“…These results showed that Mtb DNA gyrase is slower at supercoiling plasmid DNA and requires higher concentrations of ATP comparing with E. coli DNA gyrase under similar experimental conditions ( 51 ). These results are also consistent with previously published results ( 21 , 22 , 23 ). Figure 4 Steady-state kinetics of Mtb DNA gyrase in the absence or presence of glycine betaine or PEG400.…”
Section: Resultssupporting
confidence: 94%
“…Previous studies have demonstrated that Mtb DNA gyrase exhibits significantly slower enzymatic activity in supercoiling plasmid DNA templates and ATP hydrolysis than Escherichia coli DNA gyrase ( 21 , 22 , 23 ). For example, a recent single-molecule study reported that Mtb DNA gyrase displayed velocities approximately 5.5 times slower than those of E. coli DNA gyrase ( 23 ). Moreover, the K M value of Mtb DNA gyrase is also higher than that of E. coli DNA gyrase ( 22 ).…”
“…These results showed that Mtb DNA gyrase is slower at supercoiling plasmid DNA and requires higher concentrations of ATP comparing with E. coli DNA gyrase under similar experimental conditions ( 51 ). These results are also consistent with previously published results ( 21 , 22 , 23 ). Figure 4 Steady-state kinetics of Mtb DNA gyrase in the absence or presence of glycine betaine or PEG400.…”
Section: Resultssupporting
confidence: 94%
“…Previous studies have demonstrated that Mtb DNA gyrase exhibits significantly slower enzymatic activity in supercoiling plasmid DNA templates and ATP hydrolysis than Escherichia coli DNA gyrase ( 21 , 22 , 23 ). For example, a recent single-molecule study reported that Mtb DNA gyrase displayed velocities approximately 5.5 times slower than those of E. coli DNA gyrase ( 23 ). Moreover, the K M value of Mtb DNA gyrase is also higher than that of E. coli DNA gyrase ( 22 ).…”
“…This approach is exemplified by nature product inhibitors such as evybactin and albicidin and synthetic inhibitors such as the thiophene class [29][30][31]. While the catalytic functions of gyrase are conserved throughout bacteria, some sequence differences exist [22,[32][33][34], and the rate of catalysis appears tailored to the doubling time of the specific bacteria [25,35]. For example, the gyrase from E. coli is among the most active, and it and its close homologs contain an extra insertion in GyrB though to enable faster turnover [32].…”
Section: Dna Gyrase Functions As An Essential Type II Topoisomerase I...mentioning
confidence: 99%
“…DNA gyrase is one of these essential and frequently targeted nodes both within bacterial systems and in antibacterial treatments, which is exemplified by the fluoroquinolone class of antibiotics [17,18]. Bacterial (circular) chromosomal replication is completely dependent on gyrase activity, while transcriptional homeostasis is also heavily impacted [19][20][21][22]. Given the primordial nature of many of these systems, it is logical that strategies to combat these warfare and addiction strategies have co-evolved.…”
DNA gyrase is essential for the successful replication of circular chromosomes, such as those found in most bacterial species, by relieving topological stressors associated with unwinding the double-stranded genetic material. This critical central role makes gyrase a valued target for antibacterial approaches, as exemplified by the highly successful fluoroquinolone class of antibiotics. It is reasonable that the activity of gyrase could be intrinsically regulated within cells, thereby helping to coordinate DNA replication with doubling times. Numerous proteins have been identified to exert inhibitory effects on DNA gyrase, although at lower doses, it can appear readily reversible and therefore may have regulatory value. Some of these, such as the small protein toxins found in plasmid-borne addiction modules, can promote cell death by inducing damage to DNA, resulting in an analogous outcome as quinolone antibiotics. Others, however, appear to transiently impact gyrase in a readily reversible and non-damaging mechanism, such as the plasmid-derived Qnr family of DNA-mimetic proteins. The current review examines the origins and known activities of protein inhibitors of gyrase and highlights opportunities to further exert control over bacterial growth by targeting this validated antibacterial target with novel molecular mechanisms. Furthermore, we are gaining new insights into fundamental regulatory strategies of gyrase that may prove important for understanding diverse growth strategies among different bacteria.
“…14 As detailed above, the C-loop of M. tuberculosis DNA gyrase, which is absent from DNA gyrases of other bacteria, is known to be involved in functionally relevant protein−protein interactions between the GyrB ATPase domains and the DNA-binding and cleavage core of the GyrA subunit. Specifically, stabilization of the "extremely open" conformation by interactions involving the C-loop 14 impaired ATP hydrolysis, 8 appears optimized for neither DNA supercoiling nor decatenation activities, 51 and may populate additional resting states 14 or undergo additional conformational changes 16 during the reaction cycle, compared to, e.g., the more efficient Escherichia coli enzyme. Interactions involving the C-loop have been proposed to explain some of these properties.…”
DNA gyrases catalyze negative supercoiling of DNA, are
essential
for bacterial DNA replication, transcription, and recombination, and
are important antibacterial targets in multiple pathogens, including Mycobacterium tuberculosis, which in 2021 caused
>1.5 million deaths worldwide. DNA gyrase is a tetrameric (A2B2) protein formed from two subunit types: gyrase
A (GyrA)
carries the breakage-reunion active site, whereas gyrase B (GyrB)
catalyzes ATP hydrolysis required for energy transduction and DNA
translocation. The GyrB ATPase domains dimerize in the presence of
ATP to trap the translocated DNA (T-DNA) segment as a first step in
strand passage, for which hydrolysis of one of the two ATPs and release
of the resulting inorganic phosphate is rate-limiting. Here, dynamical-nonequilibrium
molecular dynamics (D-NEMD) simulations of the dimeric 43 kDa N-terminal
fragment of M. tuberculosis GyrB show
how events at the ATPase site (dissociation/hydrolysis of bound nucleotides)
are propagated through communication pathways to other functionally
important regions of the GyrB ATPase domain. Specifically, our simulations
identify two distinct pathways that respectively connect the GyrB
ATPase site to the corynebacteria-specific C-loop, thought to interact
with GyrA prior to DNA capture, and to the C-terminus of the GyrB
transduction domain, which in turn contacts the C-terminal GyrB topoisomerase-primase
(TOPRIM) domain responsible for interactions with GyrA and the centrally
bound G-segment DNA. The connection between the ATPase site and the
C-loop of dimeric GyrB is consistent with the unusual properties of M. tuberculosis DNA gyrase relative to those from
other bacterial species.
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