DNA replication in Escherichia coli: physical and kinetic studies of the replication point

Organization of ribonucleoside diphosphate reductase during multifork chromosome replication in Escherichia coli

Ribonucleoside diphosphate reductase (RNR) is located in discrete foci in a number that increases with the overlapping of replication cycles in Escherichia coli. Comparison of the numbers of RNR, DnaX and SeqA protein foci with the number of replication forks at different growth rates reveals that fork : focus ratios augment with increasing growth rates, suggesting a higher cohesion of the three protein foci with increasing number of forks per cell. Quantification of NrdB and SeqA proteins per cell showed: (i) a higher amount of RNR per focus at faster growth rates, which sustains the higher cohesion of RNR foci with higher numbers of forks per cell; and (ii) an equivalent amount of RNR per replication fork, independent of the number of the latter.

Fractionation and characterization of DNA at sites of replication from rat liver nuclei

Regenerating rat liver nuclei when sonicated and centrifuged in a Cs2SO4 gradient were fractionated into three distinct bands. These bands were designated as light band (LB), middle band (MB), and heavy band (HB) according to their density. LB and MB were shown to consist of large granular particles with varying electron densities, but LB also contained remnants of nuclear membrane. When analysed by gel electrophoresis, LB and MB displayed more than 35 bands of proteins. The third fraction, HB, consisted largely of small chromatin fibers and its proteins were predominantly the four histones of the nucleosomal core particle. Following short pulses with [3H]thymidine in vivo, the specific activity of DNA in LB and MB was significantly higher than that of bulk DNA contained in HB. DNA in all three fractions became equally labelled as the duration of the labelling interval increased beyond 30 min. Newly synthesized DNA was characterized by electrophoresis on analytical 1.7% acrylamide -0.5% agarose composite gels. After a 1-min labelling interval in vivo, 17% of the rapidly labelled DNA from LB and MB was stationary at the gel origin like replication forks from E. coli, but only 3% of HB DNA had zero mobility. Electron microscopy confirmed the presence of DNA replication forks in LB, MB, and HB. With increasing time of synthesis the proportion of labelled DNA exhibiting zero mobility decreased in all three fractions. Denaturation of DNA or digestion of single-stranded DNA with S1 nuclease released newly synthesized DNA from the gel origin. Ribonuclease was without effect. DNA recovered from LB and MB also had a higher molecular weight than the HB DNA. Together these results indicate (1) that LB and MB are enriched in newly replicated DNA; (2) that an increased proportion of newly replicated DNA in LB and MB is associated with DNA replication forks; and (3) that the replicating DNA recovered in LB and MB may be associated with other nuclear constituents in situ because this DNA appears to be protected from the more frequent chain breaks introduced into the bulk of chromatin (HB) by sonication.

Physiological modification of alkylating agent induced mutagenesis. II. Influence of the numbers of chromosome replicating forks and gene copies on the frequency of mutations induced in Escherichia coli

The frequency of reversions induced in Escherichia coli K-12 trpA58 by any of five different monofunctional alkylating agents increased as the growth rate of the organism was raised prior to mutagen treatment. The increase in mutation frequency did not correlate with growth rate-dependent changes in cell area or total cellular protein and DNA. After treatment of cells with N-methyl-N-nitrosourea (MNUA), no growth rate-dependent change was observed in the total DNA alkylation or percentage of O6-methylguanine present in the DNA extracted. The frequency of reversions induced by one mutagen, methyl methanesulphonate (MMS), increased in proportion to the average number of trpA gene copies per cell, whereas the frequency of reversions induced by the other compounds was dependent on the average number of chromosome replicating forks per cell. This difference was attributed to the different ratios of DNA base alkylation products observed, formed after treatment with MMS, an SN2-type reagent, or after treatment with the SN1-type reagents ethyl methanesulphonate (EMS), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), MNUA and N-ethyl-N-nitrosourea (ENUA). Possible reasons for the dependence of mutation frequency on the number of replicating forks per cell are discussed.

Evidence for RNA linked to nascent DNA in HeLa cells

Rapidly labeled, i.e., nascent, DNA from HeLa cells was separated from the bulk DNA by ultracentrifugation. Further characterization of the rapidly labeled component revealed that its sedimentation coefficient is in the range of 4S and that it exists in a single- and double-stranded conformation. Moreover, analysis by nitrocellulose chromatography and CsSO4 density sedimentation of the nascent DNA labeled with 3H-uridine revealed that it is covalently linked to short chains of RNA, indicating that in HeLa cells RNA primer is involved in DNA replication.

[Conformational changes before and after DNA synthesis increase cytogenetically lethal radiation damage]

Chinese hamster ovary fibroblasts were synchronized by mitotic selection and showed cytogenetic lethally acting radiation damages, which depended on age at irradiation time. The development of cell cultures was followed by counting of the killed cells in the 3rd daughter generation of the irradiated ones and by evaluation of the colony size spectra 73.5 h after innoculation. At a dose of 300 rads two narrow but high peaks of radiation sensitivity were induced, which appeared at the beginning and at the end of the S-phase of the cell cycle and therefore are reduced to conformation changes of the DNA. Consequently the DNA-super-structures linking pieces of the nucleoprotein-fibre during fastening to, and detaching from, the nuclear membrane are assumed to be the loci of the increased radiation sensitivity.

Repair by human cells of adenovirus-2 damaged by psoralen plus near ultraviolet light treatment

Adenovirus-2 is damaged by treatment with psoralen plus near-ultraviolet (UV) light is shown by reduced ability to infect human fibroblasts. The apparent sensitivity of the virus to this treatment depended upon the strain of cells used. The virus was 3-4 times more sensitive to the treatment when infecting xeroderma pigmentosum (XP complementation groups A or D) fibroblasts than when infecting normal fibroblasts. DNA extracted from virus preparations that had undergone such treatment was analyzed for treatment-induced crosslinks by gel electrophoresis and sedimentation in alkaline sucrose gradients. The fraction of adenovirus DNA molecules remaining non-crosslinked after treatment was found to correlate with the survival of the virus in normal fibroblasts. This result showed that the psoralen plus near-UV treatment gave rise to non-crosslink lesions (presumably psoralen-DNA mono-adducts), that were repairable by normal but not by XP fibroblasts, and suggested the possibility that normal fibroblasts cannot repair this type of crosslink in the DNA of an infecting adenovirion.