Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes

DiNardo, Stephen; Voelkel, Karen A.; Sternglanz, Rolf; Reynolds, Ann E.; Wright, Andrew

doi:10.1016/0092-8674(82)90403-2

Cited by 432 publications

(341 citation statements)

References 20 publications

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“…The sum of the free energies ΔG complex = ΔG oct + ΔG tetr = − 1:0 kcal/mol indicates that looping on supercoiled DNA is energetically more favorable than on linear DNA (ΔG complex = − 0:3 kcal/mol); a comparison of the values of ΔG oct and ΔG tetr from the literature is given in Table 1. A second modification of the thermodynamic parameters entering the model was that we decreased the binding energies for all operator sites while keeping the cooperative parameters constant; the reasoning behind this is that gene regulation is commonly found to be sensitive to supercoiling (32), as it can change the local structure of DNA and influence protein DNA binding. In practice we weakened all binding energies between CI dimers and operator sites by 1.5 kcal/mol.…”

Section: Resultsmentioning

confidence: 99%

DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

Nørregaard

Andersson

Sneppen

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Bacteriophage λ stably maintains its dormant prophage state but efficiently enters lytic development in response to DNA damage. The mediator of these processes is the λ repressor protein, CI, and its interactions with λ operator DNA. This λ switch is a model on the basis of which epigenetic switch regulation is understood. Using single molecule analysis, we directly examined the stability of the CI-operator structure in its natural, supercoiled state. We marked positions adjacent to the λ operators with peptide nucleic acids and monitored their movement by tethered particle tracking. Compared with relaxed DNA, the presence of supercoils greatly enhances juxtaposition probability. Also, the efficiency and cooperativity of the λ switch is significantly increased in the supercoiled system compared with a linear assay, increasing the Hill coefficient. The decision between the dormant state (the lysogenic state) and the vegetative state (the lytic state) made by bacteriophage λ upon infection of an Escherichia coli was the first epigenetic switch to be deciphered (1) and continues to provide insights into biological processes (2, 3). Once the lysogenic state is established, it is exceptionally stable and departure in the absence of the DNA damage sensing system is nearly always caused by mutation (4-6). Maintenance of lysogeny is mediated by the λ repressor protein, CI, and its formation of a complex with phage DNA. The CI protein binds at two regulatory regions called operator right (OR) and operator left (OL), located about 2.3 kbp apart on the phage genome. Each operator is a constellation of three adjacent subsites that each bind dimers of CI in a hierarchical manner (1, 7). In a lysogenic cell, CI prevents lytic growth by directly repressing the lytic promoters pR and pL. This repression is enhanced by longrange cooperative interactions between CI dimers bound to the OL1-OL2 and OR1-OR2 regions, thus looping the DNA that lies between them (8) (Fig. 1 A and B). CI-mediated DNA looping brings OR3 in proximity to OL3. This juxtaposition allows a CI dimer bound to the strong OL3 to facilitate another CI dimer to bind to the intrinsically weak OR3, thus reducing the concentration of CI necessary to occupy OR3. In this manner CI can autoregulate its own expression by binding to OR2 (activation) or by binding to OR3 (repression). This autoregulation is crucial for the phage to maintain repression while preventing excessive accumulation of CI. When DNA in the lysogen is damaged, the bacterial DNA-damage-sensing system is triggered, leading to CI inactivation by self-cleavage (9) and to an efficient switch to the lytic state, eventually leading to production of progeny phage and cell death (1).The switch from the lysogenic to the lytic state must be decisive. Partial entry into vegetative growth may kill the host without producing a full burst of progeny phage. Because the in vivo state of DNA is supercoiled (10), we sought to examine protein-mediated DNA looping on native, supercoiled DNA. In vitro single molecule exper...

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Section: Resultsmentioning

confidence: 99%

DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

Nørregaard

Andersson

Sneppen

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…In contrast, topoisomerase I is not essential: deletion mutants are viable (22). However, topoisomerase I deletion mutants of Escherichia coli grow well only because they have acquired compensatory mutations (7,23). Thus, E. coli apparently requires both DNA gyrase and topoisomerase I, but mutations can overcome the need for topoisomerase I, whereas no substitutes exist for gyrase.…”

mentioning

confidence: 99%

Topoisomerase I mutants: the gene on pBR322 that encodes resistance to tetracycline affects plasmid DNA supercoiling.

Pruss¹,

Drlica²

1986

Proc. Natl. Acad. Sci. U.S.A.

172

127

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“…The type II topoisomerases are thought to be essential for bacterial growth because of inducible lethality in temperature-sensitive mutants (16,17). The type I topoisomerases are not essential for bacterial growth, because their loss can be compensated for by alterations in type II topoisomerase genes (4,5).…”

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Comparison of inhibition of Escherichia coli topoisomerase IV by quinolones with DNA gyrase inhibition

Hoshino¹,

Kitamura²,

Morrissey³

et al. 1994

Antimicrob Agents Chemother

152

100

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In order to examine the inhibitory activities of quinolones against topoisomerase IV, both subunits of this enzyme, ParC and ParE, were purified from Escherichia coli. The specific activity of topoisomerase IV decatenation was found to be more than five times greater than that of topoisomerase IV relaxation. Thus, the decatenation activity of topoisomerase IV seems the most relevant activity for use in studies of drug inhibition of this enzyme. Although topoisomerase IV was less sensitive to quinolones than DNA gyrase, the 50% inhibitory concentrations for decatenation were significantly lower than those for type I topoisomerases. Moreover, there was a positive correlation between the inhibitory activity against topoisomerase IV decatenation and that for DNA gyrase supercoiling. These results imply that topoisomerase IV could be a target for the quinolones in intact bacteria and that quinolones could inhibit not only supercoiling of DNA gyrase but also decatenation of topoisomerase IV when high concentrations of drug exist in bacterial cells.Four topoisomerases have been isolated from Escherichia coli so far: topoisomerase I (39), topoisomerase II (DNA gyrase) (9), topoisomerase III (34), and topoisomerase IV (16). Among these enzymes, topoisomerases I, II, and IV are implicated in the control of the intracellular supercoiling density of chromosomal or plasmid DNA, affecting the efficacy of DNA replication and transcription (4, 6-8, 20, 24, 29, 36, 37). In addition, some topoisomerases are required for the segregation of daughter chromosomes or plasmid DNA (1,21,35,40). Although all of these topoisomerases are capable of changing the topology of DNA by a cleaving and rejoining step, each enzyme appears to possess a favored reaction in vitro. Type I topoisomerases, topoisomerase I and topoisomerase III, show efficient relaxing and decatenating activity, respectively, in the absence of ATP (2,3,5,11,29,30,34 subunits of DNA gyrase), respectively (16). Similar sequences are located especially around the region of DNA gyrase known as the "quinolone resistance-determining region." The quinolone antibacterial agents, in particular the fluoroquinolones, strongly inhibit DNA gyrase, which results ultimately in bacterial death (32). However, the inhibitory activities of quinolones against type I topoisomerases, topoisomerase I (25) and topoisomerase III (2) in E. coli, are weak. The inhibitory activities of fluoroquinolones against topoisomerase IV have yet to be fully investigated. The similarity in amino acid sequence between DNA gyrase and topoisomerase IV, especially around sites in the GyrA protein of DNA gyrase at positions known to produce quinolone-resistant DNA gyrases (41), implies that quinolones may be capable of inhibiting the activity of topoisomerase IV as well as against DNA gyrase.In this study, in order to define the inhibitory activities of quinolones against topoisomerase IV, both subunits of topoisomerase IV, ParC and ParE, were purified, and optimum conditions for the decatenating activity of topoi...

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Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes

Cited by 432 publications

References 20 publications

DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

Topoisomerase I mutants: the gene on pBR322 that encodes resistance to tetracycline affects plasmid DNA supercoiling.

Comparison of inhibition of Escherichia coli topoisomerase IV by quinolones with DNA gyrase inhibition

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