Formation of catenated molecules by replication of colicin E1 plasmid DNA in cell extracts

The role of ATP-dependent machines in regulating genome topology

All cells must copy and express genes in accord with internal and external cues. The proper timing and response of such events relies on the active control of higher-order genomic organization. Cells use ATP-dependent molecular machines to alter the local and global topology of DNA so as to promote and counteract the persistent effects of transcription and replication. X-ray crystallography and electron microscopy, coupled with biochemical and single molecule methods are continuing to provide a wealth of mechanistic information on how DNA remodeling factors are employed to dynamically shape and organize the genome.

Reprint of "The mechanism of negative DNA supercoiling: a cascade of DNA-induced conformational changes prepares gyrase for strand passage"

DNA topoisomerases inter-convert different DNA topoisomers in the cell. They catalyze the introduction or relaxation of DNA supercoils, as well as catenation and decatenation. Members of the type I topoisomerase family cleave a single strand of their double-stranded DNA substrate, whereas enzymes of the type II family cleave both DNA strands. Bacterial DNA gyrase, a type II topoisomerase, catalyzes the introduction of negative supercoils into DNA in an ATP-dependent reaction. Gyrase is not present in humans, and constitutes an attractive drug target for the treatment of bacterial and parasite infections. DNA supercoiling by gyrase is believed to occur by a strand passage mechanism, in which one segment of the double-stranded DNA substrate is passed through a (transient) break in a second segment. This mechanism requires the coordinated opening and closing of three protein interfaces, so-called gates, to ensure the directionality of strand passage toward negative supercoiling. Single molecule fluorescence resonance energy transfer experiments are ideally suited to investigate conformational changes during the catalytic cycle of DNA topoisomerases. In this review, we summarize the current knowledge on the cascade of DNA- and nucleotide-induced conformational changes in gyrase that lead to strand passage and negative supercoiling of DNA. We discuss how these conformational changes couple ATP hydrolysis to DNA supercoiling in gyrase, and how the common mechanistic principle of coordinated gate opening and closing is modulated to allow for the catalysis of different reactions by different type II topoisomerases.

The mechanism of negative DNA supercoiling: a cascade of DNA-induced conformational changes prepares gyrase for strand passage

DNA topoisomerases inter-convert different DNA topoisomers in the cell. They catalyze the introduction or relaxation of DNA supercoils, as well as catenation and decatenation. Members of the type I topoisomerase family cleave a single strand of their double-stranded DNA substrate, whereas enzymes of the type II family cleave both DNA strands. Bacterial DNA gyrase, a type II topoisomerase, catalyzes the introduction of negative supercoils into DNA in an ATP-dependent reaction. Gyrase is not present in humans, and constitutes an attractive drug target for the treatment of bacterial and parasite infections. DNA supercoiling by gyrase is believed to occur by a strand passage mechanism, in which one segment of the double-stranded DNA substrate is passed through a (transient) break in a second segment. This mechanism requires the coordinated opening and closing of three protein interfaces, so-called gates, to ensure the directionality of strand passage toward negative supercoiling. Single molecule fluorescence resonance energy transfer experiments are ideally suited to investigate conformational changes during the catalytic cycle of DNA topoisomerases. In this review, we summarize the current knowledge on the cascade of DNA- and nucleotide-induced conformational changes in gyrase that lead to strand passage and negative supercoiling of DNA. We discuss how these conformational changes couple ATP hydrolysis to DNA supercoiling in gyrase, and how the common mechanistic principle of coordinated gate opening and closing is modulated to allow for the catalysis of different reactions by different type II topoisomerases.

Bullied no more: when and how DNA shoves proteins around

The predominant protein-centric perspective in protein-DNA-binding studies assumes that the protein drives the interaction. Research focuses on protein structural motifs, electrostatic surfaces and contact potentials, while DNA is often ignored as a passive polymer to be manipulated. Recent studies of DNA topology, the supercoiling, knotting, and linking of the helices, have shown that DNA has the capability to be an active participant in its transactions. DNA topology-induced structural and geometric changes can drive, or at least strongly influence, the interactions between protein and DNA. Deformations of the B-form structure arise from both the considerable elastic energy arising from supercoiling and from the electrostatic energy. Here, we discuss how these energies are harnessed for topology-driven, sequence-specific deformations that can allow DNA to direct its own metabolism.

Mitochondrial DNA polymerase POLIB is essential for minicircle DNA replication in African trypanosomes

The unique mitochondrial DNA of trypanosomes is a catenated network of minicircles and maxicircles called kinetoplast DNA (kDNA). The network is essential for survival, and requires an elaborate topoisomerase-mediated release and reattachment mechanism for minicircle theta structure replication. At least seven DNA polymerases (pols) are involved in kDNA transactions, including three essential proteins related to bacterial DNA pol I (POLIB, POLIC and POLID). How Trypanosoma brucei utilizes multiple DNA pols to complete the topologically complex task of kDNA replication is unknown. To fill this gap in knowledge we investigated the cellular role of POLIB using RNA interference (RNAi). POLIB silencing resulted in growth inhibition and progressive loss of kDNA networks. Additionally, unreplicated covalently closed precursors become the most abundant minicircle replication intermediate as minicircle copy number declines. Leading and lagging strand minicircle progeny similarly declined during POLIB silencing, indicating POLIB had no apparent strand preference. Interestingly, POLIB RNAi led to the accumulation of a novel population of free minicircles that is composed mainly of covalently closed minicircle dimers. Based on these data, we propose that POLIB performs an essential role at the core of the minicircle replication machinery.

Structure of the ColE1 DNA molecule before segregation to daughter molecules

The segregation of daughter DNA molecules at the end stage of replication of plasmid ColE1 was examined. When circular ColE1 DNA replicates in a cell extract at a high KCl concentration (140 mM), a unique class of molecules accumulates. When the molecule is cleaved by a restriction enzyme that cuts the ColE1 DNA at a single site, an X-shaped molecule in which two linear components are held together around the origin of DNA replication is made. For a large fraction of these molecules, the 5' end of the leading strand remains at the origin and the 3' end of the strand is about 30 nucleotides upstream of the origin. The 3' end of the lagging strand is located at the terH site (17 nucleotides upstream of the origin) and the 5' end of the strand is a few hundred nucleotides upstream of the terH site. Thus the parental strands of the molecule intertwine with each other only once. When the KCl concentration is lowered to 70 mM, practically all of these molecules are converted to daughter circular monomers or to catenanes consisting of two singly interlocked circular units.

New topoisomerase essential for chromosome segregation in E. coli

The nucleotide sequence of the parC gene essential for chromosome partition in E. coli was determined. The deduced amino acid sequence was homologous to that of the A subunit of gyrase. We found another new gene coding for about 70 kd protein. The gene was sequenced, and the deduced amino acid sequence revealed that the gene product was homologous to the gyrase B subunit. Mutants of this gene were isolated and showed the typical Par phenotype at nonpermissive temperature; thus the gene was named parE. Enhanced relaxation activity of supercoiled plasmid molecules was detected in the combined crude cell lysates prepared from the ParC and ParE overproducers. A topA mutation defective in topoisomerase I could be compensated by increasing both the parC and the parE gene dosage. It is suggested that the parC and parE genes code for the subunits of a new topoisomerase, named topo IV.

Segregation of relaxed replicated dimers when DNA ligase and DNA polymerase I are limited during oriC-specific DNA replication

An in vitro Escherichia coli oriC-specific DNA replication system was used to investigate the DNA replication pathways of oriC plasmids. When this system was perturbed by the DNA ligase inhibitor nicotinamide mononucleotide (NMN), alterations occurred in the initiation of DNA synthesis and processing of intermediates and DNA products. Addition of high concentrations of NMN soon after initiation resulted in the accumulation of open circular dimers (OC-OC). These dimers were decatenated to open circular monomers (form II or OC), which were then processed to closed circular supercoiled monomers (form I or CC) products. After a delay, limited ligation of the interlinked dimers (OC-OC to CC-OC and CC-CC) also occurred. Similar results were obtained with replication protein extracts from polA mutants. The presence of NMN before any initiation events took place prolonged the existence of nicked template DNA and promoted, without a lag period, limited incorporation into form II molecules. This DNA synthesis was nonspecific with respect to oriC, as judged by DnaA protein dependence, and presumably occurred at nicks in the template DNA. These results are consistent with oriC-specific initiation requiring closed supercoiled molecules dependent on DNA ligase activity. The results also show that decatenation of dimers occurs readily on nicked dimer and represents an efficient pathway for processing replication intermediates in vitro.

Multiple mechanisms for initiation of ColE1 DNA replication: DNA synthesis in the presence and absence of ribonuclease H

A transcript (RNA II) of plasmid ColE1 that hybridizes with the template DNA is cleaved by RNAase H and used as a primer by DNA polymerase I. However, the plasmid can replicate in bacteria lacking both enzymes, apparently using a different mechanism of initiation of replication. Here we report in vivo and in vitro studies on initiation of DNA replication in the presence or absence of either or both enzymes. Hybridization of RNA II with the template DNA is always required for initiation. Hybridized RNA II is cleaved by RNAase H to form a primer or used as a primer without cleavage by RNAase H. Hybridization also creates a single-stranded region on the nontranscribed strand that can serve as a template for synthesis of the lagging strand in a reaction that does not require DNA polymerase I. Lagging strand synthesis terminates 17 nucleotides upstream of the normal replication origin, forcing unidirectional replication.

E. coli minichromosome replication in vitro and in vivo: comparative analyses of replication intermediates

The process of replication of Escherichia coli minichromosomes was examined by following the intermediates formed in vitro and in vivo. Replication initiated on a supercoiled closed circular (CC) monomer, proceeded rapidly to a late but incomplete stage in polymerization (the LC form) in both systems, passed more slowly through a series of open and closed circular catenated dimers with varying extents of intertwining between the monomer units, and then yielded, after decatenation, the supercoiled CC monomer. The replication patterns of two different minichromosomes were similar, although the LC form and the multiply intertwined dimers were much more evident in the smaller pAL4 than in pAL2. The same basic replication scheme was seen in vitro and in vivo but completion of polymerization and processing of the dimers were slower in vitro. Some radioactivity was detected in OC monomer early during replication, consistent with occasional decatenation of LC structures to produce OC molecules which then completed replication to form CC molecules. However, progression to CC catenated dimers prior to formation of CC monomers represented the major replication pathway.

Biochemical topology: applications to DNA recombination and replication

Processes of DNA rearrangement such as recombination or replication frequently have as products different subsets of the limitless number of distinguishable catenanes or knots. The use of gel electrophoresis and electron microscopy for analysis of these topological isomers has made it possible to deduce physical and geometric features of DNA structure and reaction mechanisms that are otherwise experimentally inaccessible. Quantitative as well as qualitative characterization is possible for any pathway in which the fate of a circular DNA can be followed. The history, theory, and techniques are reviewed and illustrative examples from recent studies are presented.

A simple topological method for describing stereoisomers of DNA catenanes and knots

Although linking number is an effective topological invariant for describing supercoiled DNA, it is inadequate for the additional interwinding in catenated or knotted DNA. We explain how the two-bridge theory of Schubert provides a powerful yet simple method for analyzing these forms by associating them with two integral invariants, alpha and beta, that measure their geometric complexity. These integers can either be determined graphically or computed with the aid of standard tables, and they allow tabulation of all possible stereoisomers of a given knot or catenane . A complete classification can then be made via a simple theorem. Stereoisomers of representative knots and catenanes are tabulated for easy reference. There are four stereoisomers of regularly interlocked catenanes that we designate right-handed parallel, right-handed antiparallel, left-handed parallel, and left-handed antiparallel according to the helical intertwining of the rings. The biological processes that form catenanes --replication, recombination, and topoisomerase action--predict distinctly different isomers.

DNA supercoiling in gyrase mutants

Nucleoids isolated from Escherichia coli strains carrying temperature-sensitive gyrA or gyrB mutations were examined by sedimentation in ethidium bromide-containing sucrose density gradients. A shift to restrictive temperature resulted in nucleoid DNA relaxation in all of the mutant strains. Three of these mutants exhibited reversible nucleoid relaxation: when cultures incubated at restrictive temperature were cooled to 0 degree C over a 4- to 5-min period, supercoiling returned to levels observed with cells grown at permissive temperature. Incubation of these three mutants at restrictive temperature also caused nucleoid sedimentation rates to increase by about 50%.

Origin, transmission, and segregation of mitochondrial DNA dimers in mouse hybrid and cybrid cell lines

Hybrid and cybrid progeny lines were constructed from mouse LA9 cells which contain almost exclusively mtDNA monomers and LDTK cells which contain only unicircular mtDNA dimers. The proportion of mtDNA monomers and dimers in the progeny lines was determined both as a function of the number of population doublings since fusion and of selection for expression of a mutant phenotype encoded on one of the parental mtDNAs. There was no preferential segregation of either parental mtDNA in early-passage progeny lines, irrespective of whether or not selection was applied. In marked contrast, there was an accumulation of mtDNA dimers in late-passage progeny lines maintained in the absence of selection for a drug-resistance marker carried by the parental mtDNA monomers. When such selection was applied, roughly equal mass proportions of both parental mtDNAs were maintained in most lines. However, in several progeny lines, new types of mtDNA dimers carrying the selected resistance marker initially encoded in the monomeric mtDNA were present. In some of these latter lines, the new mtDNA dimers apparently arose from LA9 monomers, possibly by recombination. It is hypothesized that mammalian mitochondria normally have a recombination system which maintains low steady-state levels of mtDNA unicircular oligomers by preferentially resolving dimers into two monomers.

Bacterial chromosome segregation: evidence for DNA gyrase involvement in decatenation

Nucleoids isolated from a temperature-sensitive gyrB mutant of E. coli, incubated at restrictive temperatures, exhibit increased sedimentation rates and an abnormal doublet or dumbbell-shaped morphology. Shifting cells from restrictive to permissive temperature prior to nucleoid isolation leads to decreases in the percentage of doublet nucleoids and in nucleoid sedimentation rates. When nucleoids isolated from mutant cells exposed to restrictive temperature are incubated with purified gyrase, the percentage of doublet nucleoids decreases as the total number of nucleoids increases. These results, together with the demonstrated ability of gyrase to decatenate small circular DNA molecules in vitro, suggest that gyrase participates in bacterial chromosome segregation through its decatenating activity.

Antagonism of the B subunit of DNA gyrase eliminates plasmids pBR322 and pMG110 from Escherichia coli

The constructed plasmid pBR322 and the native plasmid pMG110 were eliminated (cured) from growing Escherichia coli cells by the antagonism of the B subunit of the bacterial enzyme DNA gyrase. The antagonism may be by the growth of cells (i) at semipermissive temperatures in a bacterial mutant containing a thermolabile gyrase B subunit or (ii) at semipermissive concentrations of coumermycin A1, an antibiotic that specifically inhibits the B subunit of DNA gyrase. The kinetics of plasmid elimination indicate that plasmid loss occurs too rapidly to be explained solely by the faster growth of that plasmid-free bacteria and, therefore, represents interference with plasmid maintenance.

Kinetics of minichromosome replication in Escherichia coli B/r

Replication control of the minichromosome pAL2 was found to differ from that of the chromosome in synchronously dividing populations of Escherichia coli B/r. Initiation of minichromosome replication took place at an increasing rate throughout synchronous growth. No coupling to initiation of chromosome replication was detected. Minichromosome replication was further examined in a dnaA5(Ts) temperature-sensitive initiation mutant. When cultures held at nonpermissive temperature (41 degrees C) for 60 min were shifted to permissive temperature (25 degrees C), initiation of both pAL2 and chromosome replication ensued in two waves spaced 25 to 35 min apart. Evidence is presented that minichromosomes terminate replication by passing slowly through a series of dimeric intermediate forms before reaching the closed circular monomeric form. The consequence of this slow passage as a rate-limiting step in the initiation reaction is discussed.

Maintenance and genetic stability of vector plasmids pBR322 and pBR325 in Escherichia coli K12 strains grown in a chemostat

The maintenance and genetic stability of the vector plasmids pBR322 and pBR325 in two genetically different Escherichia coli hosts were studied during chemostat cultivation with glucose and ammonium chloride limitation and at two different dilution rates. The plasmid pBR322 was stably maintained under all growth conditions tested. However pBR325 segregated from both hosts preferentially during glucose limitation and at low dilution rate. In addition to this general segregation process a separate loss of tetracycline resistance was observed. The remaining plasmid conferred resistance to ampicillin and chloramphenicol only, without any remarkable alteration of its molecular weight. Cultivation conditions in the chemostat were found that allowed the stable genetic inheritance of both plasmids in the hosts studied.

Selection and characterization of ColE1 plasmid mutants that exhibit altered stability and replication

This report describes a method for isolating mutants of plasmid ColE1 that exhibit unstable maintenance and altered replication characteristics. It also describes the initial characterization of four mutants isolated by that method. A chimeric plasmid, pHSG124, containing a ColE1 derivative and a temperature-sensitive replication derivative of pSC101 was mutagenized in vitro, using hydroxylamine. By adjusting the growth conditions of transformants containing the mutagenized chimeric deoxyribonucleic acid, it was possible to rapidly screen colonies and identify those that had a high probability of carrying ColE1 mutants that exhibit unstable maintenance. Of those mutants, some exhibited altered copy number or accumulated catenated structures. Evidence is presented which suggests that the mutations in three of the mutants are probably located in the HaeII A fragment of ColE1.

Maintenance of some ColE1-type plasmids in chemostat culture

When cells carrying the plasmids RP1, pDS4101 (a ColK derivative) or pDS1109 (a ColE1 derivative) were maintained in chemostat culture in the absence of antibiotic selection, plasmid-free segregants were not detected after 120 generations of nutrient-limited growth. By contrast, plasmid-free segregants of pMB9- and pBR322-containing cells arose after approximately 30 generations, irrespective of the host genetic background. However, even though pDS1109 was maintained its copy-number fell five-fold during 80 generations of limited growth. It is suggested that loss of pBR322 occurs following a similar copy-number decrease which results in defective segregation of the plasmid to daughter host cells. This defective segregation was not complemented in trans by either RP1 or pDS4101.

Formation and resolution of DNA catenanes by DNA gyrase

We have discovered that DNA gyrase interlocks duplex DNA circles to form catenanes and resolves catenanes into component monomers. The reactions were inhibited by novobiocin and oxolinic acid and required ATP, Mg++ and spermidine. DNA sequence homology is not involved in catenation, since hybrid catenanes were formed efficiently between supercoiled phi X174 and Col E1 DNA. Strikingly different results were obtained with native and relaxed Col E1 DNA substrates. Up to 50-60% of input native DNA was converted into oligomeric catenanes, predominantly dimers and trimers. Relaxed substrates were instead converted into vast interlocked networks and were occasionally knotted. Optimal catenation occurred only in the narrow range of 20-35 mM KCl; increased ionic strength blocked catenation completely but activated the back reaction of decatenation. Gyrase resolved both the oligomeric catenanes and interlocked networks it produced, as well as naturally occurring catenanes. These results imply that the mechanism of gyrase involves a transient double-strand break and passage of a DNA segment through the resulting gap. Gyrase is representative of a general class of enzymes, found in both procaryotic and eucaryotic cells, that facilitate diffusion of duplex DNA segments through each other and may thereby solve topological problems arising from the replication, recombination and condensation of DNA.

DNA gyrase action involves the introduction of transient double-strand breaks into DNA

DNA gyrase from Escherichia coli, in the presence of ATP, can both separate catenated DNA circles and unknot knotted DNA. Both these reactions require passage of a DNA segment through a transient double-strand break in DNA. Evidence that transient double-strand breaks are also involved in the supercoiling and relaxing activities of DNA gyrase is derived from experiments showing that the linking number of circular DNA is changed in steps of two. A mechanism is proposed for the action of the enzyme.

Nucleotide sequence of the region required for maintenance of colicin E1 plasmid

Plasmids carrying various portions of colicin E1 plasmid (ColE1) DNA have been isolated in an attempt to determine the regions of ColE1 DNA which are required for maintenance of the plasmid in bacteria. To construct the plasmids, the DNA of a ColE1 derivative that contains a gene which controls ampicillin resistance was cleaved by the restriction endonuclease HaeII. The digestion products were joined by T4 DNA ligase and then used to transform bacteria to ampicillin resistance. The plasmid derivatives obtained in this way were always composed of certain HaeII segments. These contain approximately 10% of the ColE1 genome and include the origin of replication of ColE1. We presume that the region of ColE1 which is common to all these derivatives is required for maintenance of the plasmid. After a description of these results, the nucleotide sequence of this region is presented, and possible roles of the region in plasmid replication and maintenance are discussed.