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

Espéli, Olivier; Boccard, Frédéric

doi:10.1046/j.1365-2958.1997.6121983.x

Cited by 59 publications

(48 citation statements)

References 34 publications

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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: 99%

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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Section: What Controls Supercoil Density?mentioning

confidence: 99%

Species-specific supercoil dynamics of the bacterial nucleoid

Higgins

2016

Biophys Rev

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“…BIMEs of one category are bound by the integration host factor (IHF); these structures have been called RIBs (reiterative ihf BIMEs) (61) or RIPs (repetitive IHF-binding palindromic elements) (62). Additionally, DNA gyrase binds and cleaves some BIMEs (56,(63)(64)(65). DNA polymerase I (Pol I) also binds certain BIMEs (56,66).…”

Section: Mobile Elementsmentioning

confidence: 99%

Bacterial Genome Instability

Darmon

Leach

2014

Microbiol Mol Biol Rev

337

289

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SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease.

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“…Some of them can stabilize mRNAs (26,27) or play a role in transcription termination (14), translational control (38), and genomic rearrangements (36). However, their specific interactions with integration host factor (7,28), DNA gyrase (12,42), and DNA polymerase (16) suggest that they may play a role in the functional organization of the bacterial nucleoid.…”

mentioning

confidence: 99%

Transposition of IS 1397 in the Family Enterobacteriaceae and First Characterization of ISKpn 1 , a New Insertion Sequence Associated with Klebsiella pneumoniae Palindromic Units

et al. 2001

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IS1397 and ISKpn1 are IS3 family members which are specifically inserted into the loop of palindromic units (PUs). IS1397 is shown to transpose into PUs with sequences close or identical to the Escherichia coli consensus, even in other enterobacteria (Salmonella enterica serovar Typhimurium, Klebsiella pneumoniae, and Klebsiella oxytoca). Moreover, we show that homologous intergenic regions containing PUs constitute IS1397 transpositional hot spots, despite bacterial interspersed mosaic element structures that differ among the three species. ISKpn1, described here for the first time, is specific for PUs from K. pneumoniae, in which we discovered it. A sequence comparison between the two insertion sequences allowed us to define a motif possibly accounting for their specificity.

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

Cited by 59 publications

References 34 publications

Species-specific supercoil dynamics of the bacterial nucleoid

Species-specific supercoil dynamics of the bacterial nucleoid

Bacterial Genome Instability

Transposition of IS 1397 in the Family Enterobacteriaceae and First Characterization of ISKpn 1 , a New Insertion Sequence Associated with Klebsiella pneumoniae Palindromic Units

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