Okazaki Pieces Research Articles

Efficient in vitro replication of double-stranded DNA templates by a purified T4 bacteriophage replication system.

A wide variety of double-stranded DNA templates are replicated extensively in an in vitro DNA replication system containing the purified proteins specified by seven T4 bacteriophage DNA replication genes (32, 41, 43, 44, 62, 45, and 61). In favorable conditions, this multiprotein system catalyzes the synthesis of several copies of the input DNA template in a 30- to 60-min incubation. The replication forks produced in vitro move in a highly processive fashion, at approximately the in vivo rate of 500 nucleotides per s. The DNA synthesized on the lagging side of the in vitro replication fork is made discontinuously, as it is in vivo, giving rise to "Okazaki pieces" averaging some 10,000 nucleotides in length; in contrast, DNA is polymerized in a continuous manner on the leading side of the in vitro fork. Although the mechanism by which the seven-protein in vitro DNA replication system propagates replication forks closely resembles the in vivo mechanism, it lacks the capacity to remove RNA primers, to reseal Okazaki pieces, and to initiate replication forks at defined DNA origins; supplementation of the system with additional T4-specific replication proteins will be required to facilitate these latter three functions.

RNA priming of DNA replication by bacteriophage T4 proteins.

Bacteriophage T4 DNA replication proteins have been shown previously to require ribonucleoside triphosphates to initiator new DNA chains on unprimed single-stranded DNA templates in vitro. This DNA synthesis requires a protein controlled by T4 gene 61, as well as the T4 gene 41, 43 (DNA polymerase), 44, 45, and 62 proteins, and is stimulated by the gene 32 (helix-destabilizing) protein. In this paper, the nature of the RNA primers involved in DNA synthesis by the T4 proteins has been determined, using phi X174 and f1 DNA as model templates. The T4 41 and "61" proteins synthesize pentanucleotides with the sequence pppA-C(N)3 where N in positions 3 and 4 can be G, U, C, or A. The same group of sequences is found in the RNA at the 5' terminus of the phi X174 DNA product made by the seven T4 proteins. The DNA product chains begin at multiple discrete positions on the phi X174 DNA template. The characteristics of the T4 41 and "61" protein priming reaction are thus appropriate for a reaction required to initiate the synthesis of discontinuous "Okazaki" pieces on the lagging strand during the replication of duplex DNA.

Restoration of ligase activity in E. coli K12 lig ts7 strain by bacteriophage Mu and cloning of a DNA fragment harbouring the Mu 'lig' gene.

Restoration of ligase activity has been observed in E. coli K12 ligts7 strain lysogenic for Mu, in presence as well in absence of lysogenic immunity. This restoration consist in phenotypic reversal of temperature sensitivity of E. coli ligts7 which also regain the ability to sustain the complete growth cycle of T4 lig-phages. It is possible to put under the control of the gal operon the expression of the viral gene responsible for the restoration effect. This new gene of Mu has been named 'lig'. A 5 kb fragment responsible for the reported effects and localized between genes gam and lys of Mu genome has been cloned in pBR322. This recombinant plasmid used for transforming ligts7 strain restores in it normal behaviour for ligation of Okazaki pieces.

Deoxyribonucleic acid synthesis in isolated nuclei from baby-hamster kidney cells (BHK-21/C13). Characterization of the system

A comparative study of some commonly employed laboratory procedures for studying DNA synthesis in isolated nuclei was carried out. Nuclei isolated from baby-hamster kidney (BHK-21/C13) cells synthesize DNA for 30-60min at 37 degrees C in a reaction requiring uni- and bi-valent cations, ATP and all four deoxyribonucleoside 5'-triphosphates. The addition of either ribonucleotides or cytosol from S-phase cells had no effect, but DNA synthesis was stimulated by some dextrans (mol.wt. 5x10(6)). The extent of synthesis was influenced by apparently minor variations in experimental conditions. For example, DNA synthesis by nuclei in Tris/HCl, pH7.5, was only 50% of that observed in Hepes/NaOH, pH7.5; the presence of detergents Triton X-100, Triton N-101, Nonidet P-40, Brij 58 and Tween 80 in the incubation medium altered the amount of synthesis to different extents. Although most detergents inhibited synthesis, a stimulation occurred with Tween 80 (150% of controls). These effects were reversed on washing the nuclei, except that of Brij 58, which inhibited DNA synthesis by 90-95% irreversibly. Anomalous sucrose-density-gradient sedimentation behaviour of the DNA, and of precursor [(3)H]-dTTP, was observed when nuclei were lysed with solutions of sodium dodecyl sulphate/Mg(2+) or with Sarkosyl/Mg(2+), but consistent results, showing that the DNA synthesized in vitro sedimented exclusively at about 4S, were obtained when nuclei were lysed with sodium dodecyl sulphate (without Mg(2+))/EDTA, digested with proteinase K and heated at 100 degrees C with 11% (v/v) formaldehyde to prevent macromolecular association. These results, coupled with density-labelling studies with bromodeoxyuridine and CsCl-density-gradient analysis, showed that DNA synthesis in these nuclei was replicative and was restricted to a covalent extension of Okazaki pieces previously initiated in vivo. No new initiations were observed, and the DNA was not ligated into larger molecules. The cessation of DNA synthesis after about 60 min was due to the complete utilization of available primer/template DNA.

Discontinuous duplication of both strands of virus 2C DNA.

When Bacillus subtilis infected with virus 2C was labeled with short pulses of tritiated uracil (a specific precursor of the hydroxymethyluracil replacing thymine in 2C chromosome) and the cell lysate was fractionated in alkaline sucrose gradients, most of the radioactivity was found within a lowmolecular-weight peak of DNA (“Okazaki pieces”) of about 2×106 daltons. After longer pulses, segments of large size and full strands were the main labeled products. A shift from low to high-molecular-weight nascent DNA took place slowly during the eclipse phase, and rapidly during the maturation phase. This suggested a lagging of the ligase behind the polymerase at early stages. During the entire replication cycle, pulse-labeled DNA was present within the replication fork in its native form with no involvement of proteins. Furthermore, the amount of lowmolecular-weight pulse-labeled DNA hybridizing with the L strand was higher than that annealing with the H strand. To explain this finding it is suggested that the polymerization or the ligation of small segments is faster for one strand than for the other. Finally, the DNA fraction which is resistant to single-strand specific nuclease was about 10% when alkali-denatured Okazaki pieces were neutralized at 4C and was increased about five-fold upon selfannealing. It is concluded that both strands of 2C DNA duplicate in a discontinuous fashion through the formation of Okazaki pieces, which are held by hydrogen bonds initially and subsequently by phosphodiester linkages. It is proposed also that ligase action is faster for the L strand than for the H strand, and that this phenomenon might be related to both the polarity of chain growth and the asymmetry of transcription of 2C chromosome.

Formation of Okazaki pieces at the Escherichia coli replication fork in vitro.

Okazaki's model of discontinuous DNA synthesis, supported by the discovery of nascent DNA fragments at the replication fork (Okazaki pieces), provided a solution to the problem of how antiparallel DNA strands could be simultaneously replicated (Okazaki et al. 1969). Since Okazaki's initial observations, many investigators have shown that in a wide variety of biological systems nascent DNA at the replication fork is found in the form of Okazaki pieces which must be sealed to give normal-length mature DNA.

A Partially Single-stranded Intermediate Occuring during Synthesis of Nuclear DNA in Chlorella

Summary Pulse labelling of Chlorella DNA by incubation with uridine or guanosine resulted in labelled molecules with a higher buoyant density than the bulk of nuclear DNA. No incorporation into chloroplast DNA could be observed. The label could be chased into mature nuclear DNA indicating that the labelled molecules represent an intermediate in the synthesis of nuclear DNA. The labelled molecules have a sedimentation coefficient of less than 7S, smaller than procaryotic Okazaki pieces. In contrast to these, they do not contain RNA segments. The observed density difference is not due to posterior methylation of the labelled intermediate molecules. Two factors contribute to their high density: The labelled intermediate molecules contain single-stranded regions, and the precursors uridine and guanosine preferentially enter (GC)-rich portions of the DNA.

Map position of the replication terminus on the Escherichia coli chromosome

The directions of replication of several prophages integrated with a known orientation in the vicinity of the terminus (tre) of chromosome replication (trp::Mu, min 27; lambda rev integrated within rac, min 31, man::Mu, min 35), have been established by determining the molecular polarity of Okazaki pieces specific to these prophages. The results obtained strongly suggest that the site tre is located between rac and man, an otherwise genetically silent region.

Actinomycin D inhibits initiation of DNA replication in mammalian cells.

Mammalian (Chinese hamster ovary) cells were synchronized in the division cycle and blocked at the beginning of S phase with fluorodeoxyuridine. Traces of thymidine in the medium allowed cells to enter S phase and initiate DNA replication at some origins. For many hours after the traces of thymidine were depleted new sites for DNA replication accumulated in a small fraction of the DNA. However, these potential origins became active in bidirectional replication only when cells were released by adding [3H]thymidine to the medium. Lysis at 37 degrees C released most of the pulse-labeled DNA as linear double-stranded segments larger than Okazaki fragments and smaller than the unreplicated parental DNA. Release of the newly replicated DNA involves breakage of the template chains at or near each fork. The size of the fragments increased linearly with time of pulse labeling, but the efficiency of their release decreased. The excision could be prevented by lysis at 0 degrees C. When cells were treated with actinomycin D for 3--5 min before release, the new origins failed to function, but chain growth continued from those sites at which initiation had taken place before depletion of thymidine. We interpret these results to indicate that initiation at origins requires an actinomycin D-sensitive step, presumably RNA transcription, while chain elongation, which involves the formation of Okazaki pieces, is relatively insensitive to actinomycin D during growth over long intervals.

Simian Virus 40 DNA Replication in Isolated Replicating Viral Chromosomes

Three subnuclear systems capable of continuing many aspects of simian virus 40 (SV40) DNA replication were characterized in an effort to define the minimum requirements for "normal" DNA replication in vitro. Nuclear extracts, prepared by incubating nuclei isolated from SV40-infected CV-1 cells in a hypotonic buffer to release both SV40 replicating and mature chromosomes, were either centrifuged to separate the total SV40 nucleoprotein complexes from the soluble nucleosol or fractionated on sucrose gradients to provide purified SV40 replicating chromosomes. With nuclear extracts, CV-1 cell cytosol stimulated total DNA synthesis, elongation of nascent DNA chains, maturation and joining of "Okazaki pieces," and the conversion of replicating viral DNA into covalently closed, superhelical DNA. Nucleoprotein complexes responded similarly, but frequently the response was reduced by 10 to 30%. In contrast, isolated replicating chromosomes in the presence of cytosol appeared only to complete and join Okazaki pieces already present on the template; without cytosol, Okazaki pieces incorporated alpha-(32)P-labeled deoxynucleoside triphosphates but failed to join. Consequently, replicating chromosomes failed to extensively continue nascent DNA chain growth, and the conversion of viral replicating DNA into mature DNA was seven to eight times less than that observed in nuclear extracts. Addition of neither cytosol nor nucleosol corrected this problem. In the presence of cytosol, nonspecific endonuclease activity was not a problem in any of the three in vitro systems. Extensive purification of replicating chromosomes was limited by three as yet irreversible phenomena. First, replicating chromosomes isolated in a low-ionic-strength medium had a limited capability to continue DNA synthesis. Second, diluting either nuclear extracts or replicating chromosomes before incubation in vitro stimulated total DNA synthesis but was accompanied by the simultaneous appearance of small-molecular-weight nascent DNA not associated with intact viral DNA templates and a decrease in the synthesis of covalently closed viral DNA. Although this second phenomenon appeared similar to the first, template concentration alone could not account for the failure of purified replicating chromosomes to yield covalently closed DNA. Finally, preparation of nucleoprotein complexes in increasing concentrations of NaCl progressively decreased their ability to continue DNA replication. Exposure to 0.3 M NaCl removed one or more factors required for DNA synthesis which could be replaced by addition of cytosol. However, higher NaCl concentrations yielded nucleoprotein complexes that had relatively no endogenous DNA synthesis activity and that no longer responded to cytosol. These data demonstrate that continuation of endogenous DNA replication in vitro requires both the soluble cytosol fraction and a complex nucleoprotein template whose ability to continue DNA synthesis depends on its concentration and ionic environment during its preparation.

In vitro HeLa cell DNA synthesis II. Partial characterization of soluble factors stimulating nuclear DNA synthesis

When HeLa cells are lysed in hypotonic buffer and the lysate is fractionated by centrifugation into particulate and soluble components, the particulate component (nuclei) is deficient compared to unfractionated lysate in the extent to which it can carry out in vitro DNA synthesis. In addition, rapidly labeled short DNA chains (Okazaki pieces) accumulate in purified nuclei, and are chased into higher molecular weight DNA to a lesser degree than in unfractinated lysate. When purified nuclei were reconstituted with soluble component, the capacity of the nuclei for in vitro DNA synthesis was fully restored, as was the capacity of the nuclei for conversion of Okazaki pieces to higher molecular weight DNA. This suggests that the soluble component contains a factor or factors necessary for normal DNA replication. The major incorporation-stimulating activity was partially characterized and partially purified from the soluble component. It is heat labile, non-dialyzable, partially recoverable in the supernatant after pH 5 precipitation, found mainly in a 55–85% saturated (NH 4) 2SO 4 fraction, and is included on Sephadex G-100. After passage through Sephadex G-100, the activity displays increased instability to storage at either 4°C or −70°C. Part of the activity does not bind to phosphocellulose at pH 7.2 and low salt; no additional activity can be recovered in a 0.5 M KCl wash of the phosphocellulose column. The Okazaki-piece-joining activity was found, along with the bulk of the incorporation-stimulating activity, in the 55–85% (NH 4) 2SO 4 fraction. These findings provide some of the groundwork for future attempts to completely purify and characterize those activities in the soluble component of cell lysates which are involved in DNA replication.

Primase initiates Okazaki pieces during polyoma DNA synthesis

SHORT fragments (Okazaki pieces) are formed as intermediates during elongation of nascent DNA strands1. In isolated nuclei from polyoma-virus infected 3T6 cells Okazaki pieces are initiated by a short RNA primer (initiator RNA, iRNA) with the approximate size of a decanucleotide2. The nature of the polymerase responsible for primer synthesis is not known, but high concentrations of α-amanitin, a drug which inhibits both RNA polymerase II (ref. 3) and III (ref. 4), have no effect on primer formation (unpublished results). We now present evidence that iRNA is not synthesised by any of the known RNA polymerases, but that, instead, a mammalian enzyme is involved which in its action corresponds to the dnaG gene product of E. coli. The bacterial enzyme was named primase5. It participates in the initiation of DNA strands of some single-stranded bacteriophages and has been suggested to be involved in the synthesis of bacterial Okazaki pieces6,7. One of the distinguishing features of the E. coli enzyme is its ability to use both ribonucleotides and deoxyribonucleotides for primer synthesis5,8.

Formation of Okazaki fragments in polyoma DNA synthesis caused by misincorporation of uracil

When dUTP replaced dTTP during polyoma DNA replication in isolated cell nuclei, radioactivity from labeled deoxynucleoside triphosphates was almost exclusively recovered in very short Okazaki fragments and incorporation ceased after a short time. Addition of uracil, a known inhibitor of the enzyme uracil-DNA glycosidase (Lindahl et al., 1977), increased total synthesis and shifted the incorporation to longer progeny strands. The presence of as little as 2.5% of dUTP in a dTTP-containing system gave a distinct increase in isotope incorporation into Okazaki pieces accompanied by a corresponding decrease in longer strands. This effect was reversed completely by uracil. The short strands formed from dUTP could be chased efficiently into long strands. Our results suggest that dUTP can be incorporated in place of dTTP into polyoma DNA, and that polyoma-infected nuclei, similar to E. coli (Tye et al., 1977), contain an excision-repair system which by removal of uracil causes strand breakage and under certain circumstances may contribute to the formation of Okazaki fragments.

Okazaki pieces grow opposite to the replication fork direction during simian virus 40 DNA replication

Simian virus 40 replicating DNA was pulse labeled with alpha-32P-dATP using an acellular DNA replication system. Nascent DNA chains of less than 200 nucleotides (Okazaki pieces) were then isolated from the denatured replicating DNA by electrosieving through a polyacrylamide gel column. The purified Okazaki pieces were hybridized to separated strands of Bg1(1)+Hpa1 simian virus 40 DNA restriction fragments immobilized on nitrocellulose filters. Only strands with polarity of the DNA replication fork direction hybridized with Okazaki pieces. Hence, Okazaki pieces in simian virus 40 are synthesized against the DNA replication fork direction.

Incorporation of labelled degradation products of radioactive thymine into non DNA material

When thymine auxotrophs are grown in the presence of methyl labelled [3H] or [14C] thymine which has been stored at 4 degrees C, two classes of material are labelled which are not DNA. One class sediments on neutral sucrose gradients with spontaneously single stranded Okazaki pieces, is unstable in alkali, migrates on alkaline gels as very small material and is digested by ribonucleases and micrococcal nuclease, but not by DNAase I. This class is presumably RNA. The second class sediments more slowly on both neutral and alkaline sucrose gradients than Okazaki pieces, but co-migrates on alkaline gels with DNA whose size is between 700 and 4000 nucleotides. It is not digested by alkali, ribonucleases or deoxyribonucleases. Its identity is unknown. The proportion of the total incorporated counts in these two classes depends on the time of storage of the thymine and is already sufficient to interfere with certain types of experiments when the thymine is only a few weeks old. Thymine is easily purified by paper chromatography and this purified thymine does not label the two non DNA classes of material. It is recommended that radioactive thymine be purified in this way before use.

DNA intermediates at the Escherichia coli replication fork: effect of dUTP.

We have directly tested the hypothesis that elevated levels of dUTP cause the formation of small DNA fragments at the replication fork of Escherichia coli. Addition of increasing levels of dUTP to lysates on cellophane discs results in an increasing number of strand scissions in the newly replicated DNA. Lysates of strains defective in dUTPase produce many more scissions at the same level of dUTP. The size distribution of Okazaki pieces obtained in vivo can be reconstituted in vitro on cellophane discs if appropriate levels of dUTP are present. Although uracil excision leads to the apparent production of Okazaki pieces from both daughter strands, DNA synthesis is actually asymmetric under these conditions. De novo chain initiation events occur on only one strand. It is suggested that asymmetry of synthesis in vivo may be masked by uracil excision and other postreplication processing mechanisms.

Effect of 2',3'-dideoxythymidine-5'-triphosphate on HeLa cell in vitro DNA synthesis: evidence that DNA polymerase alpha is the only polymerase required for cellular DNA replication.

We have studied the effects of the nucleotide analogue, 2',3'-dideoxythymidine-5'-triphosphate (ddTTP) on replicative DNA synthesis in HeLa cell lysates. As previously demonstrated (1), such lysates carry out extensive DNA synthesis in vitro, at rates and in a fashion similar to in vivo DNA replication. We report here that all aspects of DNA synthesis in such lysates (total dNTP incorporation, elongation of continuous nascent strands, and the initiation, elongation, and joining of Okazaki pieces) are only slightly inhibited by concentrations of ddTTP as high as 100-500 micrometer when the dTTP concentration is maintained at 10 micrometer. This finding is consistent with the report by Edenberg, Anderson, and DePamphilis (2) that all aspects of replicative in vitro simian virus 40 DNA synthesis are also resistant to ddTTP. We also find, in agreement with Edenberg, Anderson, and DePamphilis (2), that DNA synthesis catalyzed by DNA polymerases beta or gamma is easily inhibited by ddTTP, while synthesis catalyzed by DNA polymerase alpha is very resistant. These observations suggest that DNA polymerase alpha may be the only DNA polymerase required for all aspects of cellular DNA synthesis.

Most short DNA molecules isolated from 3T3 cells are not nascent.

The population of short DNA molecules (less than 10(3) nucleotides) in 3T3 cells has been studied using in vivo and in vitro pulse labeling techniques and in vitro end-labeling. There is a large number of molecules of less than 100 nucleotides present in equal numbers in both Go and S phase cells. In S phase cells, most of these molecules are not replicating intermediates because they do not become density-labeled after a moderate period of substitution of BrdUMP, although they are detected by end-labeling in vitro. This population includes the nascent Okazaki pieces that can be labeled in a short pulse with [3H]dThd or [3H]dTTP, however, these represent less than 10% of the total population. Alkaline hydrolysis of the molecules that had been end-labeled with 32P using [gamma32P]ATP and polynucleotide kinase did not reveal significant release of [32P] 2'(3'), 5' ribonucleoside diphosphates.

Asymmetric Okazaki piece synthesis during replication of simian virus 40 DNA in vivo

We have pulse-labeled simian virus 40 (SV40)-infected monkey cells with 3H-thymidine ( 3H-dThd) and have hybridized the viral Okazaki pieces (rapidly labeled short DNA chains found during DNA replication, < 250 nucleotides long) and SV40 “intermediate sized” DNA (longer nascent strands, up to full replicon size) to the separated strands of two SV40 DNA restriction fragments, one lying to either side of the origin of bidirectional DNA replication. As much as 5 fold more Okazaki piece DNA hybridized to one strand than to the other strand of each restriction fragment. The excess Okazaki piece DNA was in the strands oriented 3′ → 5′ away from the replication origin (the strands which are expected to be synthesized discontinuously). Neither the duration of the labeling period nor the temperature of the cells during labeling significantly altered this hybridization asymmetry. With respect to the hybridization of “intermediate sized” DNA, a reverse asymmetry was detected (1.7 fold more radioactivity in the strands oriented 5′ → 3′ away from the origin for a 1 min pulse label at 22°C). The effects on these hybridization asymmetries of preincubating the infected cells with FdUrd prior to pulse-labeling were also determined. We also measured the size of the Okazaki pieces using gel electrophoresis under denaturing conditons after releasing the pieces from the filter-bound DNA strands. The size distribution of the Okazaki piece DNA from each strand was the same (∼ 145 nucleotides, weight average; 200–250 nucleotides, maximum size), indicating that the hybridization asymmetry resulted from a difference in the number rather than the size of the pieces in each strand. The simplest interpretation of our results is that SV40 DNA is synthesized semidiscontinuously: the strand with 3′ → 5′ orientation away from the origin is synthesized in short Okazaki pieces which are subsequently joined together, while the strand with 5′ → 3′ orientation away from the origin is synthesized continuously. Some models of two-strand discontinuous synthesis, however, cannot be ruled out.

Endo R DpnI restriction of Escherichia coli DNA synthesized in vitro. Evidence that the ends of Okazaki pieces are determined by template deoxynucleotide sequence

A restriction enzyme from Diplococcus pneumoniae, Endo R DpnI, cuts methylated DNA on cellophane discs into pieces which are about the same size as Okazaki pieces. DNA was synthesized in vitro on cellophane discs in the presence of β-nicotinamide mononucleotide to prevent joining of Okazaki pieces. This DNA was methylated by the addition of S-adenosyl methionine to the reaction mixture. When Endo R DpnI was used to cut methylated DNA made in vitro in the presence of S-adenosyl methionine and β-nicotinamide mononucleotide, no decrease in sedimentation of the Okazaki pieces was observed. Control experiments demonstrated that Okazaki pieces were methylated in vitro and that Endo R DpnI was capable of cutting double-stranded DNA containing methylated Okazaki pieces, that is, synthesized in β-nicotinamide mononucleotide and S-adenosyl methionine. These results are interpreted to mean that the ends of Okazaki pieces are non-randomly distributed with respect to 6-methyl adenine residues.