Roles of DNA topoisomerases in transcription

Regulation and function of R-loops at repetitive elements

R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.

Natural DNA Intercalators as Promising Therapeutics for Cancer and Infectious Diseases

Cancer and infectious diseases are one of the greatest challenges of modern medicine. An unhealthy lifestyle, the improper use of drugs, or their abuse are conducive to the increase of morbidity and mortality caused by these diseases. The imperfections of drugs currently used in therapy for these diseases and the increasing problem of drug resistance have forced a search for new substances with therapeutic potential. Throughout history, plants, animals, fungi and microorganisms have been rich sources of biologically active compounds. Even today, despite the development of chemistry and the introduction of many synthetic chemotherapeutics, a substantial part of the new compounds being tested for treatment are still of natural origin. Natural compounds exhibit a great diversity of chemical structures, and thus possess diverse mechanisms of action and molecular targets. Nucleic acids seem to be a good molecular target for substances with anticancer potential in particular, but they may also be a target for antimicrobial compounds. There are many types of interactions of small-molecule ligands with DNA. This publication focuses on the intercalation process. Intercalators are compounds that usually have planar aromatic moieties and can insert themselves between adjacent base pairs in the DNA helix. These types of interactions change the structure of DNA, leading to various types of disorders in the functioning of cells and the cell cycle. This article presents the most promising intercalators of natural origin, which have aroused interest in recent years due to their therapeutic potential.

Genome-wide mapping of Topoisomerase I activity sites reveal its role in chromosome segregation

DNA Topoisomerase I (TopoI) in eubacteria is the principle DNA relaxase, belonging to Type 1A group. The enzyme from Mycobacterium smegmatis is essential for cell survival and distinct from other eubacteria in having several unusual characteristics. To understand genome-wide TopoI engagements in vivo, functional sites were mapped by employing a poisonous variant of the enzyme and a newly discovered inhibitor, both of which arrest the enzyme activity after the first transestrification reaction, thereby leading to the accumulation of protein-DNA covalent complexes. The cleavage sites are subsets of TopoI binding sites, implying that TopoI recruitment does not necessarily lead to DNA cleavage in vivo. The cleavage protection conferred by nucleoid associated proteins in vitro suggest a similar possibility in vivo. Co-localization of binding and cleavage sites of the enzyme on transcription units, implying that both TopoI recruitment and function are associated with active transcription. Attenuation of the cleavage upon Rifampicin treatment confirms the close connection between transcription and TopoI action. Notably, TopoI is inactive upstream of the Transcription start site (TSS) and activated following transcription initiation. The binding of TopoI at the Ter region, and the DNA cleavage at the Ter indicates TopoI involvement in chromosome segregation, substantiated by its catenation and decatenation activities.

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase

Movement of the transcription machinery along a template alters DNA topology resulting in the accumulation of supercoils in DNA. The positive supercoils generated ahead of transcribing RNA polymerase (RNAP) and the negative supercoils accumulating behind impose severe topological constraints impeding transcription process. Previous studies have implied the role of topoisomerases in the removal of torsional stress and the maintenance of template topology but the in vivo interaction of functionally distinct topoisomerases with heterogeneous chromosomal territories is not deciphered. Moreover, how the transcription-induced supercoils influence the genome-wide recruitment of DNA topoisomerases remains to be explored in bacteria. Using ChIP-Seq, we show the genome-wide occupancy profile of both topoisomerase I and DNA gyrase in conjunction with RNAP in Mycobacterium tuberculosis taking advantage of minimal topoisomerase representation in the organism. The study unveils the first in vivo genome-wide interaction of both the topoisomerases with the genomic regions and establishes that transcription-induced supercoils govern their recruitment at genomic sites. Distribution profiles revealed co-localization of RNAP and the two topoisomerases on the active transcriptional units (TUs). At a given locus, topoisomerase I and DNA gyrase were localized behind and ahead of RNAP, respectively, correlating with the twin-supercoiled domains generated. The recruitment of topoisomerases was higher at the genomic loci with higher transcriptional activity and/or at regions under high torsional stress compared to silent genomic loci. Importantly, the occupancy of DNA gyrase, sole type II topoisomerase in Mtb, near the Ter domain of the Mtb chromosome validates its function as a decatenase.

The generation of DNA topological constraint is intrinsic to transcription. Although in vitro studies indicated DNA gyrase and topoisomerase I action in the removal of excess supercoils, ahead and behind the transcribing RNA polymerase, in vivo recruitment and interaction of both topoisomerases with the genome has not been investigated. Using advanced sequencing, we have mapped the genome-wide footprints of topoisomerase I and DNA gyrase along with RNAP in deadly pathogen, Mycobacterium tuberculosis. We show that in vivo distribution of topoisomerases is guided by active transcription and both the enzymes co-occupy active transcription units. We establish their interaction with the regions of genome having propensity to accumulate negative and positive supercoiled domains, validating their role in managing the twin supercoiled domains.

Topological constraints impair RNA polymerase II transcription and causes instability of plasmid-borne convergent genes

Despite the theoretical bases for the association of topoisomerases and supercoiling changes with transcription and replication, our knowledge of the impact of topological constraints on transcription and replication is incomplete. Although mutation of topoisomerases affects expression and stability of the rDNA region it is not clear whether the same is the case for RNAPII transcription and genome integrity in other regions. We developed new assays in which two convergent RNAPII-driven genes are transcribed simultaneously. Plasmid-based systems were constructed with and without a transcription terminator between the two convergent transcription units, so that the impact of transcription interference could also be evaluated. Using these assays we show that Topos I and II play roles in RNAPII transcription in vivo and reduce the stability of RNAPII-transcribed genes in Saccharomyces cerevisiae. Supercoiling accumulation in convergent transcription units impairs RNAPII transcription in top1Δ strains, but Topo II is also required for efficient transcription independent of Topo I and of detectable supercoiling accumulation. Our work shows that topological constraints negatively affect RNAPII transcription and genetic integrity, and provides an assay to study gene regulation by transcription interference.

Multiple antibiotic resistances of Enterococcus isolates from raw or sand-filtered sewage

Fifty antibiotic-resistant Enterococcus strains were isolated from raw sewage of a wastewater treatment plant and from the same sewage after trickling through a 25-cm sand column, which retained >99% of the initial population. All 50 Enterococcus isolates were resistant against triple sulfa and trimethoprim/sulfamethoxazole and none were resistant against vancomycin. Most of the isolates from raw sewage were resistant to more antibiotics than the isolates from sand column effluent. One Enterococcus isolate from raw sewage (no. 61) and one Enterococcus isolate from sand column effluent (no. 95) had ten antibiotic resistances each. Isolate no. 95 maintained its resistances in the absence of antibiotics during the whole study. It was compared with isolate no. 70, which was one of the isolates, being resistant only against the two sulfonamides. Phenotypically and biochemically, the two organisms were strains of Enterococcus faecalis. Sequence analysis of partical 16S rDNA allowed alignment of isolate no. 95 as a strain of Enterococcus faecium and of isolate no. 70 as a strain of E. faecalis. E. faecium strain no. 95 carried at least six different plasmids, whereas for E. faecalis strain no. 70, no discrete plasmid band was seen on the gels.

Leptosins isolated from marine fungus Leptoshaeria species inhibit DNA topoisomerases I and/or II and induce apoptosis by inactivation of Akt/protein kinase B

DNA topoisomerases (topo) I and II are molecular targets of several potent anticancer agents. Thus, inhibitors of these enzymes are potential candidates or model compounds for anticancer drugs. Leptosins (Leps) F and C, indole derivatives, were isolated from a marine fungus, Leptoshaeria sp. as cytotoxic substances. In vitro cytotoxic effects of Lep were measured using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide-based viability assay. Lep F inhibited the activity of topos I and II, whereas Lep C inhibited topo I in vitro. Interestingly both of the compounds were found to be catalytic inhibitors of topo I, as evidenced by the lack of stabilization of reaction intermediate cleavable complex (CC), as camptothecin (CPT) does stabilize. Furthermore, Lep C inhibited the CC stabilization induced by CPT in vitro. In vivo band depletion analysis demonstrated that Lep C likewise appeared not to stabilize CC, and inhibited CC formation by CPT, indicating that Lep C is also a catalytic inhibitor of topo I in vivo. Cell cycle analysis of Lep C-treated cells showed that Lep C appeared to inhibit the progress of cells from G(1) to S phase. Lep C induced apoptosis in RPMI8402 cells, as revealed by the accumulation of cells in sub-G(1) phase, activation of caspase-3 and the nucleosomal degradation of chromosomal DNA. Furthermore, Leps F and C inhibited the Akt pathway, as demonstrated by dose-dependent and time-dependent dephosphorylation of Akt (Ser473). Our study shows that Leps are a group of anticancer chemotherapeutic agents with single or dual catalytic inhibitory activities against topos I and II.

Camptothecins

Camptothecin analogues and derivatives appear to exert their antitumour activity by binding to topoisomerase I and have shown significant activity against a broad range of tumours. In general, camptothecins are not substrates for either the multidrug-resistance P-glycoprotein or the multidrug-resistance-associated protein (MRP). Because of manageable toxicity and encouraging activity against solid tumours, camptothecins offer promise in the clinical management of human tumours. This review illustrates the proposed mechanism(s) of action of camptothecins and presents a concise overview of current camptothecin therapy, including irinotecan and topotecan, and novel analogues undergoing clinical trails, such as exatecan (DX-8951f), IDEC-132 (9-aminocamptothecin), rubitecan (9-nitrocamptothecin), lurtotecan (GI-147211C), and the recently developed homocamptothecins diflomotecan (BN-80915) and BN-80927.

Free energy and information contents of conformons in proteins and DNA

Sequence-specific conformational strains (SSCS) of biopolymers that carry free energy and genetic information have been called conformons, a term coined independently by two groups over two and a half decades ago [Green, D.E., Ji, S., 1972. The electromechanochemical model of mitochondrial structure and function. In: Schultz, J., Cameron, B.F. (Eds.), Molecular Basis of Electron Transport. Academic Press, New York, pp. 1-44; Volkenstein, M.V., 1972. The Conformon. J. Theor. Biol. 34, 193-195]. Conformons provide the molecular mechanisms necessary and sufficient to account for all biological processes in the living cell on the molecular level in principle--including the origin of life, enzymic catalysis, control of gene expression, oxidative phosphorylation, active transport, and muscle contraction. A clear example of SSCS is provided by SIDD (strain-induced duplex destabilization) in DNA recently reported by Benham [Benham, C.J., 1996a. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425-434; Benham, C.J., 1996b. Computation of DNA structural variability--a new predictor of DNA regulatory regions. CABIOS 12(5), 375-381]. Experimental as well as theoretical evidence indicates that conformons in proteins carry 8-16 kcal/mol of free energy and 40-200 bits of information, while those in DNA contain 500-2500 kcal/mol of free energy and 200-600 bits of information. The similarities and differences between conformons and solitons have been analyzed on the basis of the generalized Franck-Condon principle [Ji, S., 1974a. A general theory of ATP synthesis and utilization. Ann. N.Y. Acad. Sci. 227, 211-226; Ji, S., 1974b. Energy and negentropy in enzymic catalysis. Ann. N.Y. Acad. Sci. 227, 419-437]. To illustrate a practical application, the conformon theory was applied to the molecular-clamp model of DNA gyrase proposed by Berger and Wang [Berger, J.M., Wang, J.C., 1996. Recent developments in DNA topoisomerases II structure and mechanism. Curr. Opin. Struct. Biol. 6(1), 84-90], leading to the proposal of an eight-step molecular mechanism for the action of the enzyme. Finally, a set of experimentally testable predictions has been formulated on the basis of the conformon theory.

Investigating the biological functions of DNA topoisomerases in eukaryotic cells

DNA topoisomerases participate in nearly all events relating to DNA metabolism including replication, transcription, and chromosome segregation. Recent studies in eukaryotic cells have led to the discovery of several novel topoisomerases, and to new questions concerning the roles of these enzymes in cellular processes. Gene knockout studies are helping to delineate the roles of topoisomerases in mammalian cells, just as similar studies in yeast established paradigms concerning the functions of topoisomerases in lower eukaryotes. The application of new technologies for identifying interacting proteins has connected the studies on topoisomerases to other areas of human biology including genome stability and aging. These studies highlight the importance of understanding how topoisomerases participate in the normal processes of transcription, DNA replication, and genome stability.

Domains of human topoisomerase I and associated functions

Human topoisomerase I can be divided into four domains based on homology alignments, physical properties, sensitivity to limited proteolysis, and fragment complementation studies. Roughly the first 197 amino acids represent the N-terminal domain that appears to be devoid of secondary structure and is likely important for targeting the enzyme to its sites of action within the nucleus of the cell. The core domain encompasses residues approximately 198 to approximately 651, is involved in catalysis, and is important for the preferential binding of the enzyme to supercoiled DNA. The C-terminal domain extends from residue approximately 697 to the end of the protein at residue 765 and contains the catalytically important active site tyrosine at position 723. The core and C-terminal domains are connected by a poorly conserved, protease-sensitive linker domain (residues approximately 652 to approximately 696) that has been implicated in DNA binding and may influence how long the enzyme remains in the nicked stated. Mutations that confer resistance to the topoisomerase I poison camptothecin are located in the core and C-terminal domains and presumably identify residues important for drug binding.

Nuclear matrix proteins and osteoblast gene expression

The molecular mechanisms that couple osteoblast structure and gene expression are emerging from recent studies on the bone extracellular matrix, integrins, the cytoskeleton, and the nucleoskeleton (nuclear matrix). These proteins form a dynamic structural network, the tissue matrix, that physically links the genes with the substructure of the cell and its substrate. The molecular analog of cell structure is the geometry of the promoter. The degree of supercoiling and bending of promoter DNA can regulate transcriptional activity. Nuclear matrix proteins may render a change in cytoskeletal organization into a bend or twist in the promoter of target genes. We review the role of nuclear matrix proteins in the regulation of gene expression with special emphasis on osseous tissue. Nuclear matrix proteins bind to the osteocalcin and type I collagen promoters in osteoblasts. One such protein is Cbfa1, a recently described transcriptional activator of osteoblast differentiation. Although their mechanisms of action are unknown, some nuclear matrix proteins may act as "architectural" transcription factors, regulating gene expression by bending the promoter and altering the interactions between other trans-acting proteins. The osteoblast nuclear matrix is comprised of cell- and phenotype-specific proteins including proteins common to all cells. Nuclear matrix proteins specific to the osteoblast developmental stage and proteins that distinguish osteosarcoma from the osteoblast have been identified. Recent studies indicating that nuclear matrix proteins mediate bone cell response to parathyroid hormone and vitamin D are discussed.

9-Nitrocamptothecin inhibits tumor recrosis factor-mediated activation of human immunodeficiency virus type 1 and enhances apoptosis in a latently infected T cell clone

Transition from latency to active replication is a crucial stage for the process of human immunodeficiency virus type 1 (HIV-1) infection and life cycle. HIV-1 replication in latently infected cells can be strongly induced by the cytokine tumor necrosis factor alpha (TNF-alpha) and the proliferation-arresting chemical sodium butyrate (NaB). We have investigated the ability of the drug 9-nitrocamptothecin (9NC), a potent cellular topoisomerase I (topo I) inhibitor currently in clinical trials in cancer patients, to regulate HIV-1 replication in latently infected lymphocytic ACH-2 cells on reactivation with either TNF-alpha or NaB. Treatment of ACH-2 cells with 9NC alone resulted in increased levels of viral transcripts, while there was a slight reduction or no change in the levels of host cell transcripts. However, pretreatment of ACH-2 cells with 9NC inhibited TNF-alpha-induced extracellular HIV-1 p24 levels up to approximately 95% and nearly 80% of the cell-associated viral RNAs. The quantitative decrease in viral products was concomitant with a decrease in cellular gene expression and induction of apoptosis in the host cells. 9NC blocked the infected cells at the boundary of the S and G2 phases, resulting in an accelerated apoptosis that was further enhanced with TNF-alpha treatment. Similar results were observed following concurrent exposure to TNF-alpha and 9NC, but 9NC failed to inhibit upregulation of HIV-1 mRNA in ACH-2 cells exposed to TNF-alpha before 9NC treatment. Further, 9NC had no inhibitory effect on NaB-induced apoptosis and upregulation of HIV-1 mRNA expression regardless of whether 9NC and NaB were used concurrently or in various treatment sequences. In uninfected lymphocytic CEM cells derived from a common parental cell line, a slight downregulation of cellular gene expression was detected along with low-level apoptosis. These results demonstrate that 9NC impairs TNF-alpha-induced, but not NaB-induced, HIV-1 activation, and suggest a means of inhibiting active HIV-1 viremia arising as a result of elevated TNF-alpha levels.

Topoisomerase function during replication-independent chromatin assembly in yeast

DNA topoisomerases I and II are the two major nuclear enzymes capable of relieving torsional strain in DNA. Of these enzymes, topoisomerase I plays the dominant role in relieving torsional strain during chromatin assembly in cell extracts from oocytes, eggs, and early embryos. We tested if the topoisomerases are used differentially during chromatin assembly in Saccharomyces cerevisiae by a combined biochemical and pharmacological approach. As measured by plasmid supercoiling, nucleosome deposition is severely impaired in assembly extracts from a yeast mutant with no topoisomerase I and a temperature-sensitive form of topoisomerase II (strain top1-top2). Expression of wild-type topoisomerase II in strain top1-top2 fully restored assembly-driven supercoiling, and assembly was equally efficient in extracts from strains expressing either topoisomerase I or II alone. Supercoiling in top1-top2 extract was rescued by adding back either purified topoisomerase I or II. Using the topoisomerase II poison VP-16, we show that topoisomerase II activity during chromatin assembly is the same in the presence and absence of topoisomerase I. We conclude that both topoisomerases I and II can provide the DNA relaxation activity required for efficient chromatin assembly in mitotically cycling yeast cells.

Detection of human topoisomerase II alpha in cell lines and tissues: characterization of five novel monoclonal antibodies

We report five novel monoclonal antibodies (Ki-S1, Ki-S4, Ki-S6, Ki-S7, and Ki-S8) reactive with a proliferation-related nuclear antigen. In immunoprecipitation and Western blot experiments using crude nuclear extracts, they recognized a protein of 170 kD that, after proteolytic digestion of the immunoprecipitate and sequencing of the resulting peptides, was identified as the alpha-isoform of human topoisomerase II. This was confirmed by testing the antibodies on a highly purified enzyme preparation. Crossreactivity with topoisomerase II beta was ruled out by testing the antibodies on crude extracts from yeast cells expressing the beta-isoform exclusively. The antibodies bind the antigen with different affinities and at different epitopes, apparently located within the carboxyl third of the enzyme. All five antibodies are suitable for archival material after adequate antigen retrieval, thereby enabling retrospective studies. This report illustrates the tissue and subcellular distribution of the antigen through the cell cycle by immunohistochemistry and confocal fluorescence microscopy. The antibodies will be useful tools in further analysis of morphological and functional aspects of topoisomerase II and may serve diagnostic purposes, as well as providing prognostic information in tumor pathology.

Roles of DNA topoisomerases in the regulation of R-loop formation in vitro

We have recently found that stable R-loop formation occurs in vivo and in vitro when a portion of the Escherichia coli rrnB operon is transcribed preferentially in its physiological orientation. Our results also suggested that the formation of such structures was more frequent in topA mutants and was sensitive to the template DNA supercoiling level. In the present report we investigated in greater detail the involvement of DNA topoisomerases in this process. By using an in vitro transcription system with phage RNA polymerases, we found that hypernegative supercoiling of plasmid DNAs in the presence of DNA gyrase is totally abolished by RNase H, suggesting that extensive R-looping occurs during transcription in the presence of DNA gyrase. When RNase A is present, significant hypernegative supercoiling occurs only when the 567-base pair rrnB HindIII fragment is transcribed in its physiological orientation. This result suggests that more stable R-loops are being produced in this orientation. Our results also suggest that DNA gyrase can participate in the process of R-loop elongation. The strong transcription-induced relaxing activity of E. coli DNA topoisomerase I is shown to efficiently counteract the effect of DNA gyrase and thus inhibit extensive R-looping. In addition, we found that an R-looped plasmid DNA is a better substrate for relaxation by E. coli DNA topoisomerase I as compared with a non-R-looped substrate.

Mechanism of topoisomerase II inhibition by staurosporine and other protein kinase inhibitors

Topoisomerase II is an essential enzyme for proliferation of eukaryotic cells. It is also a target for many antineoplastic drugs that promote stabilization of covalent complexes between topoisomerase II and DNA. Topoisomerase II and protein kinases both catalyze the transfer of phosphoester bonds from nucleotides to proteins. This similarity suggests that inhibitors may affect both classes of enzymes. In the present study, we have examined the mechanism of topoisomerase II inhibition by three different classes of protein kinase inhibitors. We report that staurosporine inhibited the catalytic activity of topoisomerase II by blocking the transfer of phosphodiester bonds from DNA to the active tyrosine site, a mechanism of inhibition not previously reported for this enzyme. In contrast, other kinase inhibitors, such as methyl 2,5-dihydroxycinnamate, most likely inactivated topoisomerase II by alkylation of essential amino acids, whereas the mechanism of inhibition of bis-indolylmaleimide possibly involved a direct interaction with DNA.

Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I

Previous biochemical studies have suggested a role for bacterial DNA topoisomerase (TOPO) I in the suppression of R-loop formation during transcription. In this report, we present several pieces of genetic evidence to support a model in which R-loop formation is dynamically regulated during transcription by activities of multiple DNA TOPOs and RNase H. In addition, our results suggest that events leading to the serious growth problems in the absence of DNA TOPO I are linked to R-loop formation. We show that the overexpression of RNase H, an enzyme that degrades the RNA moiety of an R loop, can partially compensate for the absence of DNA TOPO I. We also note that a defect in DNA gyrase can correct several phenotypes associated with a mutation in the rnhA gene, which encodes the major RNase H activity. In addition, we found that a combination of topA and rnhA mutations is lethal.