This report combines a series of papers to trace progression in the area of type-2 topoisomerase research. First, Deibler et al. show that knotted DNA is harmful to cells. Knots can block both transcription and replication, and can also act as a catalyst for mutation. Despite the fact that type-2 topoisomerases perform the important functions of unknotting and decatenating DNA, the mechanism by which they accomplish this task is still unknown. Buck and Zechiedrich propose a model in which the enzyme uses local geometry to infer global topology, and thus where to perform segment passage in order to obtain the desired results. In two articles, Liu et al. evaluate this theory quantitatively for the decatenation and unknotting problems. In both cases it is shown that the presence of certain juxtapositions is strongly correlated with global topology. This correlation is not enough, however, and Liu et al. go on to show that when segment passage operations designed to mimic type-2 topoisomerase action are performed at hooked juxtapositions, the overwhelming tendency is towards unknotting and decatenation. / text

Argonautes (AGOs) are present in all domains of life. Like their eukaryotic counterparts, archaeal and eubacterial AGOs adopt a similar global architecture and bind small nucleic acids. In many eukaryotes, AGOs, guided by short RNA sequences, defend cells against transposons and viruses. In the eubacterium Thermus thermophilus, the DNA-guided Argonaute TtAgo defends against transformation by DNA plasmids. We find that TtAgo also participates in DNA replication. In vivo, TtAgo binds 15–18 nt DNA guides derived from the chromosomal region where replication terminates, and TtAgo complexed to short DNA guides enhances target finding and prefers to bind targets with full complementarity. Additionally, TtAgo associates with proteins known to act in DNA replication. When gyrase, the sole T. thermophilus type II topoisomerase, is inhibited, TtAgo allows the bacterium to finish replicating its circular genome. In contrast, loss of both gyrase and TtAgo activity slows growth and produces long, segmented filaments in which the individual bacteria are linked by DNA. Furthermore, wild-type T. thermophilus outcompetes an otherwise isogenic strain lacking TtAgo. Finally, at physiologic temperature in vitro, we find TtAgo possesses highest affinity for fully complementary targets. We propose that terminus-derived guides binding in such a fashion localize TtAgo, and that the primary role of TtAgo is to help T. thermophilus disentangle the catenated circular chromosomes generated by DNA replication.

Maintenance of a topological homeostasis by introduction and removal of the supercoils to relieve excessive strain on the DNA is a hallmark of topoisomerase function in the cell. The requirement of the topoisomerases during DNA transaction processes marks a ubiquitous presence of the enzymes in all the life forms. Different reactions carried out by the enzymes include relaxation of positive and negative supercoils required majorly during DNA replication and transcription, decatenation at the end of DNA replication to separate the daughter chromosomes and removal of lethal knots generated in the circular chromosome. In eubacteria, the enzymes introduce negative supercoils to facilitate easier strand separation for DNA transaction processes. However, in thermophiles, a different enzyme maintains the genome in a positively supercoiled form to protect from denaturation by excessive heat. These varied functions are carried out by different topoisomerases. Therefore, each organism maintains a minimum required set of the enzymes and the absence of a certain enzyme may be compensated for by topoisomerases with dual functions. For example, Mycobacterium tuberculosis and many other slow growing mycobacteria do not possess topoisomerase IV or its homologs. In these organisms, the DNA gyrase is suggested to carry out both negative supercoiling and decatenation reactions. Therefore, the mycobacterial DNA gyrase must be able to manage between both the functions in vivo. In contrast, Mycobacterium smegmatis and few other mycobacteria contain an additional type II topoisomerase which does not resemble any known type II enzyme but could catalyze relaxation and decatenation reactions. Importantly, the enzyme displays a unique ability to introduce limited positive supercoils and may have certain functions inside the cell which remains to be studied. Owing to the indispensability for bacterial survival topoisomerases present themselves as important drug targets. A large number of inhibitors have been found to inhibit the enzyme and thereby killing the bacterial. Among these, quinolones are successfully being used as broad spectrum antibacterial drugs. Although the commonly used quinolones inhibit many bacterial pathogens, a reduced susceptibility is exhibited by some of the pathogens e.g. Mycobacterium tuberculosis. To circumvent the lower efficacy of existing drugs, new and modified quinolones have been developed which are highly effective against mycobacteria. The difference in the susceptibility may be conferred by a difference in the chemical property of the drug and the interacting residues present in the enzyme. In the present thesis efforts have been made to understand the mechanism of the type II topoisomerases from mycobacteria and drug action on these enzymes. The thesis is divided into four chapters. In Chapter I of the thesis an introduction is provided on the topoisomerases, their classification and different reactions catalyzed by these enzymes. As the work in present thesis has been carried out with type II topoisomerases, introduction of type II enzymes, their structure and mechanisms is elaborated. DNA gyrase, its mechanism of reaction and in vitro and in vivo functions are explained in great detail. DNA gyrase and topoisomerase IV are targeted by a range of different inhibitors. These different classes of inhibitors and their mechanism of action are described. Finally, the mechanism of mycobacterial DNA gyrase with structural information and the current understanding of quinolone action on the enzyme are explained. The chapter ends with the objective of the study in the present thesis. In chapter II, the studies are aimed at understanding the molecular basis for decatenation carried out by mycobacterial DNA gyrase. Previous work from the laboratory showed that the enzyme can carry out decatenation more efficiently than its homolog from E. coli. It was shown that the mycobacterial enzyme binds two DNA molecules in trans in a length dependent manner. The ability to bind the second DNA is conferred upon the holoenzyme by ATPase subunit (GyrB) subunit which alone can bind DNA. Similar studies using topo IV from E. coli, the strongest known decatenase showed binding of two DNA molecules and the second DNA binding by ATPase (ParE) subunit. However, GyrB subunit from E. coli DNA gyrase, a weaker decatenase, does not bind second DNA molecule efficiently. The results provide a general mechanism for decatenation by type II enzymes in which efficient binding of second DNA is important. In Chapter III, studies have been carried out using topo NM, an atypical type II topoisomerase from Mycobacterium smegmatis. The enzyme has been characterized previously in the laboratory. In addition to efficient decatenation and relaxation, the enzyme exhibits a unique ability to introduce positive supercoils into the DNA. As demonstrated for the mycobacterial DNA gyrase and topo IV in the Chapter II, the ATPase subunit (Topo N) of topo NM, binds second DNA efficiently. The binding of both gate and transport segments increases with the length of the DNA. Binding of two DNA molecules by the holoenzyme appears to be a cumulative effect of DNA binding to individual subunits. In the absence of any inhibitor, the enzyme accumulates cleaved DNA products with shorter DNA but not with larger DNA. The cleavage of the shorter DNA is supported only in the presence of Mg2+ and Mn2+. Another important property of the enzyme is to introduce positive supercoils which appears to be due to its efficient utilization of ATP and a high rate of reaction. Chapter IV deals with the interaction of mycobacterial gyrase with fluoroquinolones (FQs). Although DNA gyrase is the sole target of the FQs in M. tuberculosis, the lower susceptibility to commonly used FQs have led to the studies to find out more effective quinolones. Previous studies from the laboratory showed a lower susceptibility of the mycobacterial gyrase to ciprofloxacin, but moxifloxacin could inhibit the enzyme efficiently. The better inhibition by moxifloxacin appears to be due to efficient trapping of the enzyme-DNA covalent complex. Both ciprofloxacin and moxifloxacin bind the DNA gyrase from mycobacteria, E. coli and E. coli topo IV, independent of DNA. The extent of binding also correlates with the inhibition potential of the drug against a given enzyme. A general model of quinolone enzyme interaction is provided wherein the quinolones are shown to interact with GyrA subunit or holoenzyme or the enzyme- DNA complex which would finally result in the trapping of the covalent complex.

Des liens de caténation sont progressivement crées lors de la réplication de l’ADN et sont responsables de la cohésion des chromatides sœurs. La topoisomérase IV est une topoisomérase de type II impliquée dans la résolution de ces liens de caténation accumulés derrière la fourche de réplication, et lors de la dernière étape de séparation des chromatides sœurs à la fin de la réplication. Nous avons étudié la liaison de la topoIV à l’ADN ainsi que son activité catalytique à l’aide de méthodes de biologie moléculaire et de génomique. Une expérience de ChIPseq a révélé que l’interaction de la topoIV de chez E.coli avec l’ADN est contrôlée par la réplication. Durant la réplication, la topoIV a accès à des centaines de sites sur l’ADN mais ne se lie qu’à quelques sites où elle exerce son activité catalytique. La conformation locale de la chromatine et l’expression des gènes influencent la sélection de certains sites. De plus, une forte liaison et une activité catalytique renforcée a été trouvée au site de résolution des dimers, dif. Le site dif est situé à l’opposé de l’origine de réplication dans le macrodomaine ter. Nous avons montré qu’il existe une interaction physique et fonctionnelle entre la topoIV et la recombinase XerCD, qui agit au site dif. Cette interaction est médiée par MatP, une protéine essentielle dans l’organisation du macrodomaine ter. L’ensemble de ces résultats montre que la topoIV, XerCD/dif et MatP œuvrent ensemble pour permettre l’étape finale de ségrégation des chromosomes lors du cycle cellulaire. / Catenation links between sister chromatids are formed progressively during DNA replication and are involved in the establishment of sister chromatid cohesion. Topo IV is a bacterial type II topoisomerase involved in the removal of catenation links both behind replication forks and after replication during the final separation of sister chromosomes. We have investigated the global DNA-binding and catalytic activity of Topo IV in E. coli using genomic and molecular biology approaches. ChIP-seq revealed that Topo IV interaction with the E. coli chromosome is controlled by DNA replication. During replication, Topo IV has access to most of the genome but only selects a few hundred specific sites for its activity. Local chromatin and gene expression context influence site selection. Moreover strong DNA-binding and catalytic activities are found at the chromosome dimer resolution site, dif, located opposite the origin of replication. We reveal a physical and functional interaction between Topo IV and the XerCD recombinases acting at the dif site. This interaction is modulated by MatP, a protein involved in the organization of the Ter macrodomain. These results show that Topo IV, XerCD/dif and MatP are part of a network dedicated to the final step of chromosome management during the cell cycle.

Les topoisomérases I (topA) et III (topB) sont les deux topoisomérases (topos) de type IA d’Escherichia coli. La fonction principale de la topo I est la relaxation de l’excès de surenroulement négatif, tandis que peu d’information est disponible sur le rôle de la topo III. Les cellules pour lesquelles les deux topoisomérases de type IA sont manquantes souffrent d’une croissance difficile ainsi que de défauts de ségrégation sévères. Nous démontrons que ces problèmes sont majoritairement attribuables à des mutations dans la gyrase qui empêchent l’accumulation d’excès de surenroulement négatif chez les mutants sans topA. L’augmentation de l’activité de la gyrase réalisée par le remplacement de l’allèle gyrB(Ts) par le gène de type sauvage ou par l’exposition des souches gyrB(Ts) à une température permissive, permet la correction significative de la croissance et de la ségrégation des cellules topos de type IA. Nous démontrons également que les mutants topB sont hypersensibles à l’inhibition de la gyrase par la novobiocine. La réplication non-régulée en l’absence de topA et de rnhA (RNase HI) augmente la nécessité de l’activité de la topoisomérase III. De plus, en l’absence de topA et de rnhA, la surproduction de la topoisomérase III permet de réduire la dégradation importante d’ADN qui est observée en l’absence de recA (RecA). Nous proposons un rôle pour la topoisomérase III dans la ségrégation des chromosomes lorsque l’activité de la gyrase n’est pas optimale, par la réduction des collisions fourches de réplication s’observant particulièrement en l’absence de la topo I et de la RNase HI. / E. coli possesses two type IA topoisomerases (topos), namely topo I (topA) and topo III (topB). The major function of topo I is the relaxation of excess negative supercoiling. Much less is known about the function of topo III. Cells lacking both type IA topos suffer from severe chromosome segregation and growth defects. We show that these defects are mostly related to the presence of gyrase mutations that prevent excess negative supercoiling in topA null mutants. Indeed, increasing gyrase activity by spontaneous mutations, by substituting a gyrB(Ts) allele for a wild-type one or by exposing cells carrying the gyrB(Ts) allele to permissive temperatures, significantly corrected the growth and segregation defects of cells lacking type IA topo activity. We also found that topB mutants are hypersensitive to novobiocin due to gyrase inhibition. Our data also suggest that unregulated replication occurring in the absence of topA and rnhA (RNase HI) exacerbates the need for topo III activity. Moreover, when topA and rnhA were absent, we found that topo III overproduction reduced the extensive DNA degradation that took place in the absence of recA (RecA). All together, our results lead us to propose a role for topo III in chromosome segregation when gyrase activity is suboptimal, thus reducing replication forks collapse, especially when replication is unregulated due to the absence of topo I and RNase HI.

Les topoisomérases I (topA) et III (topB) sont les deux topoisomérases (topos) de type IA d’Escherichia coli. La fonction principale de la topo I est la relaxation de l’excès de surenroulement négatif, tandis que peu d’information est disponible sur le rôle de la topo III. Les cellules pour lesquelles les deux topoisomérases de type IA sont manquantes souffrent d’une croissance difficile ainsi que de défauts de ségrégation sévères. Nous démontrons que ces problèmes sont majoritairement attribuables à des mutations dans la gyrase qui empêchent l’accumulation d’excès de surenroulement négatif chez les mutants sans topA. L’augmentation de l’activité de la gyrase réalisée par le remplacement de l’allèle gyrB(Ts) par le gène de type sauvage ou par l’exposition des souches gyrB(Ts) à une température permissive, permet la correction significative de la croissance et de la ségrégation des cellules topos de type IA. Nous démontrons également que les mutants topB sont hypersensibles à l’inhibition de la gyrase par la novobiocine. La réplication non-régulée en l’absence de topA et de rnhA (RNase HI) augmente la nécessité de l’activité de la topoisomérase III. De plus, en l’absence de topA et de rnhA, la surproduction de la topoisomérase III permet de réduire la dégradation importante d’ADN qui est observée en l’absence de recA (RecA). Nous proposons un rôle pour la topoisomérase III dans la ségrégation des chromosomes lorsque l’activité de la gyrase n’est pas optimale, par la réduction des collisions fourches de réplication s’observant particulièrement en l’absence de la topo I et de la RNase HI. / E. coli possesses two type IA topoisomerases (topos), namely topo I (topA) and topo III (topB). The major function of topo I is the relaxation of excess negative supercoiling. Much less is known about the function of topo III. Cells lacking both type IA topos suffer from severe chromosome segregation and growth defects. We show that these defects are mostly related to the presence of gyrase mutations that prevent excess negative supercoiling in topA null mutants. Indeed, increasing gyrase activity by spontaneous mutations, by substituting a gyrB(Ts) allele for a wild-type one or by exposing cells carrying the gyrB(Ts) allele to permissive temperatures, significantly corrected the growth and segregation defects of cells lacking type IA topo activity. We also found that topB mutants are hypersensitive to novobiocin due to gyrase inhibition. Our data also suggest that unregulated replication occurring in the absence of topA and rnhA (RNase HI) exacerbates the need for topo III activity. Moreover, when topA and rnhA were absent, we found that topo III overproduction reduced the extensive DNA degradation that took place in the absence of recA (RecA). All together, our results lead us to propose a role for topo III in chromosome segregation when gyrase activity is suboptimal, thus reducing replication forks collapse, especially when replication is unregulated due to the absence of topo I and RNase HI.