DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences.

Yang, Young Hoon; Ames, Giovanna Ferro‐Luzzi

doi:10.1073/pnas.85.23.8850

Cited by 138 publications

(86 citation statements)

References 37 publications

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“…It is not yet known whether the degree of cleavage is correlated with the binding efficiency of DNA gyrase at these elements or whether the sequence changes affected in some way the cleavage reaction. Unlike what was observed in vitro (Yang and Ames, 1988), a single cut was observed in vivo, and in six out of seven cases was located in the Y REP. We showed that several residues were conserved in the cleavage site region of ᮊ 1997 Blackwell Science Ltd, Molecular Microbiology, 26, 767-777 Fig. 6.…”

Section: Discussioncontrasting

confidence: 73%

In vivo cleavage of Escherichia coli BIME‐2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site

Espéli

Boccard

1997

Molecular Microbiology

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SummaryThe Escherichia coli chromosome contains about 300 bacterial interspersed mosaic elements (BIMEs). These elements, located at the 3Ј end of genes, are composed of three types of alternating repetitive extragenic palindromes (REPs). Based on the type of REP they contain and on their ability to interact with the integration host factor (IHF), BIMEs are subdivided into two families: BIME-1 elements contain an IHF binding site flanked by converging Y and Z1 REPs, whereas BIME-2 elements contain a variable number of alternating Y and Z2 REPs without an IHF site. Although some BIMEs have been implicated in the protection of mRNA against 3Ј exonucleolytic degradation, the main role of elements belonging to both families remains to be elucidated. In this paper, we used oxolinic acid, a drug that reveals potential sites of DNA gyrase action, to demonstrate that DNA gyrase interacts in vivo with BIME-2 elements. The frequency of cleavage varied from one element to another, and the cleavage pattern observed in elements containing several REPs indicated that DNA gyrase cut DNA every two REPs. A single cleavage site has been identified in the Y REP in six out of seven instances, and the nucleotide sequence of a 44 bp fragment containing the scission point displayed conserved residues at six positions. The lack of one of the conserved residues accounted for the absence of cleavage in most of the Z2 REPs. Our results also showed that cleaved REPs were always associated with another REP, suggesting that a pair of diverging REPs constitutes the target of DNA gyrase. DNA gyrase cleavage at repetitive BIME-2 elements may have consequences for DNA topology and genomic rearrangements.

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Section: Discussioncontrasting

confidence: 73%

In vivo cleavage of Escherichia coli BIME‐2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site

Espéli

Boccard

1997

Molecular Microbiology

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“…Because of its stability and processive properties, the Mu SGS has been used in both rotorbead and molecular tweezers experiment to study supercoiling cycles. Unfortunately, very little is known about processivity and gyrase dynamics when gyrase is bound to sites like the BIMES of E. coli and Salmonella (Espeli and Boccard 1997;Stern et al 1984;Yang and Ames 1988). We note that when a site is too strong, it can interfere with competing DNA processes.…”

Section: What Controls Supercoil Density?mentioning

confidence: 93%

Species-specific supercoil dynamics of the bacterial nucleoid

Higgins

2016

Biophys Rev

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Bacteria organize DNA into self-adherent conglomerates called nucleoids that are replicated, transcribed, and partitioned within the cytoplasm during growth and cell division. Three classes of proteins help condense nucleoids: (1) DNA gyrase generates diffusible negative supercoils that help compact DNA into a dynamic interwound and multiply branched structure; (2) RNA polymerase and abundant small basic nucleoid-associated proteins (NAPs) create constrained supercoils by binding, bending, and forming cooperative protein-DNA complexes; (3) a multi-protein DNA condensin organizes chromosome structure to assist sister chromosome segregation after replication. Most bacteria have four topoisomerases that participate in DNA dynamics during replication and transcription. Gyrase and topoisomerase I (Topo I) are intimately involved in transcription; Topo III and Topo IV play critical roles in decatenating and unknotting DNA during and immediately after replication. RNA polymerase generates positive (+) supercoils downstream and negative (−) supercoils upstream of highly transcribed operons. Supercoil levels vary under fast versus slow growth conditions, but what surprises many investigators is that it also varies significantly between different bacterial species. The MukFEB condensin is dispensable in the high supercoil density (σ) organism Escherichia coli but is essential in Salmonella spp. which has 15 % fewer supercoils. These observations raise two questions: (1) How do different species regulate supercoil density? (2) Why do closely related species evolve different optimal supercoil levels? Control of supercoil density in E. coli and Salmonella is largely determined by differences encoded within the gyrase subunits. Supercoil differences may arise to minimalize toxicity of mobile DNA elements in the genome.

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“…Additional proposed functions have related to chromosome structure (13,14,58). It has been shown that the REP sequence binds DNA gyrase (70) and DNA polymerase I (15) and that the HU protein stimulates binding of gyrase to the REP sequence (71). These studies have led to the proposal that the PU or REP sequence is involved in the folding of the bacterial nucleoid into independent supercoiled looped domains (13,58).…”

mentioning

confidence: 99%