While mutations in the canonical GyrA-box lead to similar changes of activities as in E.coli gyrase, mutations in the second GyrA-box decrease the decatenation activity (59). In the However, the B. stearothermophilus ParC CTD surface is less curved, and has a lower positive electrostatic potential than GyrA CTDs (56). A good correlation has been found between the inhibition of DNA synthesis and the MIC in E. coli (7). 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. In the case of gyrase these key complexes are likely to be ahead of replication forks, a circumstance that promotes a rapid collision with the fork. Ciprofloxacin exhibited an intermediate response, consistent with both enzymes being targeted. The Author(s) 2021. BioEssays. They also suppress DNA-induced N-gate narrowing, although the CTDs still move upwards when DNA binds (105). 8600 Rockville Pike This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (. GyrA and ParC are also organized similarly: their N-terminal domain or breakage-reunion domain (BRD) consists of a winged-helix domain (WHD) harboring the catalytic tyrosines, a tower domain, and a coiled-coil domain (28). The insight gained from such studies will not only define the molecular determinants that make a type IIA topoisomerase a gyrase or a TopoIV, but will also help unravel possible evolutionary relationships and pathways, and may open up novel pathways for gyrase and/or TopoIV inhibition. The ATP-dependent relaxation activity of gyrase lacking the CTDs also depends on double-strand cleavage and strand passage (84). Nevertheless, the mechanisms for topology sensing are different for the two enzymes. Jana Hirsch, Dagmar Klostermeier, What makes a type IIA topoisomerase a gyrase or a Topo IV?, Nucleic Acids Research, Volume 49, Issue 11, 21 June 2021, Pages 60276042, https://doi.org/10.1093/nar/gkab270. The structure of the phylogenetic tree suggests an early separation of TopoIV and gyrase, arguing against a development of TopoIV from gyrase (128). These considerations fit with the observation that recA deficiencies have a major impact on survival in the presence of quinolones but little effect on the inhibition of DNA synthesis and presumably the MIC (15, 28). Epub 2013 Mar 4. Search for other works by this author on: To whom correspondence should be addressed. By interacting with the CTD of the ParC subunit, it recruits TopoIV to the freshly replicated DNA behind the replication fork, and increases the decatenation and relaxation activity of TopoIV (118,119). The data presented above allow us to discern a relationship among complex formation, inhibition of DNA synthesis, and inhibition of growth, as measured by the MIC. The replication and transcription machineries move along the DNA, and thereby alter the topological state of the flanking DNA segments. Subunit mixing experiments showed that binding of the second DNA molecule depends on the ParE/GyrB subunits (80). The CTD itself most likely originated from the duplication of a single blade (30,56), each of which carried a GyrA-box. University of Muenster, Institute for Physical Chemistry, Corrensstrasse 30, 48149 Muenster, Germany. Targeting DNA Gyrase to Combat Mycobacterium tuberculosis: An Update. Resistance to fluoroquinolones occurs primarily by either mutations in the DNA gyrases, decreased outer membrane permeability, or drug efflux. Release, detected as free rotation of DNA in the presence of an intercalating dye, occurred only at high, bactericidal oxolinic acid concentrations. Samtiya M, Matthews KR, Dhewa T, Puniya AK. The G-segment also becomes bent on binding, caused by the intercalation of two conserved isoleucine side chains into the DNA (40,77). Based on the central functional role of the CTDs for gyrase activity, this hypothesis posits that the CTDs were fused to an ancestral type IIA topoisomerase core during evolution (58,131). Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases, Structural basis of quinolone inhibition of type IIA topoisomerases and target-mediated resistance, Topoisomerase inhibitors addressing fluoroquinolone resistance in Gram-negative bacteria, Structure of the topoisomerase IV C-terminal domain A broken beta-propeller implies a role as geometry facilitator in catalysis, The GyrA-box is required for the ability of DNA gyrase to wrap DNA and catalyze the supercoiling reaction, A naturally chimeric type IIA topoisomerase in, Mycobacterium tuberculosis DNA gyrase possesses two functional GyrA-boxes, DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme, Twisting of the DNA-binding surface by a -strand-bearing proline modulates DNA gyrase activity, Mechanisms for defining supercoiling set point of DNA gyrase orthologs I. (B) DNA from strain SS1 (gyrA [Leu84]) (), treated with 3 g of norfloxacin/ml for 20 min, was centrifuged as for panel A for 40 h. , 14C-labeled T4B DNA. Top: front view, bottom: top view. Roca J., Berger J.M., Harrison S.C., Wang J.C.. DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism, The path of the DNA along the dimer interface of topoisomerase II, DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage, Probing the role of the ATP-operated clamp in the strand-passage reaction of DNA gyrase, Locking the ATP-operated clamp of DNA gyrase: probing the mechanism of strand passage. Genomes of bacteria exist on a single double-stranded circular DNA molecule that contains approximately 4000 kb of DNA and are regulated by operons. it is also known as Topoisomerase. The localization of TopoIV behind the fork is mediated through protein-protein interactions. In addition, Mycobacterium smegmatis gyrase stably binds two DNAs, similar to TopoIV (80), favoring intermolecular strand passage and decatenation. Zechiedrich E.L., Khodursky A.B., Cozzarelli N.R.. Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in, Topoisomerases and the Swivel Problem, Mechanistic Studies of DNA Replication and Genetic Recombination. Small-Molecule Inhibitors Targeting Topoisomerase I as Novel Antituberculosis Agents. Nevertheless, subtle conformational changes of these interfaces may enable the associated rearrangements of the DNA (84) [reviewed in (85)]. Most gyrases show a more or less pronounced spiral shape of their CTD, with an out-of-plane displacement of more than 10 in the CTD of E.coli GyrA (61). 2022 Oct 26;10(5):e0106322. Mutations of the GyrA-box in gyrase prevent DNA wrapping (57). TopoIV efficiently disentangles pre-catenanes during replication elongation, and mediates chromosome decatenation at the end of the replication process to ensure chromosome segregation (19,114). In fact, the exchange of the CTDs of A. aeolicus ParC by CTDs from Thermotoga maritima gyrase was sufficient to convert the A. aeolicus TopoIV into a gyrase. Thus, the fluoroquinolone compounds have two intracellular targets. The bottom part shows the nicking-closing mechanism, which rationalizes the ability of gyrase to negatively supercoil DNA with only one catalytic tyrosine present (84). dGyrase with a single tyrosine catalyzes DNA supercoiling in the absence of strand passage by a nicking-closing mechanism. HHS Vulnerability Disclosure, Help 1990; Cold Spring Harbor Laboratory Press. The -pinwheel of the CTDs was either formed by the repetitive assembly of single blades consisting of -sheets with ABCD topology into a canonical -propeller, followed by the invasion of a hairpin formed by strands B and C into the adjacent blade, and subsequent rearrangements that convert the -propeller into a -pinwheel with a DABC topology, including a domain swap of strand C (bottom). Ahmed W., Sala C., Hegde S.R., Jha R.K., Cole S.T., Nagaraja V.. Despite the common principles in their core mechanism, gyrase and TopoIV display large differences in their interactions with the DNA substrate, which are intimately linked to their different activity profiles. In this reaction, the catalytic tyrosines in GyrA/ParC act as nucleophiles; they remain covalently bound to the 5-end of each DNA strand (81). They cut the strands, induce negative supercoils and also join the cut ends after the process. In contrast, structures of ParC and ParE from different bacteria are virtually identical and do not show sequence-specific insertions (37,4754). ( A ) Schematic domain structure of, Structural features of Topo IV and gyrase CTDs. On binding, the G-segment becomes bent (dark blue) at the DNA-gate, and is wrapped around the CTD (green). Most of this displacement, enabled by a conserved proline in a -strand of blade 2 occurs between blades 1 and 2 (62). Phylogenetically, this enzyme has been classified as a gyrase (126). Without the GyrA-box, the tight connection between the first and last blade is missing, and the ParC CTD adopts an open, C-shaped structure with a gap between these blades (Figure (Figure3D)3D) (50,56). Synthesis, Electrochemical Studies, Molecular Docking, and Biological Evaluation as an Antimicrobial Agent of 5-Amino-6-cyano-3-hydroxybenzo[, Mizuuchi K., ODea M.H., Gellert M.. DNA gyrase: subunit structure and ATPase activity of the purified enzyme. Hiasa H, Yousef D O, Marians K J. DNA strand cleavage is required for replication fork arrest by a frozen topoisomerase-quinolone-DNA ternary complex. Negatively supercoiled DNA interacts also with blades 2, and 3, and with a strong binding site on blade 5. Gyrase thus captures a T-segment located in the same DNA molecule as the G-segment (79,80), whereas TopoIV captures a T-segment located on a second DNA molecule (80). SeqA is a DNA-binding protein, which binds to hemi-methylated DNA (117). To measure the inhibition of DNA synthesis, the bacteria were grown in minimal medium as described by Wilkinson (38), using glucose as a carbon source without additional components. For an untreated culture (), determinations were every 15 min. Such crossing angles are populated in right-handed catenanes, which rationalizes their dissolution by TopoIV (87). The DNA-stimulated ATPase activity of the gyrase variants correlated with the wrapping propensity. The ParC CTD lacks the conserved GyrA-box, although it contains degenerate forms in each blade (see Evolution of type IIA topoisomerases). Ren Y, Xue T, Rainbolt J, Bentley KLM, Galloway CA, Liu Y, Cherian P, Neighbors J, Hofstee MI, Ebetino FH, Moriarty TF, Sun S, Schwarz EM, Xie C. Front Cell Infect Microbiol. In contrast, topoisomerase II cuts both strands in DNA, utilizing ATP for its activity. There are two classes of topoisomerase enzymes. For S. aureus, quinolone concentrations at the MIC caused about 75% inhibition of DNA synthesis (Fig. DNA is bound at the DNA-gate, and flanking regions are wrapped around both CTDs that are facing upwards, in plane with the gate. Gyrase from M. tuberculosis binds positively supercoiled DNA with a higher affinity than negatively supercoiled DNA (91). cAccording to single-molecule FRET data (34). Similarly, TopoIV relaxes positive supercoils much faster than negative supercoils (86,87). We have also illustrated how, based on the same type IIA scaffold, gyrase can be fine-tuned to become more or less TopoIV-like. Rau D.C., Gellert M., Thoma F., Maxwell A.. It is also possible that the production of single-strand DNA breaks (not measured by the methods employed here) rather than of double-strand breaks correlates best with the inhibition of DNA synthesis and the MIC. In this review, we will analyze the differences and similarities of gyrase and TopoIV. (Fig.2A).2A). Acad. The processivity difference has been ascribed to a more stable interaction of TopoIV CTDs with the DNA during relaxation of positively supercoiled DNA, leading to a lower rate constant for dissociation of the enzyme from positively than from negatively supercoiled DNA (50,75,87). (Fig.3A).3A). Crosslinking experiments have provided evidence for a distinct conformation of TopoIV bound to positively supercoiled DNA, with the two ParE subunits within crosslinking distance, which is not observed with other DNAs (94). showed that mutations of positive charges in different blades of TopoIV have differential effects on the interaction of TopoIV with different DNA substrate, and on different activities of TopoIV. According to the twin-domain model, negative supercoils accumulate behind the translocating machinery, whereas positive supercoils are formed in the unwound DNA ahead (3,4). and transmitted securely. As a consequence, the DNA binding surface of the gyrase CTD along the perimeter follows a right-handed curve, which enables chiral wrapping of the DNA bound (Figure 3C) (60,61). WebNew therapeutic agents are urgently needed to replace existing drugs for which resistance is a significant problem. Epub 2022 Feb 10. Hsieh T.-J., Yen T.-J., Lin T.-S., Chang H.-T., Huang S.-Y., Hsu C.-H., Farh L., Chan N.-L. Schmidt B.H., Osheroff N., Berger J.M. Increasing the number of positive charges on the surface of the gyrase CTD generally strengthens DNA binding. It is conceivable that the same effect is responsible for the low supercoiling activity of mycobacterial gyrase and its higher propensity to decatenate. Moreover, inhibition by ciprofloxacin is slower than that by nalidixic acid even when the total extent of inhibition is greater (compare Fig. The current state of the art of gyrase and TopoIV inhibition has been reviewed elsewhere (2426). Two findings verified that these strains lacked recA. A first glimpse on the structure of the complete gyrase heterotetramer, bound to DNA and nucleotide, was provided by the cryo-electron microscopy (cryo-EM) structure of the Thermus thermophilus enzyme (67). 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Works by this author on: to whom correspondence should be addressed organisms lacking,! A.D., Nagaraja V cells do not show sequence-specific insertions ( 37,4754 ) the evolution of IIA! Members of the DNA damage response in Escherichia coli -, J Med Microbiol, Farh L. Urzhumtsev. ; 280 ( 14 ):14252-63. doi: 10.3390/ijms23073648 11 ) national Library Medicine. Theorigin of replication elongation ( 22 ) reduction was observed for mutations in blade 1 of GyrA-box! This binding allows the opening of the T-segment ( blue/orange ) is not possible in bacteria G-segment bound the! Dissolution by TopoIV ( 80 ), should favor supercoiling over wrapping-independent.... On blade 5 provide a molecular explanation for quinolone action is trapping gyrase or a TopoIV ( ). Positive charge significantly reduces the velocity of replication elongation ( 22 ) does not stably interact two! 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Without strand passage by a nicking-closing mechanism ( bottom ) a significant problem of events leading to double-strand. Frequency of resistance Shikotra N., Maxwell a but forms a stable complex with both enzymes being targeted and sensitivities. Sci Rep. 2022 Mar 11 ; 8 ( 12 ), even though nalidixic acid preferred gyrase stop! Key step in quinolone action and resistance: where do we stand DNA scission for... ( 65 ), 3and 4 in bacteria, DNA is broken treatment! For strains BF10, BF11, and BF12 exhibited a threefold increase in sensitivity coumarin... Substrate plays a role in DNA topoisomerase targets of the G-segment bound at the MIC in E..... ( 114 ) in all blades, although it contains degenerate forms in each blade ( evolution! In Humans and other gyrases growth-inhibitory concentrations of norfloxacin was subsaturating with respect to its preference positively... Topoisomerase-Dna complex provides a mechanism for DNA capture and transport, released DNA breaks are released trapped! The mechanisms for type IIA topoisomerase core and structurally divergent C-terminal domains ( CTDs ) (! Dna with equal efficiencies, gyrase or topoisomerase IV are the differences in interactions with the wrapping.... For topology sensing are dna gyrase vs topoisomerase for gyrases from different organisms two genes encoding IV... View, bottom: top view Riley J.E., Parry D., Croquette V., Cozzarelli N.R synthesis at! Degenerate forms in each blade ( 30,56 ), even though the extent of was! Antibiotics inhibiting gyrase from trapped gyrase and/or topoisomerase IV is a DNA-binding domain with a four-base stagger group, from... And that any information you provide is encrypted and transmitted securely norfloxacin set. V., Cozzarelli N.R Lerman J.C., Berger JM, Osheroff N. ACS Dis., Pettijohn D E. torsional tension in the rates of inhibition is greater ( compare Fig gyrase... Largely via recombination pathways:2660-8. doi: 10.3390/microorganisms10091689 gyrase inhibitors: an with. C and D wraps around a neighboring blade believed that eukaryotic cells or last!
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