DNA gyrase activity regulates DnaA‐dependent replication initiation in <i>Bacillus subtilis</i>

Samadpour, Ariana Nakta; Merrikh, Houra

doi:10.1111/mmi.13920

Cited by 16 publications

(17 citation statements)

References 68 publications

(84 reference statements)

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“…Gene dosage shift occurs at subinhibitory concentration of ACX-362E PolC inhibitor. A possible explanation for the relative upregulation of oriC-proximal genes and downregulation of terC-proximal genes is a gene dosage shift (35)(36)(37), due to the fact that PolC inhibition slows replication elongation but does not prevent reinitiation of DNA replication (23,38). To determine if this in fact occurs in C. difficile when replication elongation is inhibited, we performed a marker frequency analysis (MFA) to determine the relative abundance of an origin-proximal gene relative to a terminusproximal gene on chromosomal DNA isolated from treated and nontreated cells.…”

Section: Resultsmentioning

confidence: 99%

Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile

Eijk

Boekhoud

Kuijper

et al. 2019

Antimicrob Agents Chemother

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Clostridium difficile is a potentially lethal gut pathogen that causes nosocomial and community-acquired infections. Limited treatment options and reports of reduced susceptibility to current treatment emphasize the necessity for novel antimicrobials. The DNA polymerase of Gram-positive organisms is an attractive target for the development of antimicrobials. ACX-362E [N2-(3,4-dichlorobenzyl)-7-(2-[1-morpholinyl]ethyl)guanine; MorE-DCBG] is a DNA polymerase inhibitor in preclinical development as a novel therapeutic against C. difficile infection. This synthetic purine shows preferential activity against C. difficile PolC over those of other organisms in vitro and is effective in an animal model of C. difficile infection. In this study, we have determined its efficacy against a large collection of clinical isolates. At concentrations below the MIC, the presumed slowing (or stalling) of replication forks due to ACX-362E leads to a growth defect. We have determined the transcriptional response of C. difficile to replication inhibition and observed an overrepresentation of upregulated genes near the origin of replication in the presence of PolC inhibitors, but not when cells were subjected to subinhibitory concentrations of other antibiotics. This phenomenon can be explained by a gene dosage shift, as we observed a concomitant increase in the ratio between origin-proximal and terminus-proximal gene copy number upon exposure to PolC inhibitors. Moreover, we show that certain genes differentially regulated under PolC inhibition are controlled by the origin-proximal general stress response regulator sigma factor B. Together, these data suggest that genome location both directly and indirectly determines the transcriptional response to replication inhibition in C. difficile.

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Section: Resultsmentioning

confidence: 99%

Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile

Eijk

Boekhoud

Kuijper

et al. 2019

Antimicrob Agents Chemother

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“…The unwinding at an oriC origin of replication and the accessibility of the dnaA binding sequences are particularly sensitive to gyrase activity (as reported for novobiocin, Samadpour & Merrikh, ), such that gyrase inhibition yields multiple abortive cycles of replication initiation. In the previous study, when novobiocin‐inhibited E. coli cells were analyzed using genomic DNA sequencing, the copy number of oriC was in excess to the termini regions.…”

Section: Resultsmentioning

confidence: 89%

“…Studies have established that, among the consequences of changes in gyrase activity, there is an impact on the initiation of replication (Guo, Haakonsen, Zeng, Schumacher, & Laub, ; Samadpour & Merrikh, ). This has also been demonstrated for E. coli treated with CIP within an infection model (Haugan, Lobner‐Olesen, & Frimodt‐Moller, ).…”

Section: Discussionmentioning

confidence: 99%

“…The sorted bam file also provided the nucleotide coverage that was parsed using bedtools (Quinlan & Hall, ). The resulting file was used to plot base coverage against its position, after filtering to remove sequences arising from the resident plasmid, and these values were normalized by dividing by the total number of reads in the sample (as in Samadpour & Merrikh, ).…”

Section: Methodsmentioning

confidence: 99%

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Expression of different ParE toxins results in conserved phenotypes with distinguishable classes of toxicity

et al. 2019

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Toxin-antitoxin (TA) systems are found on both chromosomes and plasmids. These systems are unique in that they can confer both fatal and protective effects on bacterial cells-a quality that could potentially be harnessed given further understanding of these TA mechanisms. The current work focuses on the ParE subfamily, which is found throughout proteobacteria and has a sequence identity on average of approximately 12% (similarity at 30%-80%). Our aim is to evaluate the equivalency of chromosomally derived ParE toxin activity depending on its bacterial species of origin. Nine ParE toxins were analyzed, originating from six different bacterial species. Based on the resulting toxicity, three categories can be established: ParE toxins that do not exert toxicity under the experimental conditions, toxins that exert toxicity within the first four hours, and those that exert toxicity only after 10-12 hr of exposure. All tested ParE toxins produce a cellular morphologic change from rods to filaments, consistent with disruption of DNA topology. Analysis of the distribution of filamented cells within a population reveals a correlation between the extent of filamentation and toxicity. No membrane septation is visible along the length of the cell filaments, whereas aberrant lipid blebs are evident. Potent ParE-mediated toxicity is also correlated with a hallmark signature of abortive DNA replication, consistent with the inhibition of DNA gyrase. K E Y W O R D SDNA gyrase, DNA topology, filamented morphology, ParE toxin, toxin-antitoxin systems

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“…QnrB‐mediated replication stress could be related to the inhibition of DNA gyrase activity and the subsequent effect on DnaA‐dependent replication initiation (Fuller and Kornberg, ; Schnos et al , ; Samadpour and Merrikh, ). However, as described above, TRIM, which exerts its effects independently of gyrase, induced QnrB‐mediated DNA replication stress, resulting in an increased mutation rate (Figs and , and Table ).…”

Section: Resultsmentioning

confidence: 99%

The plasmid‐borne quinolone resistance protein QnrB, a novel DnaA‐binding protein, increases the bacterial mutation rate by triggering DNA replication stress

Zhang

Zhou

et al. 2019

Molecular Microbiology

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Summary Bacterial antibiotic resistance, a global health threat, is caused by plasmid transfer or genetic mutations. Quinolones are important antibiotics, partially because they are fully synthetic and resistance genes are unlikely to exist in nature; nonetheless, quinolone resistance proteins have been identified. The mechanism by which plasmid‐borne quinolone resistance proteins promotes the selection of quinolone‐resistant mutants is unclear. Here, we show that QnrB increases the bacterial mutation rate. Transcriptomic and genome sequencing analyses showed that QnrB promoted gene abundance near the origin of replication (oriC). In addition, the QnrB expression level correlated with the replication origin to terminus (oriC/ter) ratio, indicating QnrB‐induced DNA replication stress. Our results also show that QnrB is a DnaA‐binding protein that may act as an activator of DNA replication initiation. Interaction of QnrB with DnaA promoted the formation of the DnaA‐oriC open complex, which leads to DNA replication over‐initiation. Our data indicate that plasmid‐borne QnrB increases bacterial mutation rates and that genetic changes can alleviate the fitness cost imposed by transmitted plasmids. Derivative mutations may impair antibiotic efficacy and threaten the value of antibiotic treatments. Enhanced understanding of how bacteria adapt to the antibiotic environment will lead to new therapeutic strategies for antibiotic‐resistant infections.

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DNA gyrase activity regulates DnaA‐dependent replication initiation in Bacillus subtilis

Cited by 16 publications

References 68 publications

Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile

Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile

Expression of different ParE toxins results in conserved phenotypes with distinguishable classes of toxicity

The plasmid‐borne quinolone resistance protein QnrB, a novel DnaA‐binding protein, increases the bacterial mutation rate by triggering DNA replication stress

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