Plasmid-encoded Antirestriction Protein ArdA Can Discriminate between Type I Methyltransferase and Complete Restriction–Modification System

Nekrasov, S. V.; Agafonova, O. V.; Belogurova, Nataly G.; Delver, E. P.; Белогуров, А. А.

doi:10.1016/j.jmb.2006.09.087

Cited by 32 publications

(39 citation statements)

References 59 publications

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“…Assuming that the DNA path between the DNA bound to the HsdR and the DNA bound to the core MTase must not be any longer than ;40 bp, as determined by DNA footprinting experiments (Mernagh et al 1998;Powell et al 1998) and the minimum length of 45 bp of DNA required for ATP hydrolysis (Roberts et al 2011), then the locations of the RecA-like motor domains of the HsdR are forced to be as shown, so that their DNA-binding sites are close to the DNA-binding site of the MTase core. Placement of the HsdR on either side of the MTase and interacting directly with DNA is further supported by the length of the structure of the ArdA anti-restriction DNA mimic protein (Nekrasov et al 2007;McMahon et al 2009), which occupies the entire DNA-binding site on type I RM enzymes. This then allows the complete structures for the closed forms of EcoR124I and EcoKI to be constructed as shown in Figure 5, A and B.…”

Section: Atomic Modeling Of the Complete Rm Enzymesmentioning

confidence: 96%

Structure and operation of the DNA-translocating type I DNA restriction enzymes

Kennaway¹,

Taylor²,

Song³

et al. 2012

Genes Dev.

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Type I DNA restriction/modification (RM) enzymes are molecular machines found in the majority of bacterial species. Their early discovery paved the way for the development of genetic engineering. They control (restrict) the influx of foreign DNA via horizontal gene transfer into the bacterium while maintaining sequence-specific methylation (modification) of host DNA. The endonuclease reaction of these enzymes on unmethylated DNA is preceded by bidirectional translocation of thousands of base pairs of DNA toward the enzyme. We present the structures of two type I RM enzymes, EcoKI and EcoR124I, derived using electron microscopy (EM), small-angle scattering (neutron and X-ray), and detailed molecular modeling. DNA binding triggers a large contraction of the open form of the enzyme to a compact form. The path followed by DNA through the complexes is revealed by using a DNA mimic anti-restriction protein. The structures reveal an evolutionary link between type I RM enzymes and type II RM enzymes.

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Section: Atomic Modeling Of the Complete Rm Enzymesmentioning

confidence: 96%

Structure and operation of the DNA-translocating type I DNA restriction enzymes

Kennaway¹,

Taylor²,

Song³

et al. 2012

Genes Dev.

View full text Add to dashboard Cite

show abstract

“…The fact that ArdA existed as a dimer at low concentrations agrees with findings for another ArdA from plasmid ColIb-P9. 35 The data were fitted with a onebinding site equation, 36 and the dissociation constant K d was found to be 1.4 μM, suggesting a relatively weak interaction for this aggregation. The width of each elution peak was measured as a single peak can mask overlapping peaks.…”

Section: Size-exclusion Hplcmentioning

confidence: 99%

The Orf18 Gene Product from Conjugative Transposon Tn916 Is an ArdA Antirestriction Protein that Inhibits Type I DNA Restriction–Modification Systems

Serfiotis-Mitsa

Roberts

Cooper

et al. 2008

Journal of Molecular Biology

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“…RMSs may also cause cell death through restriction of genomic DNA or are involved in genomic rearrangements (Kobayashi, 2001). Such RMS genes are also located in GEI I of strain 2.10, and a putative anti-restriction protein (PGA2_c11710; ArdA-like) in GEI III might modulate the activity of the type I RMS (Nekrasov et al, 2007). Other genes found in GEIs are likely involved in cell envelope synthesis (rfbFGH; PGA2_c18820-_c18840; GEI IV), resistance to heavy metals (PGA2_c08910-PGA2_c08950; GEI II) and metabolism of amino acids and amines (most genes located in GEI V; for example, PGA2_c23460-PGA2_c23500).…”

Section: Geis Prophages and Gene-transfer Agents (Gtas)mentioning

confidence: 99%

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

et al. 2012

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Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.

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Plasmid-encoded Antirestriction Protein ArdA Can Discriminate between Type I Methyltransferase and Complete Restriction–Modification System

Cited by 32 publications

References 59 publications

Structure and operation of the DNA-translocating type I DNA restriction enzymes

Structure and operation of the DNA-translocating type I DNA restriction enzymes

The Orf18 Gene Product from Conjugative Transposon Tn916 Is an ArdA Antirestriction Protein that Inhibits Type I DNA Restriction–Modification Systems

Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life

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