The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery

Kaguni, Jon M.

doi:10.3390/antibiotics7010023

Cited by 24 publications

(29 citation statements)

References 286 publications

(378 reference statements)

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“…Antibiotic-resistance presents a growing threat to public health (Rice, 2008(Rice, , 2010Devasahayam et al, 2010;Moellering, 2011) and drives the need for discovery of new antibacterials that act via novel mechanisms (Robinson et al, 2012;Kaguni, 2018). A prominent group of bacteria harboring multidrug resistance and causing nosocomial infections worldwide are known as the "ESKAPE" pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.).…”

Section: Introductionmentioning

confidence: 99%

“…A rich source of potential new targets is the bacterial DNA replication machinery, which carefully orchestrates a complex series of protein-protein and protein-DNA interactions to faithfully replicate DNA prior to cell division (Robinson et al, 2012;Kaguni, 2018). Central in this process is the DNA polymerase III  subunit, also known as the  sliding clamp (), a ringshaped homodimeric protein (Kong et al, 1992) that encircles double-stranded DNA (dsDNA) (Georgescu et al, 2008a), where it serves as an interaction hub that recruits protein-binding partners to DNA.…”

Section: Introductionmentioning

confidence: 99%

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Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens

McGrath

Martyn

Whittell

et al. 2018

Journal of Structural Biology

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Bacterial sliding clamps bind to DNA and act as protein-protein interaction hubs for several proteins involved in DNA replication and repair. The partner proteins all bind to a common pocket on sliding clamps via conserved linear peptide sequence motifs, which suggest the pocket as an attractive target for development of new antibiotics. Herein we report the X-ray crystal structures and biochemical characterization of β sliding clamps from the Gram-negative pathogens Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacter cloacae. The structures reveal close similarity between the pathogen and Escherichia coli clamps and similar patterns of binding to linear clamp-binding motif peptides. The results suggest that linear motifsliding clamp interactions are well conserved and an antibiotic targeting the sliding clamp should have broadspectrum activity against Gram-negative pathogens. Crystal structures and biochemical characterization of DNA sliding clamps from three Gramnegative bacterial pathogens, Journal of Structural Biology (2018), doi: https://doi.ABSTRACT Bacterial sliding clamps bind to DNA and act as protein-protein interaction hubs for several proteins involved in DNA replication and repair. The partner proteins all bind to a common pocket on sliding clamps via conserved linear peptide sequence motifs, which suggest the pocket as an attractive target for development of new antibiotics. Herein we report the X-ray crystal structures and biochemical characterization of  sliding clamps from the Gram-negative pathogens Pseudomonas aeruginosa, Acinetobacter baumannii and Enterobacter cloacae. The structures reveal close similarity between the pathogen and Escherichia coli clamps and similar patterns of binding to linear clamp-binding motif peptides. The results suggest that linear motif-sliding clamp interactions are well conserved and an antibiotic targeting the sliding clamp should have broadspectrum activity against Gram-negative pathogens.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens

McGrath

Martyn

Whittell

et al. 2018

Journal of Structural Biology

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“…Formaldehyde produces a wide variety of lesions, so we are unsure whether it is the production of DPCs that promotes mutagenesis. Ciprofloxacin specifically inhibits type II topoisomerases [44] for which E. coli has two, DNA gyrase and Topoisomerase IV, and traps the covalent cleaved complex [45]. Because ciprofloxicin inhibits DNA replication, we do not know whether its mutagenic effect is due to general replication inhibition rather the production of DPCs.…”

Section: Discussionmentioning

confidence: 99%

Stimulation of Replication Template-Switching by DNA-Protein Crosslinks

Laranjo¹,

Klaric²,

Lovett³

2018

Preprint

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Covalent DNA protein crosslinks (DPCs) are common lesions that block replication. We examine here the consequence of DPCs on mutagenesis involving replicational template-switch reactions in Escherichia coli. 5-azacytidine (5azaC) is a potent mutagen for template-switching, dependent on DNA cytosine methylase (Dcm), implicating the trapped Dcm-DNA covalent complex as the initiator for mutagenesis. The leading strand of replication is more mutable than the lagging strand, explained by blocks to the replicative helicase and/or fork regression. We find that template-switch mutagenesis induced by 5-azaC does not require DSB repair via RecABCD. The ability to induce the SOS response is anti-mutagenic by an unknown mechanism. Mutants in recB, but not recA, exhibit high constitutive rates of template-switching and we suggest that RecBCD-mediated DNA degradation prevents template-switching associated with fork regression. A mutation in the DnaB fork helicase also promotes high levels of template-switching. We also find that other DPC-inducers, formaldehyde (a non-specific crosslinker) and ciprofloxacin (a topoisomerase II poison) are also strong mutagens for template-switching. Induction of mutations and genetic rearrangements that occur by template-switching may constitute a previously unrecognized component of the genotoxicity and genetic instability promoted by DPCs.

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“…The QS gene lasR regulates the expression of virulence factors in P. aeruginosa and therefore represents a particularly interesting therapeutic target [79]. Mutations of gyrA are common in fluroquinolone-resistant clinical strains [80] and inhibitors of gyrA expression are being explored as a pharmacological target [81,82]. In summary, 3pMap predicts regulation via transcriptional attenuation at hundreds of genes in P. aeruginosa, revealing potential new targets for molecular therapeutic intervention.…”

Section: Predicting Potential Regulatory Elements That Cause Transcrimentioning

confidence: 99%

Quantitative mapping of mRNA 3’ ends inPseudomonas aeruginosareveals a pervasive role for premature 3’ end formation in response to azithromycin

Konikkat

Scribner

Eutsey

et al. 2020

Preprint

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P. aeruginosa produces serious chronic infections in hospitalized patients and immunocompromised individuals, including cystic fibrosis patients. The molecular mechanisms by which P. aeruginosa responds to antibiotics and other stresses to promote persistent infections may provide new avenues for therapeutic intervention. Azithromycin (AZM), an antibiotic frequently used in cystic fibrosis treatment, is thought to improve clinical outcomes through a number of mechanisms including impaired biofilm growth and QS. The mechanisms underlying the transcriptional response to AZM remain unclear. Here, we interrogated the P. aeruginosa transcriptional response to AZM using an improved genomewide approach to quantitate RNA 3'-ends (3pMap). We also identified hundreds of P.aeruginosa genes subject to premature transcription termination in their transcript leaders using 3pMap. AZM treatment of planktonic and biofilm cultures alters the expression of hundreds of genes, including those involved in QS, biofilm formation, and virulence.Strikingly, most genes downregulated by AZM in biofilms had increased levels of intragenic 3'-ends indicating premature transcription termination or pausing. Reciprocally, AZM reduced premature transcription termination in many upregulated genes. Most notably, reduced termination accompanied robust induction of obgE, a GTPase involved in persister formation in P. aeruginosa. Our results support a model in which AZM-induced premature transcription termination downregulates expression of central transcriptional regulators, which in turn both impairs QS and biofilm formation, and stress responses, while upregulating genes associated with persistence.

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The Macromolecular Machines that Duplicate the Escherichia coli Chromosome as Targets for Drug Discovery

Cited by 24 publications

References 286 publications

Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens

Crystal structures and biochemical characterization of DNA sliding clamps from three Gram-negative bacterial pathogens

Stimulation of Replication Template-Switching by DNA-Protein Crosslinks

Quantitative mapping of mRNA 3’ ends inPseudomonas aeruginosareveals a pervasive role for premature 3’ end formation in response to azithromycin

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