DNA topoisomerase I controls the kinetics of promoter activation and DNA topology in Saccharomyces cerevisiae

Inactivation of the nonessential TOP1 gene, which codes for Saccharomyces cerevisiae DNA topoisomerase I, affects the rate of transcription starting at the ADH2 promoter. For both the chromosomal gene and the plasmid-borne promoter, mRNA accumulation is kinetically favored in the mutant relative to a wild-type isogenic strain. The addition of ethanol causes in wild-type yeast strains a substantial increase in linking number both on the ADH2-containing plasmid and on the resident 2 microns DNA. Evidence has been obtained that such an in vivo increase in linking number depends on (i) the activity of DNA topoisomerase I and of no other enzyme and (ii) ethanol addition, not on the release from glucose repression. A direct cause-effect relationship between the change in supercoiling and alteration of transcription cannot be defined. However, the hypothesis that a metabolism-induced modification of DNA topology in a eukaryotic cell plays a role in regulating gene expression is discussed.

DNA tridimensional context affects the reactivity of eukaryotic DNA topoisomerase I

Cleavage sites of eukaryotic DNA topoisomerase I on curved linear DNAs are clustered, map on the same side of the curve (the external one) and their distribution has the same period as the helical repeat, as observed on curved DNA tracts of Crithidia fasciculata, of Saccharomyces cerevisiae ARS1, of pT7CAT and on synthetic DNAs. The effects of the tridimensional context on both the cleavage and the topoisomerization reactions of DNA topoisomerase I were determined using serial DNA constructs made with inserts in which synthetic curves lie in a plane and in which the orientation of the planes of curvature is shifted by 72 degrees, 144 degrees, 216 degrees, 288 degrees and 360 degrees. The insertion of a curve markedly changes the reaction properties of the surrounding sequences.

The conformation of constitutive DNA interaction sites for eukaryotic DNA topoisomerase I on intrinsically curved DNAs

The analysis of the sites which are cleaved constitutively and preferentially by eukaryotic DNA topoisomerase I on two intrinsically curved DNAs reveals the conformational features that provoke the cleavage reaction on the curve-inducing sequence elements in the absence of supercoiling. This analysis is based on the observation (Caserta et al. (1989) Nucleic Acids Res. 17, 8521-8532 and (1990) Biochemistry 29, 8152-8157) that the reaction of eukaryotic DNA topoisomerase I occurs on two types of DNA sites: sites S (Supercoiled induced) and sites C (Constitutive, whose presence is topology-independent). We report that sites C are abundant on the intrinsically curved DNAs analyzed. The DNAs studied were two intrinsically curved segments of different origin: the Crithidia fasciculata kinetoplast DNA and the bent-containing domain B of the Saccharomyces cerevisiae ARS1. On these DNA segments DNA topoisomerase I cleaves at the junctions between the poly(A) tracts and mixed-sequence DNA. Analysis of the conformation of the double helix around the cleavage sites has revealed that the reaction occurs in correspondence of a defined DNA conformational motif. This motif is described by the set of Eulerian angular values that define the axial path of DNA (helical twist, deflection angle, direction) and of the orthogonal components of wedge (roll and tilt).

The over-expression of P-glycoprotein in K-562 and DAUDI cells, is associated with a high susceptibility to NK and LAK cells

We evaluated the susceptibility to natural killer (NK) or lymphokine activated killer (LAK) cell-mediated cytolysis of two pairs of drug sensitive/resistant tumor cell lines which were extensively characterized at phenotypic and genotypic level. In the DAUDI cell system, the acquired capability of tumor cell variants to grow in the presence of a relatively high concentration of vinblastine (VBL) is associated with a marked increase to NK and LAK susceptibility. In contrast in the K-562 cell system, no correlation between drug-resistance, P-glycoprotein expression and susceptibility to NK or LAK activity seems to occur.

Expression of lymphocyte homing receptor gene is lost in multi-drug-resistant variants of human T-lymphoblastoid CCRF-CEM cells

The 2.2-kb human cDNA clone PBL32, encoding for the lymphocyte homing receptor (LHR) was used to study the expression of this determinant in multi-drug-resistant (MDR) variants of human T-lymphoblastoid CCRF-CEM (CEM) cells. LHR is significantly associated with the drug-sensitive phenotype, its expression being progressively and quantitatively reduced in MDR variants of CEM cells according to the extent of drug resistance.

Regulation of the function of eukaryotic DNA topoisomerase I: analysis of the binding step and of the catalytic constants of topoisomerization as a function of DNA topology

It was previously observed that two steps of the reaction of eukaryotic DNA topoisomerase I (topoisomerization and cleavage) depend upon the conformation of the DNA substrate: in both instances the supercoiled form is a more efficient substrate than the relaxed one. This paper reports the analysis of two other steps of the reaction: the binding of DNA topoisomerase I to DNA and the catalytic constants (Kcs) of topoisomerization as a function of the topology of the substrate. Binding. Competition assays show that supercoiled DNA binds the enzyme with even slower kinetics than the relaxed form. Therefore, the preferential topoisomerization of supercoiled DNA is not due to the binding step. Additional evidence that the rate-limiting step of the topoisomerization reaction is not the binding of the enzyme to DNA is provided by the fact that the kinetics of relaxation is first order. Catalysis. The Kcs of the topoisomerization reaction have been calculated and it was shown that they do not vary as a function of the topology of the substrate or of its size. Taken together, the data on binding, cleavage, topoisomerization, and Kcs suggest that the preferential topoisomerization of torsionally strained DNA is due to the higher availability, on this topological form, of DNA sites that allow the onset of the reaction.

In vitro preferential topoisomerization of bent DNA

The steps of the topoisomerization reaction by calf thymus DNA topoisomerase I on a DNA domain containing an intrinsically bent DNA sequence have been analyzed. High preferentiality of binding, cleavage and topoisomerization on the bent segment relative to the rest of the DNA domain was observed. These studies show the importance of the local DNA conformation in the reaction of eukaryotic DNA topoisomerase I and the interest of the use of this enzyme as a tool for the analysis of DNA conformation and DNA dynamics.

Regulation of the function of eukaryotic DNA topoisomerase I: topological conditions for inactivity

The effects of supercoiling on the cleavage reaction by eukaryotic DNA topoisomerases I (wheat germ, chicken erythrocyte, and calf thymus) have been analyzed on DNA fragments (0.96 and 2.3 kilobases) encompassing an immunoglobulin kappa light-chain promoter. In one topological condition of the substrate, the absolutely relaxed state, cleavage was found to be impeded. This finding defines the topology-dependent step of the eukaryotic DNA topoisomerase I reaction and shows that for the cleavage reaction topology is more critical than sequence effects. These findings suggest a simple model for the regulation of the DNA topoisomerase I reaction based on topological factors, which may explain the regulatory function of the enzyme in in vivo eukaryotic transcription.

Cytosine methylation as an effector of right-handed to left-handed DNA structural transitions

Cytosine methylation has energetic and structural influences on left-handed Z-DNA formation in supercoiled plasmids. The restriction and modification enzymes from Haemophilus haemolyticus (HhaI and M.HhaI) provide a system to locate and analyze small segments of Z-DNA in large supercoiled plasmids. An approach is outlined that uses M.HhaI as an in vivo conformational probe for the detection of unusual DNA structures in a living cell. Also, characteristic features of the M.HhaI gene and protein are discussed.

DNA conformational variations in the in vitro torsionally strained Ig kappa light chain gene localize on consensus sequences

We have analyzed the localization and the dependence upon superhelical density of the DNA sites which modify their conformation under torsional strain in a mouse Ig L kappa gene. The conformational variations occur on DNA sites which have been defined as protein interaction sites and consensus sequence motifs: the 5'-upstream regulatory decanucleotides, the TATA sequence, the consensus heptanucleotides of the J recombinational sequences.

Eukaryotic DNA topoisomerase I reaction is topology dependent

The effects of supercoiling on the topoisomerization reaction by eukaryotic DNA topoisomerases I have been analyzed. The systems used were: DNA topoisomerase I from wheat germ, chicken erythrocyte and calf thymus on a 2.3 kb DNA fragment which encompasses the immunoglobulin kappa-light chain (L kappa) promoter of the mouse plasmacytoma MPC11; S. cerevisiae DNA topoisomerase I on a 2.2 kb DNA fragment from the same organism which encompasses the regulatory and the coding region of the ADH II gene; wheat germ DNA topoisomerase I on the plasmid pUC18. It was found in every system that lack of torsional stress prevents topoisomerization of the substrate. A simple regulatory model of DNA topoisomerase I function, based on topological considerations, is presented.

Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase

A 1476-base pair DNA fragment from Haemophilus haemolyticus containing the HhaI methyltransferase gene was isolated from a cell library and cloned into pBR322. The nucleotide sequence of this fragment was determined. The structural gene is 981 nucleotides in length coding for a protein of 327 amino acids (Mr 37,000). The translational start signal (ATG) is preceded by the putative ribosome-binding site (TAAG). Recombinant plasmids containing the 1476-basepair fragment are completely methylated when isolated from Escherichia coli, as judged by their insusceptibility to the HhaI restriction endonuclease. However, the presence of an active HhaI methylase gene in certain E. coli strains results in a very poor yield of transformants and/or in vivo-originated deletions due to the Rg1 functions of these hosts. The in vivo transcription initiation sites have been identified by S1 protection and primer-extension experiments using specific probes with total RNA prepared from E. coli cells (HB101 or RR1) which tolerate the expression of MHhaI.

Activation of in vitro transcription and topology of closed DNA domains

Activation of in vitro transcription of otherwise inert DNA sequences by purified yeast RNA polymerase II has been observed following the introduction in closed DNA domains of fragments of various origin. This enhancer-like effect on the in vitro transcriptional capacity is only detected in negatively supercoiled DNA domains and is characterized for each chimaeric plasmid by the superhelical density (- sigma) at which a sharp transition toward activation takes place. We have analyzed the topological state (as defined by localization and evaluation of the relative occurrence of secondary structures sensitive to S1 endonuclease) of the activated closed domains as a function of the conditions that determine the transcriptional enhancer effect, i.e. superhelical density, size, and nature of the components of the domains. We observe that variations in transcriptional capacity coincide with a defined pattern of secondary structures. These observations support a cause-effect relation between topology and regulation of transcription.

Transitions in topological organization of supercoiled DNA domains as a potential regulatory mechanism

We present an analysis of the influence of DNA superhelicity on the topology of chimeric plasmids. A correlation is found between topological variations and in vivo/in vitro functions. Data refer to the topological transitions observed in function of variations of the superhelical density in the three closed DNA domains that represent the three extreme examples, from the point of view of the topological organization, among many chimeric systems analyzed. The plasmids studied are ADR2-BS-pBR322 (the vector pBR322 + the yeast gene ADR2), ADR3-5c-yRp7 (containing yeast TRP1, a constitutive mutant of yeast ADR2, a fragment of 5 kilobases of unanalyzed chromosomal DNA and the vector pBR322), and p31 (pBR322 + a yeast DNA fragment encompassing the right moiety of the Ty1 element and its in vivo promoter). In the model systems analyzed, the topological transitions observed in the eukaryotic sequences (relevant in one case for activation of selective in vitro transcription (Ty), in another (ADR2) for the in vivo expression) take place in the range of superhelical densities predicted on theoretical ground (Vologodskii, A. V., Lukashin, A. V. Anshelevich, V. V. & Frank-Kamenetskii, M. D. (1979) Nucleic Acids Res. 6, 967-982).

Topological modifications and template activation are induced in chimaeric plasmids by inserted sequences

The effect of the insertion of foreign genes or gene systems in closed DNA domains has been investigated in vitro in purified systems. We observe that in chimaeric plasmids two apparently independent classes of modifications, (1) functional and (2) topological, do take place in defined instances. (1) Among the screened yeast gene systems, examples have been found of DNA sequences that upon insertion cause activation of in vitro transcription of distant genes. (2) Foreign DNA sequences may lead to new topological features of the harbouring plasmids; it is shown that more than one S1-sensitive secondary structure may be contemporaneously present on the same chimaeric plasmid. DNA superhelicity is a prerequisite of these modifications. The two classes of effects (1) functional and (2) topological are not a priori directly related one to the other but appear to be two independent consequences of the same cause: the insertion of foreign DNA sequences into closed DNA domains. These observations suggest a regulatory model of gene expression based on alternative topologies of closed DNA domains.

In vitro transcription by purified yeast RNA polymerase II. Coarse promoter mapping on homologous cloned genes

Clones of the yeast Tyl element and 2 microns plasmid have been selectively transcribed in vitro by partially or completely purified yeast RNA polymerase II. Electrophoretic analysis of whole and restricted ternary transcription complexes allows the localization of the in vitro actively transcribed regions of the analyzed genes. The DNA regions that actively promote in vitro transcription correspond to the nucleotide sequence that in the Tyl element encompasses the in vivo transcription initiation sites and that in the 2 micrometer plasmid encompasses the starting codons of two oppositely oriented potential protein coding frames. The transcription assay that we describe herein may be applied to analyze rapidly the in vitro transcription of clones genes, to localize transcription initiation sites on supercoiled templates and to evaluate the differential in vitro promoter strength in RNA polymerase II served genes. Data obtained with RNA polymerase II at two different stages of purification are presented in parallel. Studies with a completely purified enzyme should certainly be preferred although the use of a partially purified RNA polymerase II may be convenient and may reveal factors which affect specificity.