (YgfI) Is a Novel Regulator for the Stress-Response Genes in Stationary Phase in Escherichia coli K-12

  2022cites this paper
• Engineering of global transcription factor FruR to redirect the carbon flow in Escherichia coli for enhancing l-phenylalanine biosynthesis

  2022cites this paper
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli

  2021cites this paper
• Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-12

  2021cites this paper
• Fis Connects Two Sensory Pathways, Quorum Sensing and Surface Sensing, to Control Motility in Vibrio parahaemolyticus

  2021cites this paper
• Regulation of Virulence Gene Expression in Bacteria: A Review

  2021influential citation
• Importance of the 5′ regulatory region to bacterial synthetic biology applications

  2021cites this paper
• Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12

  2021cites this paper
• Hierarchy of transcription factor network in Escherichia coli K-12: H-NS-mediated silencing and Anti-silencing by global regulators.

  2021cites this paper
• Potential roles of functional bacterial amyloid proteins, bacterial biosurfactants and other putative gut microbiota products in the etiopathogeny of Parkinson’s Disease

  2021cites this paper
• Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis

  2021cites this paper
• Acetate overflow metabolism regulates a major metabolic shift after glucose depletion in Escherichia coli

  2021cites this paper
• Fis connects two sensory pathways, quorum sensing and surface sensing, to control motility in Vibrio parahaemolyticus

  2021cites this paper
• Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida

  2021cites this paper
• Escherichia coli segments its controls on carbon‐dependent gene expression into global and specific regulations

  2021cites this paper
• Development of bifunctional biosensors for sensing and dynamic control of glycolysis flux in metabolic engineering.

  2021cites this paper
• The Role of Some Transcription Factors in Expression of GyrA and GyrB Following Exposure to Ciprofloxacin

  2020cites this paper
• Engineering prokaryotic regulator IrrE to enhance stress tolerance in budding yeast

  2020cites this paper
• Structural basis of a novel repressor, SghR, controlling Agrobacterium infection by cross-talking to plants

  2020cites this paper
• Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12.

  2020cites this paper
• The two-component system, BasSR, is involved in the regulation of biofilm and virulence in avian pathogenic Escherichia coli

  2020cites this paper
• Flexible comparative genomics of prokaryotic transcriptional regulatory networks

  2020cites this paper
• Regulatory Role of the Two-Component System BasSR in the Expression of the EmrD Multidrug Efflux in Escherichia coli

  2020cites this paper
• Regulation of biofilm formation by marT in Salmonella Typhimurium

  2020cites this paper
• Unraveling the Complex Interplay of Fis and IHF Through Synthetic Promoter Engineering

  2020influential citation
• Elucidation of gene regulatory mechanisms in ageing bacterial colonies and tool development for cell factory optimization

  2020cites this paper
• Transcriptional response of mar, sox and rob regulon against concentration gradient carbapenem stress within Escherichia coli isolated from hospital acquired infection

  2020cites this paper
• Transporters of glucose and other carbohydrates in bacteria

  2020cites this paper
• The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition

  2020cites this paper
• Phylogenetic Studies on the Prodigiosin Biosynthetic Operon

  2019cites this paper
• A quantitative method for proteome reallocation using minimal regulatory interventions

  2019cites this paper
• An Alternative Platform for Protein Expression Using an Innate Whole Expression Module from Metagenomic DNA

  2019cites this paper
• Vesicles From Vibrio cholerae Contain AT-Rich DNA and Shorter mRNAs That Do Not Correlate With Their Protein Products

  2019cites this paper
• Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12

  2019cites this paper
• Modulating Fis and IHF binding specificity, crosstalk and regulatory logic through the engineering of complex promoters

  2019influential citation
• Functional Amyloids.

  2019cites this paper
• Regulatory Role of Pyruvate-Sensing BtsSR in Biofilm Formation by Escherichia coli K-12.

  2019cites this paper
• Investigating members of the Omp85 protein superfamily in Klebsiella pneumoniae

  2019cites this paper
• LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species

  2019cites this paper
• Regulatory Mechanism of Nicotine Degradation in Pseudomonas putida

  2019cites this paper
• A Small RNA and DNA Binding Protein Contribute to Biofilm Development in Bartonella henselae

  2019cites this paper
• Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli

  2019cites this paper
• Novel regulation from novel interactions: Identification of an RNA sponge that controls the levels, processing and efficacy of the RoxS riboregulator of central metabolism in Bacillus subtilis

  2019cites this paper
• Identification of new DNA-associated proteins from Waddlia chondrophila

  2019cites this paper
• Coordinated Regulation of Rsd and RMF for Simultaneous Hibernation of Transcription Apparatus and Translation Machinery in Stationary-Phase Escherichia coli

  2019cites this paper
• Discovery of novel bioactive natural products driven by genome mining.

  2018cites this paper
• Regulation of Escherichia coli Biofilm Formation (Review)

  2018cites this paper
• Title Differential Regulation of rRNA and tRNA Transcription from the rRNA-tRNA Composite Operon in Escherichia coli

  2018cites this paper
• High-Resolution, High-Throughput Analysis of Hfq-Binding Sites Using UV Crosslinking and Analysis of cDNA (CRAC).

  2018cites this paper
• Altered Distribution of RNA Polymerase Lacking the Omega Subunit within the Prophages along the Escherichia coli K-12 Genome

  2018cites this paper
• Glu571 of PheT plays a pivotal role in the thermal stability of Escherichia coli PheRS enzyme

  2018cites this paper
• Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase

  2018cites this paper