Journal articles: 'DNA Gyrase DNA Gyrase DNA Replication DNA'

1

Hashimi, Saeed M., Melisa K. Wall, Andrew B. Smith, Anthony Maxwell, and Robert G. Birch. "The Phytotoxin Albicidin is a Novel Inhibitor of DNA Gyrase." Antimicrobial Agents and Chemotherapy 51, no. 1 (January 2007): 181–87. http://dx.doi.org/10.1128/aac.00918-06.

Full text

Abstract:

ABSTRACT Xanthomonas albilineans produces a family of polyketide-peptide compounds called albicidins which are highly potent antibiotics and phytotoxins as a result of their inhibition of prokaryotic DNA replication. Here we show that albicidin is a potent inhibitor of the supercoiling activity of bacterial and plant DNA gyrases, with 50% inhibitory concentrations (40 to 50 nM) less than those of most coumarins and quinolones. Albicidin blocks the religation of the cleaved DNA intermediate during the gyrase catalytic sequence and also inhibits the relaxation of supercoiled DNA by gyrase and topoisomerase IV. Unlike the coumarins, albicidin does not inhibit the ATPase activity of gyrase. In contrast to the quinolones, the albicidin concentration required to stabilize the gyrase cleavage complex increases 100-fold in the absence of ATP. The slow peptide poisons microcin B17 and CcdB also access ATP-dependent conformations of gyrase to block religation, but in contrast to albicidin, they do not inhibit supercoiling under routine assay conditions. Some mutations in gyrA, known to confer high-level resistance to quinolones or CcdB, confer low-level resistance or hypersensitivity to albicidin in Escherichia coli. Within the albicidin biosynthesis region in X. albilineans is a gene encoding a pentapeptide repeat protein designated AlbG that binds to E. coli DNA gyrase and that confers a sixfold increase in the level of resistance to albicidin in vitro and in vivo. These results demonstrate that DNA gyrase is the molecular target of albicidin and that X. albilineans encodes a gyrase-interacting protein for self-protection. The novel features of the gyrase-albicidin interaction indicate the potential for the development of new antibacterial drugs.

APA, Harvard, Vancouver, ISO, and other styles

2

Hirsch, Jana, and Dagmar Klostermeier. "What makes a type IIA topoisomerase a gyrase or a Topo IV?" Nucleic Acids Research 49, no. 11 (April 27, 2021): 6027–42. http://dx.doi.org/10.1093/nar/gkab270.

Full text

Abstract:

Abstract Type IIA topoisomerases catalyze a variety of different reactions: eukaryotic topoisomerase II relaxes DNA in an ATP-dependent reaction, whereas the bacterial representatives gyrase and topoisomerase IV (Topo IV) preferentially introduce negative supercoils into DNA (gyrase) or decatenate DNA (Topo IV). Gyrase and Topo IV perform separate, dedicated tasks during replication: gyrase removes positive supercoils in front, Topo IV removes pre-catenanes behind the replication fork. Despite their well-separated cellular functions, gyrase and Topo IV have an overlapping activity spectrum: gyrase is also able to catalyze DNA decatenation, although less efficiently than Topo IV. The balance between supercoiling and decatenation activities is different for gyrases from different organisms. Both enzymes consist of a conserved topoisomerase core and structurally divergent C-terminal domains (CTDs). Deletion of the entire CTD, mutation of a conserved motif and even by just a single point mutation within the CTD converts gyrase into a Topo IV-like enzyme, implicating the CTDs as the major determinant for function. Here, we summarize the structural and mechanistic features that make a type IIA topoisomerase a gyrase or a Topo IV, and discuss the implications for type IIA topoisomerase evolution.

APA, Harvard, Vancouver, ISO, and other styles

3

Aedo, Sandra, and Yuk-Ching Tse-Dinh. "Isolation and Quantitation of Topoisomerase Complexes Accumulated on Escherichia coli Chromosomal DNA." Antimicrobial Agents and Chemotherapy 56, no. 11 (August 6, 2012): 5458–64. http://dx.doi.org/10.1128/aac.01182-12.

Full text

Abstract:

ABSTRACTDNA topoisomerases are important targets in anticancer and antibacterial therapy because drugs can initiate cell death by stabilizing the transient covalent topoisomerase-DNA complex. In this study, we employed a method that uses CsCl density gradient centrifugation to separate unbound from DNA-bound GyrA/ParC inEscherichia colicell lysates after quinolone treatment, allowing antibody detection and quantitation of the covalent complexes on slot blots. Using these procedures modified from thein vivocomplexes of enzyme (ICE) bioassay, we found a correlation between gyrase-DNA complex formation and DNA replication inhibition at bacteriostatic (1× MIC) norfloxacin concentrations. Quantitation of the number of gyrase-DNA complexes perE. colicell permitted an association between cell death and chromosomal gyrase-DNA complex accumulation at norfloxacin concentrations greater than 1× MIC. When comparing levels of gyrase-DNA complexes to topoisomerase IV-DNA complexes in the absence of drug, we observed that the gyrase-DNA complex level was higher (∼150-fold) than that of the topoisomerase IV-DNA complex. In addition, levels of gyrase and topoisomerase IV complexes reached a significant increase after 30 min of treatment at 1× and 1.7× MIC, respectively. These results are in agreement with gyrase being the primary target for quinolones inE. coli. We further validated the utility of this method for the study of topoisomerase-drug interactions in bacteria by showing the gyrase covalent complex reversibility after removal of the drug from the medium, and the resistant effect of the Ser83LeugyrAmutation on accumulation of gyrase covalent complexes on chromosomal DNA.

APA, Harvard, Vancouver, ISO, and other styles

4

Hiasa, Hiroshi, and Molly E. Shea. "DNA Gyrase-mediated Wrapping of the DNA Strand Is Required for the Replication Fork Arrest by the DNA Gyrase-Quinolone-DNA Ternary Complex." Journal of Biological Chemistry 275, no. 44 (August 16, 2000): 34780–86. http://dx.doi.org/10.1074/jbc.m001608200.

Full text

APA, Harvard, Vancouver, ISO, and other styles

5

Fournier, Bénédicte, Xilin Zhao, Tao Lu, Karl Drlica, and David C. Hooper. "Selective Targeting of Topoisomerase IV and DNA Gyrase in Staphylococcus aureus: Different Patterns of Quinolone- Induced Inhibition of DNA Synthesis." Antimicrobial Agents and Chemotherapy 44, no. 8 (August 1, 2000): 2160–65. http://dx.doi.org/10.1128/aac.44.8.2160-2165.2000.

Full text

Abstract:

ABSTRACT The effect of quinolones on the inhibition of DNA synthesis inStaphylococcus aureus was examined by using single resistance mutations in parC or gyrA to distinguish action against gyrase or topoisomerase IV, respectively. Norfloxacin preferentially attacked topoisomerase IV and blocked DNA synthesis slowly, while nalidixic acid targeted gyrase and inhibited replication rapidly. Ciprofloxacin exhibited an intermediate response, consistent with both enzymes being targeted. The absence of RecA had little influence on target choice by this assay, indicating that differences in rebound (repair) DNA synthesis were not responsible for the results. At saturating drug concentrations, norfloxacin and a gyrA mutant were used to show that topoisomerase IV-norfloxacin-cleaved DNA complexes are distributed on the S. aureus chromosome at intervals of about 30 kbp. If cleaved complexes block DNA replication, as indicated by previous work, such close spacing of topoisomerase-quinolone-DNA complexes should block replication rapidly (replication forks are likely to encounter a cleaved complex within a minute). Thus, the slow inhibition of DNA synthesis at growth-inhibitory concentrations suggests that a subset of more distantly distributed complexes is physiologically relevant for drug action and is unlikely to be located immediately in front of the DNA replication fork.

APA, Harvard, Vancouver, ISO, and other styles

6

Pato, M. L., and M. Banerjee. "Replacement of the Bacteriophage Mu Strong Gyrase Site and Effect on Mu DNA Replication." Journal of Bacteriology 181, no. 18 (September 15, 1999): 5783–89. http://dx.doi.org/10.1128/jb.181.18.5783-5789.1999.

Full text

Abstract:

ABSTRACT The bacteriophage Mu strong gyrase site (SGS) is required for efficient replicative transposition and functions by promoting the synapsis of prophage termini. To look for other sites which could substitute for the SGS in promoting Mu replication, we have replaced the SGS in the middle of the Mu genome with fragments of DNA from various sources. A central fragment from the transposing virus D108 allowed efficient Mu replication and was shown to contain a strong gyrase site. However, neither the strong gyrase site from the plasmid pSC101 nor the major gyrase site from pBR322 could promote efficient Mu replication, even though the pSC101 site is a stronger gyrase site than the Mu SGS as assayed by cleavage in the presence of gyrase and the quinolone enoxacin. To look for SGS-like sites in the Escherichia coli chromosome which might be involved in organizing nucleoid structure, fragments of E. coli chromosomal DNA were substituted for the SGS: first, repeat sequences associated with gyrase binding (bacterial interspersed mosaic elements), and, second, random fragments of the entire chromosome. No fragments were found that could replace the SGS in promoting efficient Mu replication. These results demonstrate that the gyrase sites from the transposing phages possess unusual properties and emphasize the need to determine the basis of these properties.

APA, Harvard, Vancouver, ISO, and other styles

7

Dar, Mohd Ashraf, Atul Sharma, Neelima Mondal, and Suman Kumar Dhar. "Molecular Cloning of Apicoplast-Targeted Plasmodium falciparum DNA Gyrase Genes: Unique Intrinsic ATPase Activity and ATP-Independent Dimerization of PfGyrB Subunit." Eukaryotic Cell 6, no. 3 (January 12, 2007): 398–412. http://dx.doi.org/10.1128/ec.00357-06.

Full text

Abstract:

ABSTRACT DNA gyrase, a typical type II topoisomerase that can introduce negative supercoils in DNA, is essential for replication and transcription in prokaryotes. The apicomplexan parasite Plasmodium falciparum contains the genes for both gyrase A and gyrase B in its genome. Due to the large sizes of both proteins and the unusual codon usage of the highly AT-rich P. falciparum gyrA (PfgyrA) and PfgyrB genes, it has so far been impossible to characterize these proteins, which could be excellent drug targets. Here, we report the cloning, expression, and functional characterization of full-length PfGyrB and functional domains of PfGyrA. Unlike Escherichia coli GyrB, PfGyrB shows strong intrinsic ATPase activity and follows a linear pattern of ATP hydrolysis characteristic of dimer formation in the absence of ATP analogues. These unique features have not been reported for any known gyrase so far. The PfgyrB gene complemented the E. coli gyrase temperature-sensitive strain, and, together with the N-terminal domain of PfGyrA, it showed typical DNA cleavage activity. Furthermore, PfGyrA contains a unique leucine heptad repeat that might be responsible for dimerization. These results confirm the presence of DNA gyrase in eukaryotes and confer great potential for drug development and organelle DNA replication in the deadliest human malarial parasite, P. falciparum.

APA, Harvard, Vancouver, ISO, and other styles

8

Rovinskiy, Nikolay, Andrews Agbleke, Olga Chesnokova, and N. Higgins. "Supercoil Levels in E. coli and Salmonella Chromosomes Are Regulated by the C-Terminal 35–38 Amino Acids of GyrA." Microorganisms 7, no. 3 (March 15, 2019): 81. http://dx.doi.org/10.3390/microorganisms7030081.

Full text

Abstract:

Prokaryotes have an essential gene—gyrase—that catalyzes negative supercoiling of plasmid and chromosomal DNA. Negative supercoils influence DNA replication, transcription, homologous recombination, site-specific recombination, genetic transposition and sister chromosome segregation. Although E. coli and Salmonella Typhimurium are close relatives with a conserved set of essential genes, E. coli DNA has a supercoil density 15% higher than Salmonella, and E. coli cannot grow at the supercoil density maintained by wild type (WT) Salmonella. E. coli is addicted to high supercoiling levels for efficient chromosomal folding. In vitro experiments were performed with four gyrase isoforms of the tetrameric enzyme (GyrA2:GyrB2). E. coli gyrase was more processive and faster than the Salmonella enzyme, but Salmonella strains with chromosomal swaps of E. coli GyrA lost 40% of the chromosomal supercoil density. Reciprocal experiments in E. coli showed chromosomal dysfunction for strains harboring Salmonella GyrA. One GyrA segment responsible for dis-regulation was uncovered by constructing and testing GyrA chimeras in vivo. The six pinwheel elements and the C-terminal 35–38 acidic residues of GyrA controlled WT chromosome-wide supercoiling density in both species. A model of enzyme processivity modulated by competition between DNA and the GyrA acidic tail for access to β-pinwheel elements is presented.

APA, Harvard, Vancouver, ISO, and other styles

9

Hardy, Christine D., and Nicholas R. Cozzarelli. "Alteration of Escherichia coli Topoisomerase IV to Novobiocin Resistance." Antimicrobial Agents and Chemotherapy 47, no. 3 (March 2003): 941–47. http://dx.doi.org/10.1128/aac.47.3.941-947.2003.

Full text

Abstract:

ABSTRACT DNA gyrase and topoisomerase IV (topo IV) are the two essential type II topoisomerases of Escherichia coli. Gyrase is responsible for maintaining negative supercoiling of the bacterial chromosome, whereas topo IV's primary role is in disentangling daughter chromosomes following DNA replication. Coumarins, such as novobiocin, are wide-spectrum antimicrobial agents that primarily interfere with DNA gyrase. In this work we designed an alteration in the ParE subunit of topo IV at a site homologous to that which confers coumarin resistance in gyrase. This parE mutation renders the encoded topo IV approximately 40-fold resistant to inhibition by novobiocin in vitro and imparts a similar resistance to inhibition of topo IV-mediated relaxation of supercoiled DNA in vivo. We conclude that topo IV is a secondary target of novobiocin and that it is very likely to be inhibited by the same mechanism as DNA gyrase.

APA, Harvard, Vancouver, ISO, and other styles

10

Pang, Zhenhua, Ray Chen, Dipankar Manna, and N. Patrick Higgins. "A Gyrase Mutant with Low Activity Disrupts Supercoiling at the Replication Terminus." Journal of Bacteriology 187, no. 22 (November 15, 2005): 7773–83. http://dx.doi.org/10.1128/jb.187.22.7773-7783.2005.

Full text

Abstract:

ABSTRACT When a mutation in an essential gene shows a temperature-sensitive phenotype, one usually assumes that the protein is inactive at nonpermissive temperature. DNA gyrase is an essential bacterial enzyme composed of two subunits, GyrA and GyrB. The gyrB652 mutation results from a single base change that substitutes a serine residue for arginine 436 (R436-S) in the GyrB protein. At 42°C, strains with the gyrB652 allele stop DNA replication, and at 37°C, such strains grow but have RecA-dependent SOS induction and show constitutive RecBCD-dependent DNA degradation. Surprisingly, the GyrB652 protein is not inactive at 42°C in vivo or in vitro and it doesn't directly produce breaks in chromosomal DNA. Rather, this mutant has a low k cat compared to wild-type GyrB subunit. With more than twice the normal mean number of supercoil domains, this gyrase hypomorph is prone to fork collapse and topological chaos near the terminus of DNA replication.

APA, Harvard, Vancouver, ISO, and other styles

11

Samadpour, A. N., and H. Merrikh. "DNA gyrase activity regulates DnaA-dependent replication initiation inBacillus subtilis." Molecular Microbiology 108, no. 2 (March 6, 2018): 115–27. http://dx.doi.org/10.1111/mmi.13920.

Full text

APA, Harvard, Vancouver, ISO, and other styles

12

Man, Ruo-Jun, Xu-Ping Zhang, Yu-Shun Yang, Ai-Qin Jiang, and Hai-Liang Zhu. "Recent Progress in Small Molecular Inhibitors of DNA Gyrase." Current Medicinal Chemistry 28, no. 28 (September 9, 2021): 5808–30. http://dx.doi.org/10.2174/1871529x21666210202113128.

Full text

Abstract:

Background: In the past few decades, with the abuse of antibiotics, bacterial resistance has enhanced constantly. More and more super species of bacteria, which are seriously threatening human health, have been discovered. Developing novel antibacterial agents to overcome the drug-resistance is an urgent duty. We all know that blocking the information-transfer of bacterial DNA and RNA is one of the effective ways to inhibit bacterial growth. Therefore, as the indispensable enzyme for DNA replication and transcription, DNA gyrase is one of the important targets for bacterial inhibitors. Accordingly, many inhibitors of DNA gyrase have also been developed. Methods: In this review, to highlight the recent progress in DNA gyrase inhibitors, the study in this field over the past three years (2017-2019) was summarized and organized based on their backbones or core moieties. Both of the subunits of DNA gyrase were taken into consideration. Results: These DNA gyrase inhibitors have been classified based on their backbones or core moieties. After the comparison of the divided 14 categories, we could achieve some clues for future modification. In particular, we found that benzodiazepines and naphthalene heterocycles were the most common structures in the drug design. On the other hand, isopropyl and cyclopropyl have also been used in drug design, which provides more inspiration for the investigations. Except for GSK2140944, which has entered the phase III clinical trial stage, other compounds here were not fully promulgated with their optimal pharmacokinetic activity. Conclusion: We briefly summed up the current situation and future challenges on this topic. Through the discussion of the design strategies and drug effect, we hope that this review can provide a focused direction for future researches.

APA, Harvard, Vancouver, ISO, and other styles

13

Zechiedrich, E. L., and N. R. Cozzarelli. "Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli." Genes & Development 9, no. 22 (November 15, 1995): 2859–69. http://dx.doi.org/10.1101/gad.9.22.2859.

Full text

APA, Harvard, Vancouver, ISO, and other styles

14

Oram, Mark, Andrew A. Travers, Alison J. Howells, Anthony Maxwell, and Martin L. Pato. "Dissection of the Bacteriophage Mu Strong Gyrase Site (SGS): Significance of the SGS Right Arm in Mu Biology and DNA Gyrase Mechanism." Journal of Bacteriology 188, no. 2 (January 15, 2006): 619–32. http://dx.doi.org/10.1128/jb.188.2.619-632.2006.

Full text

Abstract:

ABSTRACT The bacteriophage Mu strong gyrase site (SGS), required for efficient phage DNA replication, differs from other gyrase sites in the efficiency of gyrase binding coupled with a highly processive supercoiling activity. Genetic studies have implicated the right arm of the SGS as a key structural feature for promoting rapid Mu replication. Here, we show that deletion of the distal portion of the right arm abolishes efficient binding, cleavage, and supercoiling by DNA gyrase in vitro. DNase I footprinting analysis of the intact SGS revealed an adenylyl imidodiphosphate-dependent change in protection in the right arm, indicating that this arm likely forms the T segment that is passed through the cleaved G segment during the supercoiling reaction. Furthermore, in an SGS derivative with an altered right-arm sequence, the left arm showed these changes, suggesting that the selection of a T segment by gyrase is determined primarily by the sequences of the arms. Analysis of the sequences of the SGS and other gyrase sites suggests that the choice of T segment correlates with which arm possesses the more extensive set of phased anisotropic bending signals, with the Mu right arm possessing an unusually extended set of such signals. The implications of these observations for the structure of the gyrase-DNA complex and for the biological function of the Mu SGS are discussed.

APA, Harvard, Vancouver, ISO, and other styles

15

del Castillo, Francisco J., Ignacio del Castillo, and Felipe Moreno. "Construction and Characterization of Mutations at Codon 751 of the Escherichia coli gyrB Gene That Confer Resistance to the Antimicrobial Peptide Microcin B17 and Alter the Activity of DNA Gyrase." Journal of Bacteriology 183, no. 6 (March 15, 2001): 2137–40. http://dx.doi.org/10.1128/jb.183.6.2137-2140.2001.

Full text

Abstract:

ABSTRACT Microcin B17 is a peptide antibiotic that inhibits DNA replication in Escherichia coli by targeting DNA gyrase. Previously, two independently isolated microcin B17-resistant mutants were shown to harbor the same gyrB point mutation that results in the replacement of tryptophan 751 by arginine in the GyrB polypeptide. We used site-directed mutagenesis to construct mutants in which tryptophan 751 was deleted or replaced by other amino acids. These mutants exhibit altered DNA gyrase activity and different levels of resistance to microcin B17.

APA, Harvard, Vancouver, ISO, and other styles

16

Tadesse, Serkalem, and Peter L. Graumann. "Differential and Dynamic Localization of Topoisomerases in Bacillus subtilis." Journal of Bacteriology 188, no. 8 (April 15, 2006): 3002–11. http://dx.doi.org/10.1128/jb.188.8.3002-3011.2006.

Full text

Abstract:

ABSTRACT Visualization of topoisomerases in live Bacillus subtilis cells showed that Topo I, Topo IV, and DNA gyrase differentially localize on the nucleoids but are absent at cytosolic spaces surrounding the nucleoids, suggesting that these topoisomerases interact with many regions of the chromosome. While both subunits of Topo IV were uniformly distributed throughout the nucleoids, Topo I and gyrase formed discrete accumulations, or foci, on the nucleoids in a large fraction of the cells, which showed highly dynamic movements. Three-dimensional time lapse microscopy showed that gyrase foci accumulate and dissipate within a 1-min time scale, revealing dynamic assembly and disassembly of subcelluar topoisomerase centers. Gyrase centers frequently colocalized with the central DNA replication machinery, suggesting a major role for gyrase at the replication fork, while Topo I foci were frequently close to or colocalized with the structural maintenance of chromosomes (SMC) chromosome segregation complex. The findings suggest that different areas of supercoiling exist on the B. subtilis nucleoids, which are highly dynamic, with a high degree of positive supercoiling attracting gyrase to the replication machinery and areas of negative supercoiling at the bipolar SMC condensation centers recruiting Topo I.

APA, Harvard, Vancouver, ISO, and other styles

17

Garí, Eloi, Lionello Bossi, and Nara Figueroa-Bossi. "Growth-Dependent DNA Breakage and Cell Death in a Gyrase Mutant of Salmonella." Genetics 159, no. 4 (December 1, 2001): 1405–14. http://dx.doi.org/10.1093/genetics/159.4.1405.

Full text

Abstract:

Abstract A class of gyrase mutants of Salmonella enterica mimics the properties of bacteria exposed to quinolones. These mutants suffer spontaneous DNA breakage during normal growth and depend on recombinational repair for viability. Unlike quinolone-treated bacteria, however, they do not show accumulation of cleavable gyrase-DNA complexes. In recA or recB mutant backgrounds, the temperature-sensitive (ts) allele gyrA208 causes rapid cell death at 43°. Here, we isolated “suppressor-of-death” mutations, that is, secondary changes that allow a gyrA208 recB double mutant to survive a prolonged exposure to 43° and subsequently to form colonies at 28°. In most isolates, the secondary change was itself a ts mutation. Three ts alleles were mapped in genes coding for amino acyl tRNA synthetases (alaS, glnS, and lysS). Allele alaS216 completely abolished DNA breakage in a gyrA208 recA double mutant. Likewise, treating this mutant with chloramphenicol prevented death and DNA damage at 43°. Additional suppressors of gyrA208 lethality include rpoB mutations and, surprisingly, icd mutations inactivating isocitrate dehydrogenase. We postulate that the primary effect of the gyrase alteration is to hamper replication fork movement. Inhibiting DNA replication under conditions of continuing macromolecular synthesis (“unbalanced growth”) activates a mechanism that causes DNA breakage and cell death, reminiscent of “thymineless” lethality.

APA, Harvard, Vancouver, ISO, and other styles

18

Wentzell, Lois M., and Anthony Maxwell. "The Complex of DNA Gyrase and Quinolone Drugs on DNA Forms a Barrier to the T7 DNA Polymerase Replication Complex." Journal of Molecular Biology 304, no. 5 (December 2000): 779–91. http://dx.doi.org/10.1006/jmbi.2000.4266.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Patil, Tejaswini D. "DESIGN, INSILICO SCREENING, MOLECULAR DOCKING, SYNTHESIS AND BIOLOGICAL EVALUATION OF BENZO-FUSED FIVE MEMBERED NITROGEN CONTAINING HETEROCYCLE AGAINST DNA GYRASE SUBUNIT B AS POTENTIAL ANTIMICROBIAL AGENT." Journal of Medical pharmaceutical and allied sciences 10, no. 3 (July 15, 2021): 3016–23. http://dx.doi.org/10.22270/jmpas.v10i3.1176.

Full text

Abstract:

Because of its function in DNA replication, DNA gyrase subunit B (1KZN) is a promising target for antimicrobial drug development. There is an urgent requirement for the designing and improvement of novel antimicrobial drugs due to the rapid development of antimicrobial drug resistance. The aim of this study is to use molecular docking to design, synthesise, and identify benzo-fused five-membered nitrogen containing heterocycle against DNA gyrase subunit B (1KZN). Using an effective procedure, 2-(1H-1,2,3-Benzotriazol-1-yl)-N-substituted acetamide was synthesised based on the literature review. The antimicrobial activity of all synthesised compounds was tested against four different organisms: E. coli, P. aeruginosa, S. aureus, and Candida albicans. The compound binds to the active site of DNA gyrase subunit B (1KZN) in a docking study, indicating that it may have antimicrobial activity. The compounds BT4 and BT6 have the antimicrobial capacity, according to the findings of this report. BT3 has the ability to be an antibacterial agent for Staphylococcus aureus.

APA, Harvard, Vancouver, ISO, and other styles

20

Yi, Lanhua, and Xin Lü. "New Strategy on Antimicrobial-resistance: Inhibitors of DNA Replication Enzymes." Current Medicinal Chemistry 26, no. 10 (June 20, 2019): 1761–87. http://dx.doi.org/10.2174/0929867324666171106160326.

Full text

Abstract:

Background:Antimicrobial resistance is found in all microorganisms and has become one of the biggest threats to global health. New antimicrobials with different action mechanisms are effective weapons to fight against antibiotic-resistance.Objective:This review aims to find potential drugs which can be further developed into clinic practice and provide clues for developing more effective antimicrobials.Methods:DNA replication universally exists in all living organisms and is a complicated process in which multiple enzymes are involved in. Enzymes in bacterial DNA replication of initiation and elongation phases bring abundant targets for antimicrobial development as they are conserved and indispensable. In this review, enzyme inhibitors of DNA helicase, DNA primase, topoisomerases, DNA polymerase and DNA ligase were discussed. Special attentions were paid to structures, activities and action modes of these enzyme inhibitors.Results:Among these enzymes, type II topoisomerase is the most validated target with abundant inhibitors. For type II topoisomerase inhibitors (excluding quinolones), NBTIs and benzimidazole urea derivatives are the most promising inhibitors because of their good antimicrobial activity and physicochemical properties. Simultaneously, DNA gyrase targeted drugs are particularly attractive in the treatment of tuberculosis as DNA gyrase is the sole type II topoisomerase in Mycobacterium tuberculosis. Relatively, exploitation of antimicrobial inhibitors of the other DNA replication enzymes are primeval, in which inhibitors of topo III are even blank so far.Conclusion:This review demonstrates that inhibitors of DNA replication enzymes are abundant, diverse and promising, many of which can be developed into antimicrobials to deal with antibioticresistance.

APA, Harvard, Vancouver, ISO, and other styles

21

Bellon, Steven, Jonathan D. Parsons, Yunyi Wei, Koto Hayakawa, Lora L. Swenson, Paul S. Charifson, Judith A. Lippke, Robert Aldape, and Christian H. Gross. "Crystal Structures of Escherichia coli Topoisomerase IV ParE Subunit (24 and 43 Kilodaltons): a Single Residue Dictates Differences in Novobiocin Potency against Topoisomerase IV and DNA Gyrase." Antimicrobial Agents and Chemotherapy 48, no. 5 (May 2004): 1856–64. http://dx.doi.org/10.1128/aac.48.5.1856-1864.2004.

Full text

Abstract:

ABSTRACT Topoisomerase IV and DNA gyrase are related bacterial type II topoisomerases that utilize the free energy from ATP hydrolysis to catalyze topological changes in the bacterial genome. The essential function of DNA gyrase is the introduction of negative DNA supercoils into the genome, whereas the essential function of topoisomerase IV is to decatenate daughter chromosomes following replication. Here, we report the crystal structures of a 43-kDa N-terminal fragment of Escherichia coli topoisomerase IV ParE subunit complexed with adenylyl-imidodiphosphate at 2.0-Å resolution and a 24-kDa N-terminal fragment of the ParE subunit complexed with novobiocin at 2.1-Å resolution. The solved ParE structures are strikingly similar to the known gyrase B (GyrB) subunit structures. We also identified single-position equivalent amino acid residues in ParE (M74) and in GyrB (I78) that, when exchanged, increased the potency of novobiocin against topoisomerase IV by nearly 20-fold (to 12 nM). The corresponding exchange in gyrase (I78 M) yielded a 20-fold decrease in the potency of novobiocin (to 1.0 μM). These data offer an explanation for the observation that novobiocin is significantly less potent against topoisomerase IV than against DNA gyrase. Additionally, the enzyme kinetic parameters were affected. In gyrase, the ATP Km increased ≈5-fold and the V max decreased ≈30%. In contrast, the topoisomerase IV ATP Km decreased by a factor of 6, and the V max increased ≈2-fold from the wild-type values. These data demonstrate that the ParE M74 and GyrB I78 side chains impart opposite effects on the enzyme's substrate affinity and catalytic efficiency.

APA, Harvard, Vancouver, ISO, and other styles

22

Oram, Mark, and Martin L. Pato. "Mu-Like Prophage Strong Gyrase Site Sequences: Analysis of Properties Required for Promoting Efficient Mu DNA Replication." Journal of Bacteriology 186, no. 14 (July 15, 2004): 4575–84. http://dx.doi.org/10.1128/jb.186.14.4575-4584.2004.

Full text

Abstract:

ABSTRACT The bacteriophage Mu genome contains a centrally located strong gyrase site (SGS) that is required for efficient prophage replication. To aid in studying the unusual properties of the SGS, we sought other gyrase sites that might be able to substitute for the SGS in Mu replication. Five candidate sites were obtained by PCR from Mu-like prophage sequences present in Escherichia coli O157:H7 Sakai, Haemophilus influenzae Rd, Salmonella enterica serovar Typhi CT18, and two strains of Neisseria meningitidis. Each of the sites was used to replace the natural Mu SGS to form recombinant prophages, and the effects on Mu replication and host lysis were determined. The site from the E. coli prophage supported markedly enhanced replication and host lysis over that observed with a Mu derivative lacking the SGS, those from the N. meningitidis prophages allowed a small enhancement, and the sites from the Haemophilus and Salmonella prophages gave none. Each of the candidate sites was cleaved specifically by E. coli DNA gyrase both in vitro and in vivo. Supercoiling assays performed in vitro, with the five sites or the Mu SGS individually cloned into a pUC19 reporter plasmid, showed that the Mu SGS and the E. coli or N. meningitidis sequences allowed an enhancement of processive, gyrase-dependent supercoiling, whereas the H. influenzae or Salmonella serovar Typhi sequences did not. While consistent with a requirement for enhanced processivity of supercoiling for a site to function in Mu replication, these data suggest that other factors are also important. The relevance of these observations to an understanding of the function of the SGS is discussed.

APA, Harvard, Vancouver, ISO, and other styles

23

Stein, Daniel C. "Transformation of Neisseria gonorrhoeae: physical requirements of the transforming DNA." Canadian Journal of Microbiology 37, no. 5 (May 1, 1991): 345–49. http://dx.doi.org/10.1139/m91-056.

Full text

Abstract:

The 1600-bp (base pair) fragment encoding a portion of the nalidixic acid resistant DNA gyrase, subunit B, was characterized to determine what parameters effect transformation in the gonococcus. When this DNA (pSY2) was isolated from Escherichia coli, it was able to transform a variety of gonococcal strains to resistance to nalidixic acid via DNA-mediated transformation, irrespective of their restriction–modification phenotype. Nalidixic acid resistant transformants contained no plasmid DNA sequences that corresponded to the vector, as measured by plasmid screening procedures and colony hybridization techniques. Supercoiled and linear DNA transformed the gonococcus at the same efficiency. DNA fragments as small as 615 bp were able to transform the gonococcus. The presence of a 10-bp uptake sequence enhanced a DNA fragment's ability to transform the gonococcus by four orders of magnitude. When the fragment encoding the nalidixic acid resistant DNA gyrase was subcloned into M13mp18, both the replicative form and the single-stranded form of the phage were able to transform the gonococcus to nalidixic acid resistance. Key words: sequence-specific uptake, gyrase, restriction and modification.

APA, Harvard, Vancouver, ISO, and other styles

24

Shapiro, Adam, Haris Jahic, Swati Prasad, David Ehmann, Jason Thresher, Ning Gao, and Laurel Hajec. "A Homogeneous, High-Throughput Fluorescence Anisotropy-Based DNA Supercoiling Assay." Journal of Biomolecular Screening 15, no. 9 (October 2010): 1088–98. http://dx.doi.org/10.1177/1087057110378624.

Full text

Abstract:

The degree of supercoiling of DNA is vital for cellular processes, such as replication and transcription. DNA topology is controlled by the action of DNA topoisomerase enzymes. Topoisomerases, because of their importance in cellular replication, are the targets of several anticancer and antibacterial drugs. In the search for new drugs targeting topoisomerases, a biochemical assay compatible with automated high-throughput screening (HTS) would be valuable. Gel electrophoresis is the standard method for measuring changes in the extent of supercoiling of plasmid DNA when acted upon by topoisomerases, but this is a low-throughput and laborious method. A medium-throughput method was described previously that quantitatively distinguishes relaxed and supercoiled plasmids by the difference in their abilities to form triplex structures with an immobilized oligonucleotide. In this article, the authors describe a homogeneous supercoiling assay based on triplex formation in which the oligonucleotide strand is labeled with a fluorescent dye and the readout is fluorescence anisotropy. The new assay requires no immobilization, filtration, or plate washing steps and is therefore well suited to HTS for inhibitors of topoisomerases. The utility of this assay is demonstrated with relaxation of supercoiled plasmid by Escherichia coli topoisomerase I, supercoiling of relaxed plasmid by E. coli DNA gyrase, and inhibition of gyrase by fluoroquinolones and nalidixic acid.

APA, Harvard, Vancouver, ISO, and other styles

25

We˛grzyn, Alicja, Anna Herman-Antosiewicz, Karol Taylor, and Grzegorz We˛grzyn. "Molecular Mechanism of Heat Shock-Provoked Disassembly of the Coliphage λ Replication Complex." Journal of Bacteriology 180, no. 9 (May 1, 1998): 2475–83. http://dx.doi.org/10.1128/jb.180.9.2475-2483.1998.

Full text

Abstract:

ABSTRACT We have found previously that, in contrast to the free O initiator protein of λ phage or plasmid rapidly degraded by theEscherichia coli ClpP/ClpX protease, the λO present in the replication complex (RC) is protected from proteolysis. However, in cells growing in a complete medium, a temperature shift from 30 to 43°C resulted in the decay of the λO fraction, which indicated disassembly of RC. This process occurred due to heat shock induction of the groE operon, coding for molecular chaperones of the Hsp60 system. Here we demonstrate that an increase in the cellular concentration of GroEL and GroES proteins is not in itself sufficient to cause RC disassembly. Another requirement is a DNA gyrase-mediated negative resupercoiling of λ plasmid DNA, which counteracts DNA relaxation and starts to dominate 10 min after the temperature upshift. We presume that RC dissociates from λ DNA during the negative resupercoiling, becoming susceptible to the subsequent action of GroEL/S and ClpP/ClpX proteins. In contrast to λcro +, in λcro −plasmid-harboring cells, the RC reveals heat shock resistance. After temperature upshift of the λcrots plasmid-harboring cells, a Cro repressor-independent control of λ DNA replication and heat shock resistance of RC are established before the period of DNA gyrase-mediated negative supercoiling. We suggest that the tight binding of RC to λ DNA is due to interaction of RC with other DNA-bound proteins, and is related to the molecular basis of the λcro − plasmid replication control.

APA, Harvard, Vancouver, ISO, and other styles

26

SMITH, JAMES L., and PINA M. FRATAMICO. "Fluoroquinolone Resistance in Campylobacter." Journal of Food Protection 73, no. 6 (June 1, 2010): 1141–52. http://dx.doi.org/10.4315/0362-028x-73.6.1141.

Full text

Abstract:

Campylobacter is a commensal in poultry, and therefore, poultry and poultry products are major sources of Campylobacter infections in humans. Fluoroquinolones inhibit the growth of Campylobacter and other microorganisms by binding to bacterial DNA gyrase and DNA topoisomerase IV. These enzymes are associated with bacterial transcription, replication, and chromosome condensation and segregation. Selection pressure in the presence of fluoroquinolones rapidly leads to resistance in Campylobacter, due to the selection for mutations in DNA gyrase. Fluoroquinolone-resistant campylobacters have been found in poultry feces and carcasses, and in retail poultry meat products in most areas of the world. In addition, other food animals and the meat products from those animals have been shown contaminated with fluoroquinolone-resistant campylobacters. Even the removal of fluoroquinolones from use in treating animal diseases has not entirely eliminated the presence of resistant Campylobacter jejuni and Campylobacter coli from animals and animal products. Human exposure to Campylobacter infection could be reduced by using strategies that decrease colonization of chickens by the pathogen.

APA, Harvard, Vancouver, ISO, and other styles

27

Hiasa, H., R. J. DiGate, and K. J. Marians. "Decatenating activity of Escherichia coli DNA gyrase and topoisomerases I and III during oriC and pBR322 DNA replication in vitro." Journal of Biological Chemistry 269, no. 3 (January 1994): 2093–99. http://dx.doi.org/10.1016/s0021-9258(17)42140-5.

Full text

APA, Harvard, Vancouver, ISO, and other styles

28

Portolani, Mariella, Paola Pietrosemoli, Claudio Cermelli, Anna Mannini-Palenzona, Maria Pia Grossi, Lorella Paolini, and Giuseppe Barbanti-Brodano. "Suppression of BK virus replication and cytopathic effect by inhibitors of prokaryotic DNA gyrase." Antiviral Research 9, no. 3 (April 1988): 205–18. http://dx.doi.org/10.1016/0166-3542(88)90004-6.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

Bhatnagar, Kamya, Aaron Hinz, Melissa Kohlman, and Alex Wong. "An sRNA Screen for Reversal of Quinolone Resistance in Escherichia coli." G3: Genes|Genomes|Genetics 10, no. 1 (November 19, 2019): 79–88. http://dx.doi.org/10.1534/g3.119.400199.

Full text

Abstract:

In light of the rising prevalence of antimicrobial resistance (AMR) and the slow pace of new antimicrobial development, there has been increasing interest in the development of adjuvants that improve or restore the effectiveness of existing drugs. Here, we use a novel small RNA (sRNA) screening approach to identify genes whose knockdown increases ciprofloxacin (CIP) sensitivity in a resistant strain of Escherichia coli. 5000 sRNA constructs were initially screened on a gyrA S83L background, ultimately leading to 30 validated genes whose disruption reduces CIP resistance. This set includes genes involved in DNA replication, repair, recombination, efflux, and other regulatory systems. Our findings increase understanding of the functional interactions of DNA Gyrase, and may aid in the development of new therapeutic approaches for combating AMR.

APA, Harvard, Vancouver, ISO, and other styles

30

González-Huici, Víctor, Martín Alcorlo, Margarita Salas, and José M. Hermoso. "Phage φ29 Proteins p1 and p17 Are Required for Efficient Binding of Architectural Protein p6 to Viral DNA In Vivo." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8401–6. http://dx.doi.org/10.1128/jb.186.24.8401-8406.2004.

Full text

Abstract:

ABSTRACT Bacteriophage φ29 protein p6 is a viral architectural protein, which binds along the whole linear φ29 DNA in vivo and is involved in initiation of DNA replication and transcription control. Protein p1 is a membrane-associated viral protein, proposed to attach the viral genome to the cell membrane. Protein p17 is involved in pulling φ29 DNA into the cell during the injection process. We have used chromatin immunoprecipitation and real-time PCR to analyze in vivo p6 binding to DNA in cells infected with φ29 sus1 or sus17 mutants; in both cases p6 binding is significantly decreased all along φ29 DNA. φ29 DNA is topologically constrained in vivo, and p6 binding is highly increased in the presence of novobiocin, a gyrase inhibitor that produces a loss of DNA negative superhelicity. Here we show that, in cells infected with φ29 sus1 or sus17 mutants, the increase of p6 binding by novobiocin is even higher than in cells containing p1 and p17, alleviating the p6 binding deficiency. Therefore, proteins p1 and p17 could be required to restrain the proper topology of φ29 DNA, which would explain the impaired DNA replication observed in cells infected with sus1 or sus17 mutants.

APA, Harvard, Vancouver, ISO, and other styles

31

Lahiri, Sushmita D., Amy Kutschke, Kathy McCormack, and Richard A. Alm. "Insights into the Mechanism of Inhibition of Novel Bacterial Topoisomerase Inhibitors from Characterization of Resistant Mutants of Staphylococcus aureus." Antimicrobial Agents and Chemotherapy 59, no. 9 (June 15, 2015): 5278–87. http://dx.doi.org/10.1128/aac.00571-15.

Full text

Abstract:

ABSTRACTThe type II topoisomerases DNA gyrase and topoisomerase IV are clinically validated bacterial targets that catalyze the modulation of DNA topology that is vital to DNA replication, repair, and decatenation. Increasing resistance to fluoroquinolones, which trap the topoisomerase-DNA complex, has led to significant efforts in the discovery of novel inhibitors of these targets. AZ6142 is a member of the class of novel bacterial topoisomerase inhibitors (NBTIs) that utilizes a distinct mechanism to trap the protein-DNA complex. AZ6142 has very potent activity against Gram-positive organisms, includingStaphylococcus aureus,Streptococcus pneumoniae, andStreptococcus pyogenes. In this study, we determined the frequencies of resistance to AZ6142 and other representative NBTI compounds inS. aureusandS. pneumoniae. The frequencies of selection of resistant mutants at 4× the MIC were 1.7 × 10−8forS. aureusand <5.5 × 10−10forS. pneumoniae. To improve our understanding of the NBTI mechanism of inhibition, the resistantS. aureusmutants were characterized and 20 unique substitutions in the topoisomerase subunits were identified. Many of these substitutions were located outside the NBTI binding pocket and impact the susceptibility of AZ6142, resulting in a 4- to 32-fold elevation in the MIC over the wild-type parent strain. Data on cross-resistance with other NBTIs and fluoroquinolones enabled the differentiation of scaffold-specific changes from compound-specific variations. Our results suggest that AZ6142 inhibits both type II topoisomerases inS. aureusbut that DNA gyrase is the primary target. Further, the genotype of the resistant mutants suggests that domain conformations and DNA interactions may uniquely impact NBTIs compared to fluoroquinolones.

APA, Harvard, Vancouver, ISO, and other styles

32

Levine, Cindy, Hiroshi Hiasa, and Kenneth J. Marians. "DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities." Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 1400, no. 1-3 (October 1998): 29–43. http://dx.doi.org/10.1016/s0167-4781(98)00126-2.

Full text

APA, Harvard, Vancouver, ISO, and other styles

33

Uhlin, B. E., and K. Nordström. "Preferential inhibition of plasmid replication in vivo by altered DNA gyrase activity in Escherichia coli." Journal of Bacteriology 162, no. 2 (1985): 855–57. http://dx.doi.org/10.1128/jb.162.2.855-857.1985.

Full text

APA, Harvard, Vancouver, ISO, and other styles

34

Limban, Carmen, Diana Camelia Nuta, Alexandru Vasile Missir, Roxana Roman, Miron Teodor Caproiu, Florea Dumitrascu, Lucia Pintilie, et al. "Synthesis and Characterization of New Fluoro/Trifluoromethyl-Substituted Acylthiourea Derivatives with Promising Activity against Planktonic and Biofilm-Embedded Microbial Cells." Processes 8, no. 5 (April 26, 2020): 503. http://dx.doi.org/10.3390/pr8050503.

Full text

Abstract:

The aim of this study was preparation of new derivatives based on 2-((4-chlorophenoxy)methyl)-N-(arylcarbamothioyl)benzamide structure; the new compounds were characterized by IR, NMR (1H, 13C) spectroscopy, and elemental analysis. The obtained compounds were evaluated for their in vitro antimicrobial activity against planktonic and biofilm-embedded microbial cells (Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, Candida albicans), by qualitative and quantitative assays. Some of the compounds revealed promising antibacterial and antifungal activities, with low minimum inhibitory concentration values between 0.15 and 2.5 mg/mL and minimal biofilm eradication concentrations of 0.019–2.5 mg/mL. To investigate the potential target of their antibacterial activity, in silico drug-likeness and molecular docking screenings on Staphylococcus aureus DNA gyrase were performed. The compound with the best antibacterial activity (1g) was docked into topoisomerase II DNA gyrase enzymes (PDB ID: 2XCS) and showed valuable interactions with the target protein along with good docking scores, suggesting that it can act by the inhibition of DNA replication. The tested compounds exhibited only a poor antioxidant activity, as revealed by the in vitro assay using 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay.

APA, Harvard, Vancouver, ISO, and other styles

35

Johnson, Erik P., Shiyin Yao, and Donald R. Helinski. "Gyrase Inhibitors and Thymine Starvation Disrupt the Normal Pattern of Plasmid RK2 Localization in Escherichia coli." Journal of Bacteriology 187, no. 10 (May 15, 2005): 3538–47. http://dx.doi.org/10.1128/jb.187.10.3538-3547.2005.

Full text

Abstract:

ABSTRACT Multicopy plasmids in Escherichia coli are not randomly distributed throughout the cell but exist as defined clusters that are localized at the mid-cell, or at the 1/4 and 3/4 cell length positions. To explore the factors that contribute to plasmid clustering and localization, E. coli cells carrying a plasmid RK2 derivative that can be tagged with a green fluorescent protein-LacI fusion protein were subjected to various conditions that interfere with plasmid superhelicity and/or DNA replication. The various treatments included thymine starvation and the addition of the gyrase inhibitors nalidixic acid and novobiocin. In each case, localization of plasmid clusters at the preferred positions was disrupted but the plasmids remained in clusters, suggesting that normal plasmid superhelicity and DNA synthesis in elongating cells are not required for the clustering of individual plasmid molecules. It was also observed that the inhibition of DNA replication by these treatments produced filaments in which the plasmid clusters were confined to one or two nucleoid bodies, which were located near the midline of the filament and were not evenly spaced throughout the filament, as is found in cells treated with cephalexin. Finally, the enhanced yellow fluorescent protein-RarA fusion protein was used to localize the replication complex in individual E. coli cells. Novobiocin and nalidixic acid treatment both resulted in rapid loss of RarA foci. Under these conditions the RK2 plasmid clusters were not disassembled, suggesting that a completely intact replication complex is not required for plasmid clustering.

APA, Harvard, Vancouver, ISO, and other styles

36

Pohlhaus, Jennifer Reineke, David T. Long, Erin O'Reilly, and Kenneth N. Kreuzer. "The ε Subunit of DNA Polymerase III Is Involved in the Nalidixic Acid-Induced SOS Response in Escherichia coli." Journal of Bacteriology 190, no. 15 (June 6, 2008): 5239–47. http://dx.doi.org/10.1128/jb.00173-08.

Full text

Abstract:

ABSTRACT Quinolone antibacterial drugs such as nalidixic acid target DNA gyrase in Escherichia coli. These inhibitors bind to and stabilize a normally transient covalent protein-DNA intermediate in the gyrase reaction cycle, referred to as the cleavage complex. Stabilization of the cleavage complex is necessary but not sufficient for cell killing—cytotoxicity apparently results from the conversion of cleavage complexes into overt DNA breaks by an as-yet-unknown mechanism(s). Quinolone treatment induces the bacterial SOS response in a RecBC-dependent manner, arguing that cleavage complexes are somehow converted into double-stranded breaks. However, the only proteins known to be required for SOS induction by nalidixic acid are RecA and RecBC. In hopes of identifying additional proteins involved in the cytotoxic response to nalidixic acid, we screened for E. coli mutants specifically deficient in SOS induction upon nalidixic acid treatment by using a dinD::lacZ reporter construct. From a collection of SOS partially constitutive mutants with disruptions of 47 different genes, we found that dnaQ insertion mutants are specifically deficient in the SOS response to nalidixic acid. dnaQ encodes DNA polymerase III ε subunit, the proofreading subunit of the replicative polymerase. The deficient response to nalidixic acid was rescued by the presence of the wild-type dnaQ gene, confirming involvement of the ε subunit. To further characterize the SOS deficiency of dnaQ mutants, we analyzed the expression of several additional SOS genes in response to nalidixic acid using real-time PCR. A subset of SOS genes lost their response to nalidixic acid in the dnaQ mutant strain, while two tested SOS genes (recA and recN) continued to exhibit induction. These results argue that the replication complex plays a role in modulating the SOS response to nalidixic acid and that the response is more complex than a simple on/off switch.

APA, Harvard, Vancouver, ISO, and other styles

37

Alcorlo, Martín, Margarita Salas, and José M. Hermoso. "In Vivo DNA Binding of Bacteriophage GA-1 Protein p6." Journal of Bacteriology 189, no. 22 (September 14, 2007): 8024–33. http://dx.doi.org/10.1128/jb.01047-07.

Full text

Abstract:

ABSTRACT Bacteriophage GA-1 infects Bacillus sp. strain G1R and has a linear double-stranded DNA genome with a terminal protein covalently linked to its 5′ ends. GA-1 protein p6 is very abundant in infected cells and binds DNA with no sequence specificity. We show here that it binds in vivo to the whole viral genome, as detected by cross-linking, chromatin immunoprecipitation, and real-time PCR analyses, and has the characteristics of a histone-like protein. Binding to DNA of GA-1 protein p6 shows little supercoiling dependency, in contrast to the ortholog protein of the evolutionary related Bacillus subtilis phage φ29. This feature is a property of the protein rather than the DNA or the cellular background, since φ29 protein p6 shows supercoiling-dependent binding to GA-1 DNA in Bacillus sp. strain G1R. GA-1 DNA replication is impaired in the presence of the gyrase inhibitors novobiocin and nalidixic acid, which indicates that, although noncovalently closed, the viral genome is topologically constrained in vivo. GA-1 protein p6 is also able to bind φ29 DNA in B. subtilis cells; however, as expected, the binding is less supercoiling dependent than the one observed with the φ29 protein p6. In addition, the nucleoprotein complex formed is not functional, since it is not able to transcomplement the DNA replication deficiency of a φ29 sus6 mutant. Furthermore, we took advantage of φ29 protein p6 binding to GA-1 DNA to find that the viral DNA ejection mechanism seems to take place, as in the case of φ29, with a right to left polarity in a two-step, push-pull process.

APA, Harvard, Vancouver, ISO, and other styles

38

Defant, Andrea, Alessandro Vozza, and Ines Mancini. "Design, Synthesis and Antimicrobial Evaluation of New Norfloxacin-Naphthoquinone Hybrid Molecules." Proceedings 41, no. 1 (November 14, 2019): 9. http://dx.doi.org/10.3390/ecsoc-23-06480.

Full text

Abstract:

Although the wide arsenal of drugs available to treat bacterial infections, emerging drug-resistant bacterial pathogens have recently highlighted an urgent need to find new more effective and less toxic therapeutic agents. Fluoroquinolones, including norfloxacin, are antibiotics showing a concentration-dependent bactericidal capacity due to the activity inhibition of DNA-gyrase and topoisomerase IV, which are enzymes essential for bacterial DNA replication. Naphthoquinones are secondary metabolites showing different biological activities, including cytotoxic, antibacterial and antifungal effects. In particular, the efficacy of natural and synthetic 1,4-naphthoquinone derivatives is likely due to their oxidizing/reducing capability, through which they destroy cellular targets as nucleic acids. Hybrid molecules are produced combining structural features of two or more bioactive compounds, in order to obtain new therapeutic agents able, not only to reduce undesirable side effects of the parent drugs, but also to inhibit more biological targets, hopefully with a better therapeutic property than the administration of combined single-target drugs. With the aim to apply this strategy in the study of new potential antimicrobial agents, we have synthesized four hybrid molecules by the reaction of norfloxacin with suitable quinones and their activities have been evaluated against both bacteria and fungi, in comparison with synthetic precursors. The experimental data are supported by docking calculations on S. aureus DNA-gyrase, discussing the interactions involved for each hybrid molecule, in comparison with norfloxacin and the original ligand moxifloxacin.

APA, Harvard, Vancouver, ISO, and other styles

39

Butler, Michelle M., William A. LaMarr, Kimberly A. Foster, Marjorie H. Barnes, Donna J. Skow, Patrick T. Lyden, Lauren M. Kustigian, et al. "Antibacterial Activity and Mechanism of Action of a Novel Anilinouracil-Fluoroquinolone Hybrid Compound." Antimicrobial Agents and Chemotherapy 51, no. 1 (January 2007): 119–27. http://dx.doi.org/10.1128/aac.01311-05.

Full text

Abstract:

ABSTRACT The anilinouracils (AUs) such as 6-(3-ethyl-4-methylanilino)uracil (EMAU) are a novel class of gram-positive, selective, bactericidal antibacterials which inhibit pol IIIC, the gram-positive-specific replicative DNA polymerase. We have linked various fluoroquinolones (FQs) to the N-3 position of EMAU to generate a variety of AU-FQ “hybrids” offering the potential for targeting two distinct steps in DNA replication. In this study, the properties of a hybrid, “251D,” were compared with those of representative AUs and FQs in a variety of in vitro assays, including pol IIIC and topoisomerase/gyrase enzyme assays, antibacterial, bactericidal, and mammalian cytotoxicity assays. Compound 251D potently inhibited pol IIIC and topoisomerase/gyrase, displayed gram-positive antibacterial potency at least 15 times that of the corresponding AU compound, and as expected, acted selectively on bacterial DNA synthesis. Compound 251D was active against a broad panel of antibiotic-resistant gram-positive pathogens as well as several gram-negative organisms and was also active against both AU- and FQ-resistant gram-positive organisms, demonstrating its capacity for attacking both of its potential targets in the bacterium. 251D also was bactericidal for gram-positive organisms and lacked toxicity in vitro. Although we obtained strains of Staphylococcus aureus resistant to the individual parent compounds, spontaneous resistance to 251D was not observed. We obtained 251D resistance in multiple-passage experiments, but resistance developed at a pace comparable to those for the parent compounds. This class of AU-FQ hybrids provides a promising new pharmacophore with an unusual dual mechanism of action and potent activity against antibiotic-sensitive and -resistant gram-positive pathogens.

APA, Harvard, Vancouver, ISO, and other styles

40

Raghu Ram, E. V. S., Ambrish Kumar, Subir Biswas, Ashutosh Kumar, Sushma Chaubey, Mohammad Imran Siddiqi, and Saman Habib. "Nuclear gyrB encodes a functional subunit of the Plasmodium falciparum gyrase that is involved in apicoplast DNA replication." Molecular and Biochemical Parasitology 154, no. 1 (July 2007): 30–39. http://dx.doi.org/10.1016/j.molbiopara.2007.04.001.

Full text

APA, Harvard, Vancouver, ISO, and other styles

41

Sutherland, Jeanette H., and Yuk-Ching Tse-Dinh. "Analysis of RuvABC and RecG Involvement in the Escherichia coli Response to the Covalent Topoisomerase-DNA Complex." Journal of Bacteriology 192, no. 17 (July 2, 2010): 4445–51. http://dx.doi.org/10.1128/jb.00350-10.

Full text

Abstract:

ABSTRACT Topoisomerases form a covalent enzyme-DNA intermediate after initial DNA cleavage. Trapping of the cleavage complex formed by type IIA topoisomerases initiates the bactericidal action of fluoroquinolones. It should be possible also to identify novel antibacterial lead compounds that act with a similar mechanism on type IA bacterial topoisomerases. The cellular response and repair pathways for trapped topoisomerase complexes remain to be fully elucidated. The RuvAB and RecG proteins could play a role in the conversion of the initial protein-DNA complex to double-strand breaks and also in the resolution of the Holliday junction during homologous recombination. Escherichia coli strains with ruvA and recG mutations are found to have increased sensitivity to low levels of norfloxacin treatment, but the mutations had more pronounced effects on survival following the accumulation of covalent complexes formed by mutant topoisomerase I defective in DNA religation. Covalent topoisomerase I and DNA gyrase complexes are converted into double-strand breaks for SOS induction by the RecBCD pathway. SOS induction following topoisomerase I complex accumulation is significantly lower in the ruvA and recG mutants than in the wild-type background, suggesting that RuvAB and RecG may play a role in converting the initial single-strand DNA-protein cleavage complex into a double-strand break prior to repair by homologous recombination. The use of a ruvB mutant proficient in homologous recombination but not in replication fork reversal demonstrated that the replication fork reversal function of RuvAB is required for SOS induction by the covalent complex formed by topoisomerase I.

APA, Harvard, Vancouver, ISO, and other styles

42

Drlica, K., C. Xu, J. Y. Wang, R. M. Burger, and M. Malik. "Fluoroquinolone action in mycobacteria: similarity with effects in Escherichia coli and detection by cell lysate viscosity." Antimicrobial Agents and Chemotherapy 40, no. 7 (July 1996): 1594–99. http://dx.doi.org/10.1128/aac.40.7.1594.

Full text

Abstract:

Fluoroquinolones are potent antibacterial agents that are being used as therapeutic agents for the treatment of multidrug-resistant tuberculosis. To better understand fluoroquinolone action in mycobacteria, the effects of ciprofloxacin were examined. DNA synthesis was inhibited rapidly in Mycobacterium smegmatis, DNA cleavage was readily observed by an empirical assay of cell lysate viscosity, and cell growth was blocked. These data are explained by the formation of gyrase-DNA-ciprofloxacin complexes that block replication fork movement. The bactericidal action of ciprofloxacin against M. smegmatis, Mycobacterium bovis BCG, and Escherichia coli occurred more slowly in cells with longer doubling times. The bactericidal effect against M. bovis BCG was partially blocked by pretreatment with chloramphenicol, an inhibitor of protein synthesis, and by very high concentrations of ciprofloxacin itself. Similar responses occur when E. coli is treated with ciprofloxacin. These similarities between E. coli and mycobacteria indicate that results from extensive fluoroquinolone studies with E. coli can be applied to mycobacteria. A simple viscometric assay of DNA cleavage is described. The assay is expected to be useful for screening new fluoroquinolone derivatives for increased effectiveness against clinically important bacteria.

APA, Harvard, Vancouver, ISO, and other styles

43

Duguet, M. "When helicase and topoisomerase meet!" Journal of Cell Science 110, no. 12 (June 15, 1997): 1345–50. http://dx.doi.org/10.1242/jcs.110.12.1345.

Full text

Abstract:

Several examples of direct interactions between helicases and topoisomerases have recently been described. The data suggest a possible cooperation between these enzymes in major DNA events such as the progression of a replication fork, segregation of newly replicated chromosomes, disruption of nucleosomal structure, DNA supercoiling, and finally recombination, repair, and genomic stability. A first example is the finding of a strong interaction between T antigen and topoisomerase I in mammalian cells, that may trigger unwinding of the parental DNA strands at the replication forks of Simian Virus 40. A second example is the reverse gyrase from thermophilic prokaryotes, composed of a putative helicase domain, and a topoisomerase domain in the same polypeptide. This enzyme may be required to maintain genomic stability at high temperature. A third example is the finding of an interaction between type II topoisomerase and the helicase Sgs1 in yeast. This interaction possibly allows the faithful segregation of newly replicated chromosomes in eukaryotic cells. A fourth example is the interaction between the same helicase Sgs1 and topoisomerase III in yeast, that may control recombination level and genetic stability of repetitive sequences. Recently, in humans, mutations in genes similar to Sgs1 have been found to be responsible for Bloom's and Werner's syndromes. The cooperation between helicases and topoisomerases is likely to be extended to many aspects of DNA mechanisms including chromatin condensation/decondensation.

APA, Harvard, Vancouver, ISO, and other styles

44

Pinkney, Michael, Ramon Diaz, Erich Lanka, and Christopher M. Thomas. "Replication of mini RK2 plasmid in extracts of Escherichia coli requires plasmid-encoded protein TrfA and host-encoded proteins DnaA, B, G DNA gyrase and DNA polymerase III." Journal of Molecular Biology 203, no. 4 (October 1988): 927–38. http://dx.doi.org/10.1016/0022-2836(88)90118-0.

Full text

APA, Harvard, Vancouver, ISO, and other styles

45

Szafran, Marcin Jan, Martyna Gongerowska, Paweł Gutkowski, Jolanta Zakrzewska-Czerwińska, and Dagmara Jakimowicz. "The Coordinated Positive Regulation of Topoisomerase Genes Maintains Topological Homeostasis in Streptomyces coelicolor." Journal of Bacteriology 198, no. 21 (August 22, 2016): 3016–28. http://dx.doi.org/10.1128/jb.00530-16.

Full text

Abstract:

ABSTRACTMaintaining an optimal level of chromosomal supercoiling is critical for the progression of DNA replication and transcription. Moreover, changes in global supercoiling affect the expression of a large number of genes and play a fundamental role in adapting to stress. Topoisomerase I (TopA) and gyrase are key players in the regulation of bacterial chromosomal topology through their respective abilities to relax and compact DNA. Soil bacteria such asStreptomycesspecies, which grow as branched, multigenomic hyphae, are subject to environmental stresses that are associated with changes in chromosomal topology. The topological fluctuations modulate the transcriptional activity of a large number of genes and inStreptomycesare related to the production of antibiotics. To better understand the regulation of topological homeostasis inStreptomyces coelicolor, we investigated the interplay between the activities of the topoisomerase-encoding genestopAandgyrBA. We show that the expression of both genes is supercoiling sensitive. Remarkably, increased chromosomal supercoiling induces thetopApromoter but only slightly influencesgyrBAtranscription, while DNA relaxation affects thetopApromoter only marginally but strongly activates thegyrBAoperon. Moreover, we showed that exposure to elevated temperatures induces rapid relaxation, which results in changes in the levels of both topoisomerases. We therefore propose a unique mechanism ofS. coelicolorchromosomal topology maintenance based on the supercoiling-dependent stimulation, rather than repression, of the transcription of both topoisomerase genes. These findings provide important insight into the maintenance of topological homeostasis in an industrially important antibiotic producer.IMPORTANCEWe describe the unique regulation of genes encoding two topoisomerases, topoisomerase I (TopA) and gyrase, in a modelStreptomycesspecies. Our studies demonstrate the coordination of topoisomerase gene regulation, which is crucial for maintenance of topological homeostasis.Streptomycesspecies are producers of a plethora of biologically active secondary metabolites, including antibiotics, antitumor agents, and immunosuppressants. The significant regulatory factor controlling the secondary metabolism is the global chromosomal topology. Thus, the investigation of chromosomal topology homeostasis inStreptomycesstrains is crucial for their use in industrial applications as producers of secondary metabolites.

APA, Harvard, Vancouver, ISO, and other styles

46

Tachedjian, G., D. Tyssen, D. Jardine, S. Locarnini, and C. Birch. "Synergistic Inhibition of Human Immunodeficiency Virus Type 1 in vitro by Interferon Alpha and Coumermycin A1." Antiviral Chemistry and Chemotherapy 3, no. 3 (June 1992): 183–88. http://dx.doi.org/10.1177/095632029200300309.

Full text

Abstract:

Interferon alpha, either leukocyte derived or the recombinant form, and the DNA gyrase inhibitor coumermycin A1 both inhibited human immunodeficiency virus type 1 (HIV) replication in vitro. We have found that combinations of these two agents synergistically inhibited HIV replication in human peripheral blood leucocytes (PBL). Significant inhibition was detected when both virion-associated reverse transcriptase activity and p24 levels were used as markers of replication. Mathematical analysis of data using the procedure of Chou and Chou (1987) produced combination indices of less than 1.0 for most effect levels at several combination ratios. Synergy was also evident when the classical isobologram technique was used for data analysis. Synergistic drug interactions were observed at concentrations not associated with cytotoxicity or anti-proliferative effects, and were seen at concentrations achievable in vivo.

APA, Harvard, Vancouver, ISO, and other styles

47

Scherler, Aurélie, Nicolas Jacquier, Carole Kebbi-Beghdadi, and Gilbert Greub. "Diverse Stress-Inducing Treatments cause Distinct Aberrant Body Morphologies in the Chlamydia-Related Bacterium, Waddlia chondrophila." Microorganisms 8, no. 1 (January 9, 2020): 89. http://dx.doi.org/10.3390/microorganisms8010089.

Full text

Abstract:

Chlamydiae, such as Chlamydia trachomatis and Chlamydia pneumoniae, can cause chronic infections. It is believed that persistent forms called aberrant bodies (ABs) might be involved in this process. AB formation seems to be a common trait of all members of the Chlamydiales order and is caused by distinct stress stimuli, such as β-lactam antibiotics or nutrient starvation. While the diverse stimuli inducing ABs are well described, no comprehensive morphological characterization has been performed in Chlamydiales up to now. We thus infected mammalian cells with the Chlamydia-related bacterium Waddlia chondrophila and induced AB formation using different stimuli. Their morphology, differences in DNA content and in gene expression were assessed by immunofluorescence, quantitative PCR, and reverse transcription PCR, respectively. All stimuli induced AB formation. Interestingly, we show here for the first time that the DNA gyrase inhibitor novobiocin also caused appearance of ABs. Two distinct patterns of ABs could be defined, according to their morphology and number: (i) small and multiple ABs versus (ii) large and rare ABs. DNA replication of W. chondrophila was generally not affected by the different treatments. Finally, no correlation could be observed between specific types of ABs and expression patterns of mreB and rodZ genes.

APA, Harvard, Vancouver, ISO, and other styles

48

Koch, Birgit, Xiaofang Ma, and Anders Løbner-Olesen. "Replication of Vibrio cholerae Chromosome I in Escherichia coli: Dependence on Dam Methylation." Journal of Bacteriology 192, no. 15 (May 28, 2010): 3903–14. http://dx.doi.org/10.1128/jb.00311-10.

Full text

Abstract:

ABSTRACT We successfully substituted Escherichia coli's origin of replication oriC with the origin region of Vibrio cholerae chromosome I (oriCIVc ). Replication from oriCIVc initiated at a similar or slightly reduced cell mass compared to that of normal E. coli oriC. With respect to sequestration-dependent synchrony of initiation and stimulation of initiation by the loss of Hda activity, replication initiation from oriC and oriCIVc were similar. Since Hda is involved in the conversion of DnaAATP (DnaA bound to ATP) to DnaAADP (DnaA bound to ADP), this indicates that DnaA associated with ATP is limiting for V. cholerae chromosome I replication, which similar to what is observed for E. coli. No hda homologue has been identified in V. cholerae yet. In V. cholerae, dam is essential for viability, whereas in E. coli, dam mutants are viable. Replacement of E. coli oriC with oriCIVc allowed us to specifically address the role of the Dam methyltransferase and SeqA in replication initiation from oriCIVc . We show that when E. coli's origin of replication is substituted by oriCIVc , dam, but not seqA, becomes important for growth, arguing that Dam methylation exerts a critical function at the origin of replication itself. We propose that Dam methylation promotes DnaA-assisted successful duplex opening and replisome assembly at oriCIVc in E. coli. In this model, methylation at oriCIVc would ease DNA melting. This is supported by the fact that the requirement for dam can be alleviated by increasing negative supercoiling of the chromosome through oversupply of the DNA gyrase or loss of SeqA activity.

APA, Harvard, Vancouver, ISO, and other styles

49

Singh, Sheo B., Priya Dayananth, Carl J. Balibar, Charles G. Garlisi, Jun Lu, Ryuta Kishii, Masaya Takei, Yasumichi Fukuda, Sookhee Ha, and Katherine Young. "Kibdelomycin Is a Bactericidal Broad-Spectrum Aerobic Antibacterial Agent." Antimicrobial Agents and Chemotherapy 59, no. 6 (April 6, 2015): 3474–81. http://dx.doi.org/10.1128/aac.00382-15.

Full text

Abstract:

ABSTRACTBacterial resistance to antibiotics continues to grow and pose serious challenges, while the discovery rate for new antibiotics declines. Kibdelomycin is a recently discovered natural-product antibiotic that inhibits bacterial growth by inhibiting the bacterial DNA replication enzymes DNA gyrase and topoisomerase IV. It was reported to be a broad-spectrum aerobic Gram-positive agent with selective inhibition of the anaerobic bacteriumClostridium difficile. We have extended the profiling of kibdelomycin by using over 196 strains of Gram-positive and Gram-negative aerobic pathogens recovered from worldwide patient populations. We report the MIC50s, MIC90s, and bactericidal activities of kibdelomycin. We confirm the Gram-positive spectrum and report for the first time that kibdelomycin shows strong activity (MIC90, 0.125 μg/ml) against clinical strains of the Gram-negative nonfermenterAcinetobacter baumanniibut only weak activity againstPseudomonas aeruginosa. We confirm that well-characterized resistant strains ofStaphylococcus aureusandStreptococcus pneumoniaeshow no cross-resistance to kibdelomycin and quinolones and coumarin antibiotics. We also show that kibdelomycin is not subject to efflux inPseudomonas, though it is inEscherichia coli, and it is generally affected by the outer membrane permeability entry barrier in the nonfermentersP. aeruginosaandA. baumannii, which may be addressable by structure-based chemical modification.

APA, Harvard, Vancouver, ISO, and other styles

50

Martins-Duarte, Érica S., Lilach Sheiner, Sarah B. Reiff, Wanderley de Souza, and Boris Striepen. "Replication and partitioning of the apicoplast genome of Toxoplasma gondii is linked to the cell cycle and requires DNA polymerase and gyrase." International Journal for Parasitology 51, no. 6 (May 2021): 493–504. http://dx.doi.org/10.1016/j.ijpara.2020.11.004.

Full text

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'DNA Gyrase DNA Gyrase DNA Replication DNA'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles