DNA Binding Proteins of the Filamentous Phages CTXφ and VGJφ of Vibrio cholerae

ABSTRACT The native product of open reading frame 112 (orf112) and a recombinant variant of the RstB protein, encoded by Vibrio cholerae pathogen-specific bacteriophages VGJφ and CTXφ, respectively, were purified to more than 90% homogeneity. Orf112 protein was shown to specifically bind single-stranded genomic DNA of VGJφ; however, RstB protein unexpectedly bound double-stranded DNA in addition to the single-stranded genomic DNA. The DNA binding properties of these proteins may explain their requirement for the rolling circle replication of the respective phages and RstB's requirement for single-stranded-DNA chromosomal integration of CTXφ phage dependent on XerCD recombinases.

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Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase ɛ and of the Dpb3p-Dpb4p subassembly

Genes to Cells ◽

10.1046/j.1365-2443.2003.00683.x ◽

2003 ◽

Vol 8 (11) ◽

pp. 873-888 ◽

Cited By ~ 24

Author(s):

Toshiaki Tsubota ◽

Satoko Maki ◽

Hajime Kubota ◽

Akio Sugino ◽

Hisaji Maki

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Binding ◽

Dna Polymerase ◽

Binding Properties ◽

Double Stranded Dna ◽

Dna Binding Properties

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Rolling circle replication requires single-stranded DNA binding protein to avoid termination and production of double-stranded DNA

Nucleic Acids Research ◽

10.1093/nar/gku737 ◽

2014 ◽

Vol 42 (16) ◽

pp. 10596-10604 ◽

Cited By ~ 21

Author(s):

Cosimo Ducani ◽

Giulio Bernardinelli ◽

Björn Högberg

Keyword(s):

Dna Binding ◽

Binding Protein ◽

Dna Binding Protein ◽

Rolling Circle Replication ◽

Single Stranded Dna ◽

Rolling Circle ◽

Double Stranded Dna

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Identification of a Replicon from pTXL1, a Small Cryptic Plasmid from Leuconostoc mesenteroides subsp. mesenteroides Y110, and Development of a Food-Grade Vector

Applied and Environmental Microbiology ◽

10.1128/aem.68.12.6451-6456.2002 ◽

2002 ◽

Vol 68 (12) ◽

pp. 6451-6456 ◽

Cited By ~ 20

Author(s):

Franck Biet ◽

Yves Cenatiempo ◽

Christophe Fremaux

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Leuconostoc Mesenteroides ◽

Class Ii ◽

Open Reading Frame ◽

Cryptic Plasmid ◽

Rolling Circle Replication ◽

Rolling Circle ◽

Reading Frame ◽

Food Grade

ABSTRACT A 2,665-bp cryptic plasmid, pTXL1, isolated from Leuconostoc mesenteroides subsp. mesenteroides Y110 was identified. This plasmid harbors a replicon localized on a 1,300-bp fragment. Two observations suggested that pTXL1 does not belong to rolling-circle replication (RCR)-type plasmids and most likely replicates via a theta mechanism. These hypotheses are supported by the observation that no detectable single-stranded intermediate was found for the replicon and that, unlike in RCR-type plasmids, the pTXL1 replicon sequence lacks an open reading frame encoding a replicase. The small-sized pTXL1 plasmid is stable and, according to its origin, can be considered in the “generally recognized as safe” category. Its ability to replicate in several lactic acid bacteria was exploited to develop a vector producing mesentericin Y105, a class II anti-Listeria bacteriocin. With this new vector, a recombinant industrial Leuconostoc cremoris strain able to produce mesentericin Y105 was constructed.

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Synthesis and evaluation of the in vitro DNA-binding properties of chiral cis-dichloro(pyridyloxazoline)platinum(II) complexes

Canadian Journal of Chemistry ◽

10.1139/v08-131 ◽

2009 ◽

Vol 87 (1) ◽

pp. 321-327 ◽

Cited By ~ 3

Author(s):

David W Dodd ◽

Heather E Toews ◽

Michael J Trevail ◽

Michael C Jennings ◽

Robert HE Hudson ◽

...

Keyword(s):

Dna Binding ◽

Hplc Analysis ◽

Polyacrylamide Gel Electrophoresis ◽

Metal Exposure ◽

Binding Studies ◽

Binding Properties ◽

Double Stranded Dna ◽

Dna Binding Studies ◽

Dna Binding Properties

A series of chiral cis-dichloro(pyridyloxazoline)platinum(II) and palladium(II) complexes were synthesized and their reactivity towards a defined sequence of single-stranded and double-stranded DNA was investigated in comparison to cisplatin. The compounds differed in the nature and absolute configuration of the substituent at the C4 position of the oxazoline ring. The DNA-binding ability of these compounds was evaluated by HPLC analysis, post metal exposure, of enzymatic digests of an undecamer duplex containing one putative metallation site. Polyacrylamide gel electrophoresis (PAGE) and thermal denaturation confirmed the results of the HPLC analysis, which showed that the stereochemistry and character of the substituent at the C4 position of the oxazoline ring had little effect on DNA binding, possibly due to the formation of monofunctional adducts.Key words: cisplatin, chiral, pyridyloxazoline, DNA-binding studies, platinum, palladium.

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A Plasmid Isolated from Phytopathogenic Onion Yellows Phytoplasma and Its Heterogeneity in the Pathogenic Phytoplasma Mutant

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.1998.11.11.1031 ◽

1998 ◽

Vol 11 (11) ◽

pp. 1031-1037 ◽

Cited By ~ 32

Author(s):

Tsutomu Kuboyama ◽

Chieh-Chen Huang ◽

Xiaoyun Lu ◽

Toshimi Sawayanagi ◽

Tokiko Kanazawa ◽

...

Keyword(s):

Copy Number ◽

Open Reading Frame ◽

Extrachromosomal Dna ◽

Rolling Circle Replication ◽

Banding Patterns ◽

Rolling Circle ◽

Rep Protein ◽

Reading Frame ◽

Dna And Rna ◽

Dna Fragment

A 3.6-kbp DNA fragment was cloned from the extrachromosomal DNA of a pathogenic plant mollicute, onion yellows phytoplasma (OY-W). Sequence analysis of the fragment revealed an open reading frame (ORF) encoding the replication (Rep) protein of rolling-circle replication (RCR)-type plasmids. This result suggests the existence of a plasmid (pOYW1) in OY-W that uses the RCR mechanism. This assumption was confirmed by detecting the single-stranded DNA (ssDNA) of a replication intermediate that is specifically produced by the RCR mechanism. This is the first report on the identification of the replication system of this plasmid and the genes encoded in it. With a DNA fragment including the Rep gene region of pOYW1 used as a probe, Southern and Northern (RNA) blot hybridizations were employed to examine the heterogeneity between the plasmids found in OY-W and a pathogenic mutant (OY-M) isolated from OY-W. Multiple bands were detected in the DNA and RNA extracted from both OY-W and OY-M infected plants, although the banding patterns were different. Moreover, the copy number of plasmids from OY-W was about 4.2 times greater than that from OY-M. These results indicate constructive heterogeneity between OY-W and OY-M plasmids, and the possibility of a relationship between the plasmid-encoded genes and the pathogenicity of the phytoplasma was suggested.

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Identification and Characterization of Saccharomyces cerevisiae Cdc6 DNA-binding Properties

Molecular Biology of the Cell ◽

10.1091/mbc.11.5.1673 ◽

2000 ◽

Vol 11 (5) ◽

pp. 1673-1685 ◽

Cited By ~ 15

Author(s):

Luo Feng ◽

Bin Wang ◽

Barbara Driscoll ◽

Ambrose Jong

Keyword(s):

Dna Replication ◽

Dna Binding ◽

Binding Activity ◽

Temperature Sensitive ◽

Sequence Specificity ◽

Binding Properties ◽

Dna Binding Activity ◽

Double Stranded Dna ◽

Dna Binding Properties ◽

Mutant Cells

Recent studies have shown that Cdc6 is an essential regulator in the formation of DNA replication complexes. However, the biochemical nature of the Cdc6 molecule is still largely unknown. In this report, we present evidence that the Saccharomyces cerevisiaeCdc6 protein is a double-stranded DNA-binding protein. First, we have demonstrated that the purified yeast Cdc6 can bind to double-stranded DNA (dissociation constant ∼ 1 × 10−7 M), not to single-stranded DNA, and that the Cdc6 molecule is a homodimer in its native form. Second, we show that GST-Cdc6 fusion proteins expressed in Escherichia coli bind DNA in an electrophoretic mobility shift assay. Cdc6 antibodies and GST antibodies, but not preimmune serum, induce supershifts of GST-Cdc6 and DNA complexes in these assays, which also showed that GST-Cdc6 binds to various DNA probes without apparent sequence specificity. Third, the minimal requirement for the binding of Cdc6 to DNA has been mapped within its N-terminal 47-amino acid sequence (the NP6 region). This minimal binding domain shows identical DNA-binding properties to those possessed by full-length Cdc6. Fourth, the GST-NP6 protein competes for DNA binding with distamycin A, an antibiotic that chelates DNA within the minor groove of the A+T-rich region. Finally, site-direct mutagenesis studies revealed that the29KRKK region of Cdc6 is essential for Cdc6 DNA-binding activity. To further elucidate the function of Cdc6 DNA binding in vivo, we demonstrated that a binding mutant of Cdc6 fails to complement either cdc6-1 temperature-sensitive mutant cells orΔcdc6 null mutant cells at the nonpermissive temperature. The mutant gene also conferred growth impairments and increased the plasmid loss in its host, indicative of defects in DNA synthesis. Because the mutant defective in DNA binding also fails to stimulate Abf1 ARS1 DNA-binding activity, our results suggest that Cdc6 DNA-binding activity may play a pivotal role in the initiation of DNA replication.

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