The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes

scientific article

The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1030749434
P356DOI10.1038/NRMICRO2283
P698PubMed publication ID20140025
P5875ResearchGate publication ID41414533

P2093author name stringMichael P Jennings
Yogitha N Srikhanta
Kate L Fox
P2860cites workType I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)Q24548508
Short-sequence DNA repeats in prokaryotic genomesQ24548611
Nucleoside triphosphate-dependent restriction enzymesQ24555228
Structure and function of type II restriction endonucleasesQ24555230
Phase and antigenic variation in bacteriaQ24561666
Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymesQ24655282
Epigenetic gene regulation in the bacterial worldQ24669987
Characterization of the Type III restriction endonuclease PstII from Providencia stuartii.Q24816456
Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitroQ24816467
Slipped-strand mispairing: a major mechanism for DNA sequence evolutionQ28295992
The major phase-variable outer membrane protein of Escherichia coli structurally resembles the immunoglobulin A1 protease class of exported protein and is regulated by a novel mechanism involving Dam and oxyRQ30175814
Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and loopingQ30479841
Characterization of a CACAG pentanucleotide repeat in Pasteurella haemolytica and its possible role in modulation of a novel type III restriction-modification systemQ30642496
Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systemsQ30662423
Reassortment of pilin genes in Neisseria gonorrhoeae occurs by two distinct mechanismsQ56984407
Variations in the surface proteins and restriction enzyme systems of Mycoplasma pulmonis in the respiratory tract of infected ratsQ57916398
Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58Q57976193
Restriction-modification systems in Mycoplasma sppQ61037744
DNA cleavage by the type IC restriction-modification enzyme EcoR124IIQ64389312
The outer membrane protein, antigen 43, mediates cell-to-cell interactions within Escherichia coli biofilmsQ64449674
DNA restriction--modification genes of phage P1 and plasmid p15B. Structure and in vitro transcriptionQ67286988
DNA restriction--modification enzymes of phage P1 and plasmid p15B. Subunit functions and structural homologiesQ67286996
DNA Modification and RestrictionQ69353381
Host specificity of DNA produced by Escherichia coli. XII. The two restriction and modification systems of strain 15T-Q69920009
Phase variation of Ag43 in Escherichia coli: Dam-dependent methylation abrogates OxyR binding and OxyR-mediated repression of transcriptionQ73486820
Comparative whole-genome analyses reveal over 100 putative phase-variable genes in the pathogenic Neisseria sppQ74339153
Kinetic models of translocation, head-on collision, and DNA cleavage by type I restriction endonucleasesQ77594570
Direct observation of DNA translocation and cleavage by the EcoKI endonuclease using atomic force microscopyQ77787225
The role of Dam methylation in phase variation of Haemophilus influenzae genes involved in defence against phage infectionQ81317030
Methylation and cleavage sequences of the EcoP1 restriction-modification enzymeQ40218789
DNA recognition and cleavage by the EcoP15 restriction endonucleaseQ40289784
Phase-variable lipopolysaccharide structures enhance the invasive capacity of Haemophilus influenzaeQ40428771
An essential role for DNA adenine methylation in bacterial virulenceQ40639021
Translational frameshifting in the control of transposition in bacteriaQ40852573
Characterization of a restriction enzyme from Escherichia coli K carrying a mutation in the modification subunitQ40934053
DNA adenine methylation regulates virulence gene expression in Salmonella enterica serovar Typhimurium.Q41063123
Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domainQ41131058
Overproduction of DNA adenine methyltransferase alters motility, invasion, and the lipopolysaccharide O-antigen composition of Yersinia enterocoliticaQ41447666
Oral immunization with a dam mutant of Yersinia pseudotuberculosis protects against plagueQ41458134
Regulation of Pap phase variation. Lrp is sufficient for the establishment of the phase off pap DNA methylation pattern and repression of pap transcription in vitroQ41716758
Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding bacteriophage 933W of enterohemorrhagic Escherichia coli O157:H7Q41911686
DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymesQ42002446
The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases.Q42617085
A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA.Q42645045
Molecular characterization of LbpB, the second lactoferrin-binding protein of Neisseria meningitidis.Q42673499
Simple sequence repeats in the Helicobacter pylori genomeQ42676800
High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzaeQ43056361
S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymesQ43648772
Genomic comparisons among gamma-proteobacteriaQ43674825
DNA cleavage by type III restriction-modification enzyme EcoP15I is independent of spacer distance between two head to head oriented recognition sitesQ43749963
Envelope instability in DNA adenine methylase mutants of Salmonella entericaQ43947009
Posttranscriptional regulation of EcoP1I and EcoP15I restriction activityQ43980444
S-Adenosyl Methionine Prevents Promiscuous DNA Cleavage by the EcoP1I type III Restriction EnzymeQ44608364
The bacteriophage P1 restriction endonucleaseQ44914916
Stopped-flow and mutational analysis of base flipping by the Escherichia coli Dam DNA-(adenine-N6)-methyltransferaseQ44995080
The DNA translocation and ATPase activities of restriction-deficient mutants of Eco KI.Q45070688
Phase variable restriction-modification systems in Moraxella catarrhalisQ45183866
Host specificity of DNA in Haemophilus influenzae: the restriction and modification systems in strains Rb and Rf.Q45240020
Effect of repeated in vivo passage (in mice) on Salmonella typhimurium dam mutant virulence and fitnessQ46821029
The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pyloriQ47792946
Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymesQ48069333
Alteration of DNA adenine methylase (Dam) activity in Pasteurella multocida causes increased spontaneous mutation frequency and attenuation in miceQ48233604
Type III DNA restriction and modification systems EcoP1 and EcoP15. Nucleotide sequence of the EcoP1 operon, the EcoP15 mod gene and some EcoP1 mod mutantsQ48327658
Sequence diversity among related genes for recognition of specific targets in DNA moleculesQ48398543
2001 Fred Griffith review lecture. Immigration control of DNA in bacteria: self versus non-selfQ48575149
DNA methylation-dependent regulation of pef expression in Salmonella typhimuriumQ50122267
Increased adherence and actin pedestal formation by dam-deficient enterohaemorrhagic Escherichia coli O157:H7.Q50696981
Microbial genetics. The tinkerer's evolving tool-box.Q52262067
A Dam methylation mutant of Klebsiella pneumoniae is partially attenuated.Q52577360
Scanning force microscopy of DNA translocation by the Type III restriction enzyme EcoP15I.Q52943618
Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori.Q54038143
Restriction-modification system differences in Helicobacter pylori are a barrier to interstrain plasmid transfer.Q54038147
Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavageQ55043499
BASE FLIPPINGQ56256582
Signature Tagged Mutagenesis of Haemophilus influenzae identifies genes required for in vivo survivalQ30873470
KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification systemQ30969015
The proteolytic control of restriction activity in Escherichia coli K-12.Q31795891
Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I.Q31937862
Phasevarions mediate random switching of gene expression in pathogenic NeisseriaQ33434451
Salmonella DNA adenine methylase mutants confer cross-protective immunityQ33552366
Molecular characterization of the 98-kilodalton iron-regulated outer membrane protein of Neisseria meningitidisQ33614142
ATP-dependent restriction enzymesQ33851803
DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymesQ33890885
Regulation of pap pilin phase variation by a mechanism involving differential dam methylation statesQ33923349
The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genesQ33936713
Roles of DNA adenine methylation in regulating bacterial gene expression and virulenceQ34009521
DNA adenine methylase is essential for viability and plays a role in the pathogenesis of Yersinia pseudotuberculosis and Vibrio choleraeQ34009783
Inside a living cellQ34014156
Deoxyribonucleic acid restriction and modification systems in Salmonella: chromosomally located systems of different serotypesQ34111951
DNA adenine methylase overproduction in Yersinia pseudotuberculosis alters YopE expression and secretion and host immune responses to infectionQ34117830
Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more.Q34135626
Complex restriction enzymes: NTP-driven molecular motorsQ34178514
DNA Restriction Enzyme from E. coliQ34220586
DNA restriction and modification mechanisms in bacteriaQ34224398
Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambdaQ34251434
S-Adenosyl-L-methionine-dependent restriction enzymesQ34317912
Transcriptional phase variation of a type III restriction-modification system in Helicobacter pyloriQ34320449
Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymesQ34358530
Phase variation of H. influenzae fimbriae: transcriptional control of two divergent genes through a variable combined promoter region.Q34366696
Playing Dr Jekyll and Mr Hyde: combined mechanisms of phase variation in bacteriaQ34392578
Recognition and cleavage of DNA by type-II restriction endonucleasesQ34431350
Comparative genomics of the restriction-modification systems in Helicobacter pyloriQ34489772
Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression.Q34659322
How to proteins move along DNA? Lessons from type-I and type-III restriction endonucleasesQ35020190
Genetic variation in pathogenic bacteriaQ35277088
Variable expression of class 1 outer membrane protein in Neisseria meningitidis is caused by variation in the spacing between the -10 and -35 regions of the promoter.Q35584590
DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicityQ35657182
The biology of restriction and anti-restrictionQ36175695
Functional analysis of the M.HpyAIV DNA methyltransferase of Helicobacter pyloriQ36314651
The GATC-binding protein SeqA is required for bile resistance and virulence in Salmonella enterica serovar typhimuriumQ36315344
Natural transformation of Neisseria gonorrhoeae: from DNA donation to homologous recombinationQ36359422
Re-examining the role and random nature of phase variationQ36381528
N6-methyl-adenine: an epigenetic signal for DNA-protein interactionsQ36401376
Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogensQ36524212
Structure, function and mechanism of exocyclic DNA methyltransferasesQ36598928
Bacterial contingency loci: the role of simple sequence DNA repeats in bacterial adaptationQ36649037
A family of phase-variable restriction enzymes with differing specificities generated by high-frequency gene rearrangementsQ36812335
The restriction-modification system of Pasteurella haemolytica is a member of a new family of type I enzymesQ36832889
Phase variable type III restriction-modification systems of host-adapted bacterial pathogensQ36917132
Role of the Campylobacter jejuni Cj1461 DNA methyltransferase in regulating virulence characteristicsQ36933207
Regulation of the Salmonella enterica std fimbrial operon by DNA adenine methylation, SeqA, and HdfR.Q36958056
Type III restriction enzymes communicate in 1D without looping between their target sitesQ37078204
DNA repeats identify novel virulence genes in Haemophilus influenzaeQ37312114
ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12Q37589808
Differential binding of Lrp to two sets of pap DNA binding sites mediated by Pap I regulates Pap phase variation in Escherichia coli.Q37625420
A mutational analysis of the two motifs common to adenine methyltransferases.Q37635562
Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysisQ37698719
Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a correlation between host responses and HsdS components of type I restriction-modification systemsQ38287381
Molecular analysis of a locus for the biosynthesis and phase-variable expression of the lacto-N-neotetraose terminal lipopolysaccharide structure in Neisseria meningitidisQ38289637
DNA recognition by the EcoP15I and EcoPI modification methyltransferasesQ38295255
Interaction of EcoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5'-CAGCAG-3'.Q38304144
Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequenceQ38312746
Functional analysis of conserved motifs in type III restriction-modification enzymesQ38336578
Mutations in the Res subunit of the EcoPI restriction enzyme that affect ATP-dependent reactionsQ38345023
Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695Q39501893
Heat-inducible surface stress protein (Hsp70) mediates sulfatide recognition of the respiratory pathogen Haemophilus influenzae.Q39520129
Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genomeQ39584191
Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolutionQ39600720
Purification and properties of the P15 specific restriction endonuclease from Escherichia coliQ39799531
Brief heat shock treatment induces a long-lasting alteration in the glycolipid receptor binding specificity and growth rate of Haemophilus influenzaeQ39829711
Transfer of the genes for the StyLTI restriction-modification system of Salmonella typhimurium to strains lacking modification ability results in death of the recipient cells and degradation of their DNAQ39939110
DNA communications by Type III restriction endonucleases--confirmation of 1D translocation over 3D loopingQ39946292
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)196-206
P577publication date2010-02-08
P1433published inNature Reviews MicrobiologyQ1071797
P1476titleThe phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes
P478volume8

Reverse relations

cites work (P2860)
Q30659946A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae
Q36323846A genetic switch controls the production of flagella and toxins in Clostridium difficile
Q34310334A random six-phase switch regulates pneumococcal virulence via global epigenetic changes
Q52648650A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions.
Q34400711A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori
Q37070358Analysis of nontypeable haemophilus influenzae phase-variable genes during experimental human nasopharyngeal colonization
Q35120837Antisense RNA associated with biological regulation of a restriction-modification system
Q39003514Bacterial DNA Methylation and Methylomes
Q36537965Broad conditions favor the evolution of phase-variable loci.
Q53076840Campylobacter jejuni transcriptional and genetic adaptation during human infection.
Q33812805Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant
Q42108715Cleavage of a model DNA replication fork by a methyl-specific endonuclease.
Q40285952Comparative genome analysis reveals important genetic differences among serotype O1 and serotype O2 strains of Y. ruckeri and provides insights into host adaptation and virulence
Q58085053Comparative genomic and methylome analysis of non-virulent D74 and virulent Nagasaki Haemophilus parasuis isolates
Q89930481Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease
Q99585781Contribution of DNA adenine methylation to gene expression heterogeneity in Salmonella enterica
Q90463939Deciphering bacterial epigenomes using modern sequencing technologies
Q21134930Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis
Q35598777Deletion of one nucleotide within the homonucleotide tract present in the hsdS gene alters the DNA sequence specificity of type I restriction-modification system NgoAV
Q34513606Distribution of the type III DNA methyltransferases modA, modB and modD among Neisseria meningitidis genotypes: implications for gene regulation and virulence.
Q33886643Domain movement within a gene: a novel evolutionary mechanism for protein diversification.
Q24629701Entering the era of bacterial epigenomics with single molecule real time DNA sequencing
Q36079875Epigenetic Switch Driven by DNA Inversions Dictates Phase Variation in Streptococcus pneumoniae.
Q35153520Evidence for an evolutionary antagonism between Mrr and Type III modification systems
Q51326292Evolution of simple sequence repeat-mediated phase variation in bacterial genomes.
Q37253104Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1.
Q36250210Expression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease
Q37798011Genetic shifts ofNeisseria meningitidisserogroup B antigens and the quest for a broadly cross-protective vaccine
Q90663459Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae
Q30419110Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences
Q30437973Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle
Q42283711Horizontal transfer of DNA methylation patterns into bacterial chromosomes
Q26782340How the Knowledge of Interactions between Meningococcus and the Human Immune System Has Been Used to Prepare Effective Neisseria meningitidis Vaccines
Q42357253Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics
Q30541484Identification of the nature of reading frame transitions observed in prokaryotic genomes
Q93380766Kinetic and catalytic properties of M.HpyAXVII, a phase-variable DNA methyltransferase from Helicobacter pylori
Q90629856Localized Hypermutation is the Major Driver of Meningococcal Genetic Variability during Persistent Asymptomatic Carriage
Q60912015Metaepigenomic analysis reveals the unexplored diversity of DNA methylation in an environmental prokaryotic community
Q57900155Metatranscriptome analysis of the reef-building coral Orbicella faveolata indicates holobiont response to coral disease
Q38088545Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution
Q36305686Movement of DNA sequence recognition domains between non-orthologous proteins.
Q91199458Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis
Q30080007Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Q64967673Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria.
Q34211653Origin of the diversity in DNA recognition domains in phasevarion associated modA genes of pathogenic Neisseria and Haemophilus influenzae
Q89481909Panel 3: Genomics, precision medicine and targeted therapies
Q36525717Passage of Campylobacter jejuni through the chicken reservoir or mice promotes phase variation in contingency genes Cj0045 and Cj0170 that strongly associates with colonization and disease in a mouse model
Q34509855Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168
Q40075220Phase-variable methylation and epigenetic regulation by type I restriction-modification systems
Q34097569Phasevarion mediated epigenetic gene regulation in Helicobacter pylori
Q47744169Phasevarion-Regulated Virulence in the Emerging Pediatric Pathogen Kingella kingae
Q41082178Phasevarions mediate epigenetic regulation of antimicrobial susceptibility in Neisseria meningitidis.
Q49917740Phasevarions of Bacterial Pathogens: Methylomics Sheds New Light on Old Enemies
Q38099632Programmed heterogeneity: epigenetic mechanisms in bacteria
Q51575920Pseudomonas syringae Differentiates into Phenotypically Distinct Subpopulations During Colonization of a Plant Host.
Q34273732STM2209-STM2208 (opvAB): a phase variation locus of Salmonella enterica involved in control of O-antigen chain length
Q90418149Selective and non-selective bottlenecks as drivers of the evolution of hypermutable bacterial loci
Q35813616Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes
Q61800366Single-molecule sequencing detection of N6-methyladenine in microbial reference materials
Q36539205Specific IgA and metalloproteinase activity in bronchial secretions from stable chronic obstructive pulmonary disease patients colonized by Haemophilus influenzae
Q34470436Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N(6)-adenine DNA methyltransferases of Neisseria meningitidis.
Q33808990Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host
Q57285690Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution
Q28074750The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development
Q28550136The Epigenomic Landscape of Prokaryotes
Q38998285The Helicobacter pylori Methylome: Roles in Gene Regulation and Virulence
Q34557738The ModA2 Phasevarion of nontypeable Haemophilus influenzae Regulates Resistance to Oxidative Stress and Killing by Human Neutrophils
Q35084650The Pathobiology of Neisseria gonorrhoeae Lower Female Genital Tract Infection
Q91287194The bacterial epigenome
Q30572851The complex methylome of the human gastric pathogen Helicobacter pylori
Q64254964The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori
Q34722544The dam replacing gene product enhances Neisseria gonorrhoeae FA1090 viability and biofilm formation.
Q41923111The impact of bottlenecks on microbial survival, adaptation and phenotypic switching in host-pathogen interactions
Q34433472The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts
Q24598577The methylomes of six bacteria
Q38663969The modA10 phasevarion of nontypeable Haemophilus influenzae R2866 regulates multiple virulence-associated traits.
Q26998736The role of variable DNA tandem repeats in bacterial adaptation
Q26865951To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems
Q36387438Type III Methyltransferase M.NgoAX from Neisseria gonorrhoeae FA1090 Regulates Biofilm Formation and Interactions with Human Cells
Q34358103Type III restriction-modification enzymes: a historical perspective
Q36158458Whole-genome sequencing identifies emergence of a quinolone resistance mutation in a case of Stenotrophomonas maltophilia bacteremia.
Q30870320qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data

Search more.