AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesInformation ScienceHealth Care
Replication Protein ATranscription FactorsDNA-Binding ProteinsDNA HelicasesTranscription, GeneticReplication OriginDNA ReplicationMolecular Sequence DataBase SequencePlasmidsTrans-ActivatorsNanovirusBacterial ProteinsEscherichia coliOrigin Recognition ComplexProtein BindingBinding SitesAmino Acid SequenceMutationPromoter Regions, GeneticDnaB HelicasesCell LineRepliconDNA, BacterialViral ProteinsDNADNA, ViralGene Expression RegulationSp1 Transcription FactorChromosomes, BacterialRepressor ProteinsGene Expression Regulation, BacterialNuclear ProteinsGeminiviridaeRNA, MessengerProtein Structure, TertiaryHeLa CellsTranscriptional ActivationNucleic Acid ConformationEscherichia coli ProteinsRNA, ViralCell NucleusDNA, Single-StrandedSequence Homology, Amino AcidTransfectionCells, CulturedSequence AlignmentBasic Helix-Loop-Helix Transcription FactorsSignal TransductionTranscription Factor AP-1Cloning, MolecularHomeodomain ProteinsSaccharomyces cerevisiaeDNA Replication TimingGene Expression Regulation, DevelopmentalGene Expression Regulation, ViralForkhead Transcription FactorsBasic-Leucine Zipper Transcription FactorsSaccharomyces cerevisiae ProteinsGenes, ReporterChromatinRegulatory Sequences, Nucleic AcidRecombinant Fusion ProteinsAdenosine TriphosphatasesCell Cycle ProteinsCell DifferentiationTranscription Factor AP-2ProteinsModels, MolecularChromatin ImmunoprecipitationModels, GeneticTranscription Factors, TFIICell CycleS PhaseReverse Transcriptase Polymerase Chain ReactionGenome, ViralTranscription Factor TFIIDModels, BiologicalEnhancer Elements, GeneticYY1 Transcription FactorKruppel-Like Transcription FactorsReplication Protein CGene ExpressionTranscription Initiation SiteHIV-1Electrophoretic Mobility Shift AssayCell Line, TumorPhosphorylationNF-kappa BZinc FingersSTAT3 Transcription FactorSequence DeletionMutagenesisGene Expression ProfilingTATA BoxRestriction MappingPhenotypeVirus ReplicationGATA4 Transcription FactorKinetics
LysRInitiationRegulatorBacterialSequencesChromosomeForksSubunitElongationProcessesBacteriaStrandsTerminationTimelyCellularSpeciesStartFunctionHighChromosomalFlipping to initiate replicationDirectly or indirectlyRepressorProkaryotesATPaseRibosomal proteinGenomeDynamicsHypothetical proteinColiSequenceSubsequentlyMutationsRecombinationConsistentPutativeOriginSynthesisHelixRepliconObservationsSitesComplementCoordinationCellControlPromoteSystem
LysR1
  • LysR substrate binding domain, Bacterial regulatory helix-turn-helix protein [Interproscan]. (ntu.edu.sg)
Initiation5
  • During initiation, the replication machineries - termed replisomes - are assembled on DNA in a bidirectional fashion. (wikipedia.org)
  • The replicator thereby specifies the location of replication initiation events, and the chromosome region that is replicated from a single origin or initiation event is defined as the replicon. (wikipedia.org)
  • Obviously, the initiation of chromosome replication is essential to bacterial reproduction, but this process is not inhibited by any of the currently-used antimicrobial agents. (mdpi.com)
  • Translation initiation factor 1A / IF-1 [Interproscan]. (ntu.edu.sg)
  • Translation initiation factor SUI1 [Interproscan]. (ntu.edu.sg)
Regulator1
  • protein_coding" "AAC74319","hns","Escherichia coli","global DNA-binding transcriptional dual regulator H-NS [Ensembl]. (ntu.edu.sg)
Bacterial2
  • A fundamental feature of the replicon hypothesis is that it relies on positive regulation to control DNA replication onset, which can explain many experimental observations in bacterial and phage systems. (wikipedia.org)
  • proposed a 206 protein-coding gene core of aminimal bacterial gene set based on analysis of several free-living andendosymbiotic bacterial genomes (3). (fullblog.com.ar)
Sequences1
  • The concept of the replicator as a genetic entity has proven very useful in the quest to identify replicator DNA sequences and initiator proteins in prokaryotes, and to some extent also in eukaryotes, although the organization and complexity of replicators differ considerably between the domains of life. (wikipedia.org)
Chromosome1
  • Chromosome replication is triggered when a nucleoprotein complex, termed the orisome, assembles, unwinds the duplex DNA, and recruits the proteins required to establish new replication forks. (mdpi.com)
Forks1
  • In the elongation phase, replisomes travel in opposite directions with the replication forks, unwinding the DNA helix and synthesizing complementary daughter DNA strands using both parental strands as templates. (wikipedia.org)
Subunit2
  • Nonetheless,some of the putatively disrupted genes, such as isoleucyl andtyrosyl-tRNA synthetases (MG345 & MG455), DNA replication gene dnaA(MG469), and DNA polymerase HI, subunit alpha (MG261) are thought toperform essential functions. (fullblog.com.ar)
  • protein_coding" "AAC73960","hcp","Escherichia coli","hybrid-cluster [4Fe-2S-2O] subunit of anaerobic terminal reductases [Ensembl]. (ntu.edu.sg)
Elongation1
Processes2
  • The necessity to regulate origin location likely arises from the need to coordinate DNA replication with other processes that act on the shared chromatin template to avoid DNA strand breaks and DNA damage. (wikipedia.org)
  • p)ppGpp not only controls various stages of central dogma processes (replication, transcription, ribosome maturation and translation) and central metabolism but also regulates various physiological processes such as pathogenesis, persistence, motility and competence. (bvsalud.org)
Bacteria2
  • Nonetheless, research subsequent to Jacob's, Brenner's and Cuzin's proposal of the replicon model has discovered many additional layers of replication control in bacteria and eukaryotes that comprise both positive and negative regulatory elements, highlighting both the complexity and the importance of restricting DNA replication temporally and spatially. (wikipedia.org)
  • Tight coordination between transcription and translation has long been recognized as the hallmark of gene expression in bacteria. (bvsalud.org)
Strands1
  • Synthesis of daughter strands starts at discrete sites, termed replication origins, and proceeds in a bidirectional manner until all genomic DNA is replicated. (wikipedia.org)
Termination2
  • Once replication is complete, specific termination events lead to the disassembly of replisomes. (wikipedia.org)
  • In Escherichia coli cells, disruption of the transcription-translation coordination leads to the loss of transcription processivity via triggering Rho-mediated premature transcription termination. (bvsalud.org)
Timely2
  • Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. (wikipedia.org)
  • During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. (bvsalud.org)
Cellular1
  • To ensure complete and accurate duplication of the entire genome and the correct flow of genetic information to progeny cells, all DNA replication events are not only tightly regulated with cell cycle cues but are also coordinated with other cellular events such as transcription and DNA repair. (wikipedia.org)
Species2
  • Although the specific replication origin organization structure and recognition varies from species to species, some common characteristics are shared. (wikipedia.org)
  • The1999 report by some of the present inventors on the essential microbialgene for M. genitalium and its closest relative, Mycoplasma pneumoniae,mapped ~2200 transposon insertion sites in these two species, andidentified 130 putatively non-essential M. genitalium protein-codinggenes or M. pneumoniae orthologs of M. genitalium genes. (fullblog.com.ar)
Start1
Function4
  • Protein of unknown function (DUF1158) [Interproscan]. (ntu.edu.sg)
  • Protein of unknown function (DUF2526) [Interproscan]. (ntu.edu.sg)
  • Protein of unknown function (DUF441) [Interproscan]. (ntu.edu.sg)
  • Protein of unknown function (DUF2511) [Interproscan]. (ntu.edu.sg)
High2
  • A key prerequisite for DNA replication is that it must occur with extremely high fidelity and efficiency exactly once per cell cycle to prevent the accumulation of genetic alterations with potentially deleterious consequences for cell survival and organismal viability. (wikipedia.org)
  • The genome atlases allowed for distinguishing distinct DNA structures and highlighted suspicious high transcription zones. (mdpi.com)
Chromosomal1
  • Incomplete, erroneous, or untimely DNA replication events can give rise to mutations, chromosomal polyploidy or aneuploidy, and gene copy number variations, each of which in turn can lead to diseases, including cancer. (wikipedia.org)
Flipping to initiate replication1
  • This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription. (nih.gov)
Directly or indirectly2
  • It is often unclear as to whether host proteins directly or indirectly regulate transposition reactions. (biomedcentral.com)
  • The fact that the size of these anucleate cells is relatively constant (but see [ 9 ] ) is consistent with the idea that DnaA is involved, directly or indirectly, in the positioning of the division site. (encyclopedia.pub)
Repressor1
  • H-NS typically regulates cellular functions through its potent transcriptional repressor function. (biomedcentral.com)
Prokaryotes2
  • This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses. (wikipedia.org)
  • The concept of the replicator as a genetic entity has proven very useful in the quest to identify replicator DNA sequences and initiator proteins in prokaryotes, and to some extent also in eukaryotes, although the organization and complexity of replicators differ considerably between the domains of life. (wikipedia.org)
ATPase1
Ribosomal protein2
  • 23209 ribosomal protein S12 methylthiotransferase rimO BBZA01000003 CDS ARMA_0051 23344. (go.jp)
  • RS20_BEII9 30S ribosomal protein S20 OS=Beijerinckia indica subsp. (isoelectricpointdb.org)
Genome7
  • The origin of replication (also called the replication origin) is a particular sequence in a genome at which replication is initiated. (wikipedia.org)
  • To ensure complete and accurate duplication of the entire genome and the correct flow of genetic information to progeny cells, all DNA replication events are not only tightly regulated with cell cycle cues but are also coordinated with other cellular events such as transcription and DNA repair. (wikipedia.org)
  • Transcription of all required genes has to take place simultaneously with genome duplication. (frontiersin.org)
  • In addition, the existing data also demonstrate that the replication fork trap in E. coli imposes significant constraints to genome duplication if ectopic origins are active. (frontiersin.org)
  • We describe the current models of how replication fork fusion events can cause serious problems for genome duplication, as well as models of how such problems might be alleviated both by a number of repair pathways as well as the replication fork trap system. (frontiersin.org)
  • Considering the problems associated both with head-on replication-transcription conflicts as well as head-on replication fork fusion events might provide clues of how these genome trafficking issues have contributed to shape the distinct architecture of bacterial chromosomes. (frontiersin.org)
  • Overall, protein-coding density of bacterial genomes is with 85-90% high ( McCutcheon and Moran, 2011 ) and the correlation between genome size and the number of genes is surprisingly constant ( Touchon and Rocha, 2016 ). (frontiersin.org)
Dynamics2
  • Norris, V. DnaA and Hyperstructure Dynamics in the Cell Cycle. (encyclopedia.pub)
  • DnaA and Hyperstructure Dynamics in the Cell Cycle" Encyclopedia , https://encyclopedia.pub/entry/49596 (accessed December 02, 2023). (encyclopedia.pub)
Hypothetical protein45
  • 4628 hypothetical protein BBZA01000001 CDS ARMA_0005 5077. (go.jp)
  • 5685 hypothetical protein BBZA01000001 CDS ARMA_0006 5873. (go.jp)
  • 7021 hypothetical protein BBZA01000001 CDS ARMA_0007 complement(7097. (go.jp)
  • 7504) hypothetical protein BBZA01000001 CDS ARMA_0008 complement(7590. (go.jp)
  • 11958) hypothetical protein BBZA01000001 CDS ARMA_0012 12170. (go.jp)
  • 578 hypothetical protein BBZA01000002 CDS ARMA_0016 684. (go.jp)
  • 2342 hypothetical protein BBZA01000002 CDS ARMA_0017 2339. (go.jp)
  • 3094 hypothetical protein BBZA01000002 CDS ARMA_0018 3478. (go.jp)
  • 4371 hypothetical protein BBZA01000002 CDS ARMA_0019 complement(4468. (go.jp)
  • 5751) hypothetical protein BBZA01000002 CDS ARMA_0021 complement(5880. (go.jp)
  • 6020) hypothetical protein BBZA01000002 CDS ARMA_0020 6069. (go.jp)
  • 7490 hypothetical protein BBZA01000002 CDS ARMA_0022 complement(7569. (go.jp)
  • 10130) hypothetical protein BBZA01000002 CDS ARMA_0023 10363. (go.jp)
  • 12985 hypothetical protein BBZA01000002 CDS ARMA_0025 13067. (go.jp)
  • 13828 hypothetical protein BBZA01000002 CDS ARMA_0026 13840. (go.jp)
  • 15584 hypothetical protein BBZA01000003 CDS ARMA_0028 complement(2147. (go.jp)
  • 2662) hypothetical protein BBZA01000003 CDS ARMA_0030 complement(2909. (go.jp)
  • 3070) hypothetical protein BBZA01000003 CDS ARMA_0029 3089. (go.jp)
  • 3247 hypothetical protein BBZA01000003 CDS ARMA_0031 3817. (go.jp)
  • 11054 hypothetical protein BBZA01000003 CDS ARMA_0036 11082. (go.jp)
  • 11983 hypothetical protein BBZA01000003 CDS ARMA_0038 complement(11960. (go.jp)
  • 12616) hypothetical protein BBZA01000003 CDS ARMA_0039 12726. (go.jp)
  • 13859 hypothetical protein BBZA01000003 CDS ARMA_0040 13859. (go.jp)
  • 14554 hypothetical protein BBZA01000003 CDS ARMA_0041 14582. (go.jp)
  • 15289 hypothetical protein BBZA01000003 CDS ARMA_0042 15306. (go.jp)
  • 15746 hypothetical protein BBZA01000003 CDS ARMA_0043 complement(15750. (go.jp)
  • 16253) hypothetical protein BBZA01000003 CDS ARMA_0044 complement(16376. (go.jp)
  • 16723) hypothetical protein BBZA01000003 tRNA ARMA_tRNA01 complement(16745. (go.jp)
  • 17762 hypothetical protein BBZA01000003 CDS ARMA_0046 17875. (go.jp)
  • 19373 hypothetical protein BBZA01000003 CDS ARMA_0048 complement(19431. (go.jp)
  • 20651) hypothetical protein BBZA01000003 CDS ARMA_0049 20873. (go.jp)
  • 21793 hypothetical protein BBZA01000003 CDS ARMA_0050 21812. (go.jp)
  • 24549 hypothetical protein BBZA01000003 CDS ARMA_0052 24709. (go.jp)
  • 25812 hypothetical protein BBZA01000003 CDS ARMA_0053 25854. (go.jp)
  • 27638 hypothetical protein BBZA01000003 CDS ARMA_0054 27690. (go.jp)
  • 29561 hypothetical protein BBZA01000003 CDS ARMA_0055 29551. (go.jp)
  • 30963 hypothetical protein BBZA01000003 CDS ARMA_0056 30956. (go.jp)
  • 32158 hypothetical protein BBZA01000003 CDS ARMA_0057 32158. (go.jp)
  • 35130 hypothetical protein BBZA01000003 CDS ARMA_0058 35127. (go.jp)
  • 35501 hypothetical protein BBZA01000003 CDS ARMA_0059 35523. (go.jp)
  • 38051 hypothetical protein BBZA01000003 CDS ARMA_0060 38048. (go.jp)
  • 38443 hypothetical protein BBZA01000003 CDS ARMA_0061 38445. (go.jp)
  • 40466 hypothetical protein BBZA01000003 CDS ARMA_0063 complement(40556. (go.jp)
  • 42784) hypothetical protein BBZA01000004 CDS ARMA_0066 23. (go.jp)
  • 493 hypothetical protein BBZA01000004 CDS ARMA_0067 664. (go.jp)
Coli7
  • protein_coding" "AAC73204","ftsQ","Escherichia coli","divisome assembly protein, membrane anchored protein involved in growth of wall at septum [Ensembl]. (ntu.edu.sg)
  • protein_coding" "AAC73303","nlpE","Escherichia coli","lipoprotein involved with copper homeostasis and adhesion [Ensembl]. (ntu.edu.sg)
  • protein_coding" "AAC73572","dnaX","Escherichia coli","DNA polymerase III/DNA elongation factor III, tau and gamma subunits [Ensembl]. (ntu.edu.sg)
  • protein_coding" "AAC73733","dacA","Escherichia coli","D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5) [Ensembl]. (ntu.edu.sg)
  • protein_coding" "AAC73976","ftsK","Escherichia coli","DNA translocase at septal ring sorting daughter chromsomes [Ensembl]. (ntu.edu.sg)
  • protein_coding" "AAC74007","cmoM","Escherichia coli","putative S-adenosyl-L-methionine-dependent methyltransferase [Ensembl]. (ntu.edu.sg)
  • protein_coding" "AAC74207","potD","Escherichia coli","spermidine/putrescine ABC transporter periplasmic binding protein [Ensembl]. (ntu.edu.sg)
Sequence2
  • The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. (nih.gov)
  • Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). (nih.gov)
Subsequently1
  • Once bound to replicators, initiators (often with the help of co-loader proteins) deposit replicative helicases onto DNA, which subsequently drive the recruitment of additional replisome components and the assembly of the entire replication machinery. (wikipedia.org)
Mutations1
  • These mutations were mapped to the same locus and the gene was called dnaA [ 7 ] . (encyclopedia.pub)
Recombination1
  • 1833 recombination protein RecA recA BBZA01000004 CDS ARMA_0068 complement(1901. (go.jp)
Consistent1
  • We also show that H-NS forms cross-links with the Tn5 transposase protein specifically in the transpososome, an observation consistent with the two proteins occupying overlapping binding sites in the transposon ends. (biomedcentral.com)
Putative2
  • 10614) putative ABC transport system permease protein BBZA01000001 CDS ARMA_0010 complement(10625. (go.jp)
  • 11353) putative ABC transport system ATP-binding protein BBZA01000001 CDS ARMA_0011 complement(11350. (go.jp)
Origin2
  • Although the specific replication origin organization structure and recognition varies from species to species, some common characteristics are shared. (wikipedia.org)
  • The model postulates that a diffusible, trans-acting factor, a so-called initiator, interacts with a cis-acting DNA element, the replicator, to promote replication onset at a nearby origin. (wikipedia.org)
Synthesis1
  • Synthesis of daughter strands starts at discrete sites, termed replication origins, and proceeds in a bidirectional manner until all genomic DNA is replicated. (wikipedia.org)
Helix1
  • The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. (nih.gov)
Replicon2
  • A fundamental feature of the replicon hypothesis is that it relies on positive regulation to control DNA replication onset, which can explain many experimental observations in bacterial and phage systems. (wikipedia.org)
  • By contrast, a model of negative regulation (analogous to the replicon-operator model for transcription) fails to explain the above findings. (wikipedia.org)
Observations1
Sites1
Complement4
  • Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. (wikipedia.org)
  • 14478 3-oxoacyl-[acyl-carrier protein] reductase fabG BBZA01000001 CDS ARMA_0014 complement(14430. (go.jp)
  • 41314) energy-coupling factor transport system permease protein ecfT BBZA01000003 CDS ARMA_0064 complement(41356. (go.jp)
  • 41931) energy-coupling factor transport system substrate-specific component qrtT BBZA01000003 CDS ARMA_0065 complement(42026. (go.jp)
Coordination1
  • During carbon downshift, a lack of stringent response in relA deficient strain leads to disruption of the transcription-translation coordination, thus compromising the transcription processivity and further the timely expression of related catabolic operons for utilizing secondary carbon sources. (bvsalud.org)
Cell2
  • A key prerequisite for DNA replication is that it must occur with extremely high fidelity and efficiency exactly once per cell cycle to prevent the accumulation of genetic alterations with potentially deleterious consequences for cell survival and organismal viability. (wikipedia.org)
  • POTRA domain, Cell division protein FtsQ [Interproscan]. (ntu.edu.sg)
Control1
  • Despite the fundamental nature of these events, organisms have evolved surprisingly divergent strategies that control replication onset. (wikipedia.org)
Promote1
  • On the other hand there are some examples where transposons appear to have co-opted host proteins to promote their transposition. (biomedcentral.com)
System1
  • 14787 ABC-2 type transport system ATP-binding protein BBZA01000002 CDS ARMA_0027 14784. (go.jp)