The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI

Davies, Graham P; Kemp, Priscilla; Molineux, Ian J.; Murray, Noreen E.

doi:10.1006/jmbi.1999.3081

Cited by 54 publications

(70 citation statements)

References 43 publications

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“…Amino acid substitutions in the DEAD-box motifs do not prevent the conformational change associated with tight binding to the target sequences in the presence of AdoMet and ATP. These proteins, however, are all deficient in ATPase activity and DNA translocation, consistent with a role for the DEAD-box motifs in the coupling of ATP hydrolysis to DNA translocation (35,37). The failure to translocate DNA was demonstrated by an in vivo assay in which wild-type EcoKI translocates the T7 genome from the phage particle into the bacterial cell (57).…”

Section: R-m Complexmentioning

confidence: 80%

“…5) has similarities with motifs associated with DNA nicking in both type II restriction enzymes and the RecB family of nucleases. Sitedirected mutagenesis proved the relevance of this motif to the endonuclease activities of EcoAI (78) and EcoKI (36,37).…”

Section: Restriction Subunit-hsdrmentioning

confidence: 94%

“…Conservative substitutions within the amino acid sequence characteristic of endonucleases do not block either the ATPase or DNA translocase activities of EcoAI (78) and EcoKI (37). These mutations are believed to be within a separate domain from those of the DEAD-box motifs (37), and, as expected from their sequence identity with the active sites of type II restriction endonucleases, they block the nicking and cutting activity of the R-M complex.…”

Section: R-m Complexmentioning

confidence: 96%

“…These mutations are believed to be within a separate domain from those of the DEAD-box motifs (37), and, as expected from their sequence identity with the active sites of type II restriction endonucleases, they block the nicking and cutting activity of the R-M complex. This implies a common mechanism for the hydrolysis of phosphodiester bonds by type I and type II systems.…”

Section: R-m Complexmentioning

confidence: 99%

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Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Murray

2000

Microbiol Mol Biol Rev

403

481

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SUMMARY Restriction enzymes are well known as reagents widely used by molecular biologists for genetic manipulation and analysis, but these reagents represent only one class (type II) of a wider range of enzymes that recognize specific nucleotide sequences in DNA molecules and detect the provenance of the DNA on the basis of specific modifications to their target sequence. Type I restriction and modification (R-M) systems are complex; a single multifunctional enzyme can respond to the modification state of its target sequence with the alternative activities of modification or restriction. In the absence of DNA modification, a type I R-M enzyme behaves like a molecular motor, translocating vast stretches of DNA towards itself before eventually breaking the DNA molecule. These sophisticated enzymes are the focus of this review, which will emphasize those aspects that give insights into more general problems of molecular and microbial biology. Current molecular experiments explore target recognition, intramolecular communication, and enzyme activities, including DNA translocation. Type I R-M systems are notable for their ability to evolve new specificities, even in laboratory cultures. This observation raises the important question of how bacteria protect their chromosomes from destruction by newly acquired restriction specifities. Recent experiments demonstrate proteolytic mechanisms by which cells avoid DNA breakage by a type I R-M system whenever their chromosomal DNA acquires unmodified target sequences. Finally, the review will reflect the present impact of genomic sequences on a field that has previously derived information almost exclusively from the analysis of bacteria commonly studied in the laboratory.

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Section: R-m Complexmentioning

confidence: 80%

Section: Restriction Subunit-hsdrmentioning

confidence: 94%

Section: R-m Complexmentioning

confidence: 96%

Section: R-m Complexmentioning

confidence: 99%

See 2 more Smart Citations

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Murray

2000

Microbiol Mol Biol Rev

403

481

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“…An assortment of assays have been used to obtain evidence that the DNA translocating subunits of type I restriction enzymes can translocate along DNA (18,22,23,27,37,48,59,63). Also of particular interest is recent evidence suggesting that the yeast Mot1 and Rad54 proteins, which are more closely related to the ATP-dependent chromatin-remodeling enzymes, are able to translocate along DNA (16,50).…”

mentioning

confidence: 99%

Evidence for DNA Translocation by the ISWI Chromatin-Remodeling Enzyme

Whitehouse

Stockdale

Flaus

et al. 2003

Molecular and Cellular Biology

138

134

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The ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin-remodeling activities. Here, we studied the interaction of the ISWI protein with nucleosomal substrates. We found that the ability of nucleic acids to bind and stimulate the ATPase activity of ISWI depends on length. We also found that ISWI is able to displace triplex-forming oligonucleotides efficiently when they are introduced at sites close to a nucleosome but successively less efficiently 30 to 60 bp from its edge. The ability of ISWI to direct triplex displacement was specifically impeded by the introduction of 5-or 10-bp gaps in the 3-5 strand between the triplex and the nucleosome. In combination, these observations suggest that ISWI is a 3-5-strand-specific, ATP-dependent DNA translocase that may be capable of forcing DNA over the surface of nucleosomes.A general feature of eukaryotes is that their genomic DNA associates with proteins to form chromatin. In addition to providing a means of packaging DNA within nuclei, chromatin provides an additional level at which gene expression can be regulated. Active regions of the genome tend to be maintained in a more accessible state than inactive regions, and the manipulation of chromatin structure has been found to play an important role in the regulation of many genes. In order to be able to regulate gene expression at this level, eukaryotes have devised a number of strategies by which they can manipulate chromatin structure. These include the covalent modification of chromatin structure by posttranslational modification, the manipulation of the protein content of chromatin through the association of variant histone and nonhistone proteins, and the noncovalent alteration of chromatin structure by ATP-dependent chromatin-remodeling activities (2,7,38,67).It now appears likely that all eukaryotes encode multiple yet distinct ATPases with homology to the yeast SNF2 protein (Snf2p). These include the Sth1p, Chd1p, Isw1p, Isw2p, and Ino80p proteins in budding yeast and a spectrum of related proteins in higher eukaryotes (2, 66). Among these, the ISWI proteins represent a discrete class of ATPase involved in chromatin remodeling. The founding member of the ISWI group was identified in Drosophila melanogaster due to its similarity to Snf2p. As the homology is restricted to the helicase-like domain, it was named imitation SWI/SNF (ISWI) (21). Biochemical characterization of ISWI proteins began with the identification of ISWI as the catalytic subunit of three distinct complexes, nucleosome-remodeling factor (NuRF), chromatin accessibility complex (ChrAC), and the ATP-utilizing chromatin assembly and modifying factor (ACF) isolated from Drosophila embryo extracts (36,60,64). Subsequently, ISWI-related proteins have been found to be components of chromatin-remodeling complexes in organisms ranging from yeast to humans, suggesting that these proteins fulfill important functions conserved throughout evolution (5,42,43,49,61). Within each of these complexes, the ISWI protein is associated with a...

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DNA supercoiling during ATP-dependent DNA translocation by the type I restriction enzyme EcoAI

Janscak

Bickle

2000

Journal of Molecular Biology

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The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI

Cited by 54 publications

References 43 publications

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Type I Restriction Systems: Sophisticated Molecular Machines (a Legacy of Bertani and Weigle)

Evidence for DNA Translocation by the ISWI Chromatin-Remodeling Enzyme

DNA supercoiling during ATP-dependent DNA translocation by the type I restriction enzyme EcoAI

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