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© 1996 Oxford University Press 3149-3157

Footnote

Inhibition of initiation of simian virus 40 DNA replication during acute response of cells irradiated by ultraviolet light

Inhibition of initiation of simian virus 40 DNA replication during acute response of cells irradiated by ultraviolet light Yi-Ching Wang and Ming-Ta Hsu 1, *

Institute of Toxicology, Chung Shan Medical and Dental College, Taichung 40203, Taiwan , Republic of China and 1 School of Life Science, National Yang-Ming University, Pei-Tou, Taipei , Taiwan 112, Republic of China

Received May 23, 1996; Revised and Accepted June 28, 1996

ABSTRACT

To study the mechanism by which ultraviolet (UV) light inhibits DNA replication, we examined the effects of UV 254 nm irradiation on the replication of simian virus 40 (SV40) DNA and SV40-based plasmid in monkey cells. The study was designed to determine the relative contributions made by inhibition of replication initiation and chain elongation to the immediate inhibition of DNA replication following UV irradiation. We used two-dimensional neutral-alkaline electrophoresis to examine the behaviour of replication intermediates unambiguously. Kinetic analysis using this technique showed that initiation of replication started to decline at 15 min post-irradiation. When the pulse label incorporated in SV40 replication intermediates before irradiation was chased for 1 h, most of the label was found in mature Form I and II molecules. This indicated that replication elongation took place on damaged template. We also used a transfection technique to show that heavily irradiated plasmids replicated efficiently in unirradiated transfected cells. By the transfection technique, we observed that UV irradiation of host cells dose-dependently inhibited replication of transfected non-irradiated plasmids, suggesting that the inhibition of DNA replication is due to a global change in cellular physiology induced by UV. This change was also apparent from poor staining of the chromatin by fluorescent-DNA-binding dyes immediately after UV irradiation of intact cells. We conclude that a significant fraction of chain elongation proceeds on damaged templates and DNA replication during the acute response of cells irradiated with UV is mainly controlled by the inhibition of replication initiation.

INTRODUCTION

Organisms must replicate their DNA with high accuracy so as to maintain their genetic identity. However, DNA is subject to damage by many chemical and physical agents. Ultraviolet (UV) light is one of the best-studied DNA-damaging agents causing inhibition of DNA replication. Recent studies have demonstrated three regulatory pathways for controlling DNA replication after radiation damage. Two are cell cycle regulation pathways which arrest cells at either the late G 1 phase or the G 2 -M interface, and are mediated by p53 tumor suppressor ( 1 , 2 ) or Cdc2 protein kinase ( 3 ) respectively. The third pathway accounts for the immediate inhibition of replication after radiation damage known as the acute response after irradiation ( 4 , 5 ).

Several different mechanisms have been proposed to explain the immediate inhibition of replication after UV irradiation in the acute response. Early observations by Kaufmann and Cleaver ( 4 ) demonstrate that UV induces inhibition of replication specifically at the level of initiation after low (0.3-2.6 J/m 2 ) doses. The effect is detected by velocity sedimentation of pulse-labeled, newly synthesized DNA in alkaline sucrose gradients, and is reflected by a selective inhibition of synthesis of daughter DNA with the same length as an average replicon within 30-60 min after irradiation. Recently, inhibition of initiation by X-ray irradiation has been demonstrated in a defined mammalian gene ( 5 ); initiation in the dihydrofolate reductase (DHFR) gene of an irradiated Chinese hamster cell (CHO) is completely inhibited within 30 min and does not resume for 3-4 h. On the other hand, inhibition of chain elongation by UV has also been observed. For example, DNA synthesis during a 15-min pulse immediately after irradiation of a simple eukaryote, Dictyostelium discoideum , is of single-stranded low molecular weight DNA, and the size of nascent strand generated after UV depends on radiation dose ( 6 ). Similarly, in the SV40 chromosome in UV-irradiated cells, the daughter strands of SV40 DNA grow only to a size equal to the interdimer distance along the parental strands, suggesting an elongation blocking at dimer ( 7 ). However, explanations for how elongation is affected remain controversial. An early model proposed that damage in the leading strand blocks chain elongation and replication fork progression, whereas damage in the lagging strand merely causes small gaps opposite the damage without blocking the replication ( 8 ). However, analysis of DNA replication started from an origin near DHFR gene in UV-irradiated CHO cells indicated that replication can efficiently bypass UV lesions in a 15 kb region without significant repair or recombination and pyrimidine dimer containing DNA can be completely replicated in UV irradiated CHO cells ( 9 ).

In view of the controversy in the mechanisms of inhibition of DNA replication in mammalian cells and the recent report that initiation of DNA replication in mammalian cells is the main step inhibited by ionizing radiation ( 5 ), we examined the effects of UV light on the replication of SV40 and SV40-based plasmid in monkey cells using experimental protocols specifically to address the effect of UV irradiation on chain elongation and initiation. SV40 is a small double-stranded DNA virus that replicates in the nucleus, has a chromatin structure very similar to that of host cells, and uses host enzymes for its bidirectional replication ( 10 ). It thus provides an excellent model of a single mammalian replicon. Previous studies have indicated that, like cellular DNA replication, viral DNA replication is inhibited by UV irradiation in a dose-dependent fashion as measured by incorporation of [ 3 H]TdR ( 11 - 13 ). In the present study, we used two-dimensional neutral-alkaline electrophoretic analysis to define the replication intermediates and therefore to differentiate DNA replication from DNA repair synthesis. Using this technique we show that SV40 DNA replication is rapidly shut off following UV irradiation, with a concomitant rise of repair synthesis. However, DNA chains initiated before irradiation can be elongated into complete SV40 molecules within 1 h. Using a transfection technique, we also found that SV40-based plasmid irradiated with a high dose of UV can replicate efficiently in non-irradiated host cells, albeit in an error-prone manner. In contrast, when the host cells were irradiated with a low dose of UV before transfection of non-irradiated SV40 plasmid, the plasmid's replication was dose-dependently inhibited. The data suggest that the acute response observed immediately after UV irradiation is mainly controlled by inhibition of replication initiation. Mechanisms involved in producing a microenvironment in damaged cells that inhibits the overall DNA replication are also discussed.

MATERIALS AND METHODS

Cells, virus, plasmids and enzymes

CV-1 African Green Monkey kidney cells and Cos-1 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum and 50 [mu]g/ml gentamicin (Gibco). SV40 viral stocks were prepared as described ( 14 ). pSV2CAT and pBKCMV plasmids were purchased from American Type Culture Collection. All restriction enzymes were obtained from New England Biolabs.

Virus infection and plasmid transfection procedures

CV-1 cells were infected with SV40 virus at 10 p.f.u./cell as described ( 14 ). Double-stranded SV40 DNA or SV40-based plasmid was transfected into subconfluent cells by the DEAE-dextran method ( 15 ).

UV irradiation of cells and DNA

Cells were irradiated with 254 nm UV light from a low pressure mercury germicidal lamp at an incident dose rate of 2.5 J/m 2 /s, measured with a model UVX digital radiometer (Ultraviolet Products, San Gabriel, CA) using a UVX-254 midrange sensor. For irradiation of DNA, SV40-based plasmid was irradiated at a concentration of 1 [mu]g/ml immediately before it was transfected into cells. The UV source was from a spectrolinker #XL-1000 at an incident dose rate of 25-30 J/m 2 /s, measured as described previously.

Pulse labeling procedure

For in vivo pulse-labeling with [ 3 H]TdR, cells were incubated with 5 mCi/ml [ 3 H]TdR in DMEM medium supplemented with 2% fetal calf serum for the time periods indicated in the figure legends. At the end of the labeling period, isotope solution was quickly removed then cells were lysed with buffer containing 1% sodium dodecyl sulfate (SDS). For pulse-chase experiments, cells were pulse-labeled for either 10 or 15 min with [ 3 H]thymidine before irradiation. Following irradiation, cells were chased for 1 h with medium containing 10 mM thymidine. For nuclear run-on assay, cells were first lysed with NP-40 lysis buffer (0.2% NP-40, 10 mM Tris-HCl, pH 7.4, 0.2 mM ZnCl 2 ) to remove cytoplasm, and subsequently incubated with reaction buffer containing 10 mM HEPES, 10% glycerol, 20 mM KCl, 7.5 mM MgCl 2 , 0.25 mM dithiothreitol, 5 mM ATP, 1.25 mM GTP, CTP and UTP, 0.6 mM each of dGTP, dATP, dTTP and 10 [mu]Ci of [ 32 P]dCTP. The reaction was performed at 37oC for 20 min in a culture plate where nuclei stayed firmly on the plate throughout the labeling period. At the end of the reaction nuclei were extracted by the Hirt method ( 16 ).

Neutral-alkaline two-dimensional gel electrophoresis

The neutral-alkaline two-dimensional electrophoresis technique was modified from Sundin and Varshavsky ( 17 ) and Nawotka and Huberman ( 18 ). DNA was first electrophoresed in a 1.0% agarose gel in TAE buffer (40 mM Tris-acetate, 1 mM EDTA, pH 7.4). After electrophoresis, the marker lane was cut off and stained with ethidium bromide (0.5 [mu]g/ml) to determine the position of SV40 DNA in the unstained part of the gel. The lanes containing the samples were cut with a razor blade and orientated horizontally in the second dimensional gel tray (20 * 20 cm). DNA was electrophoresed in 1.3% agarose gel in 40 mM NaOH, 1 mM EDTA. The alkaline gel was run at 4oC with magnetic stirring. Electrophoresis was done at 200 mA for 20 h with one change of buffer. After electrophoresis, the gel was washed with distilled water three times, neutralized with 0.1 M Tris-HCl, pH 7.0 and stained with ethidium bromide. After photography, the gel was processed for autoradiography or fluorography as described previously ( 19 ).

Bacterial transformation

SV40-based plasmid was harvested from the cells by the Hirt method ( 16 ). Purified DNA was treated with Dpn I or Mbo I to remove all non-replicated DNA or newly replicated DNA respectively. Escherichia coli MC1061 or HB101 was transformed with enzyme-digested DNA by electroporation using a Gene Pulser apparatus at 24 [mu]F and 2.5 kV with the pulse controller set to 200 ohms. The yield of plasmid DNA was calculated from the bacterial transformation efficiency using standard plasmid DNA as a control of transformation efficiency.

Fluorescence microscopy

Cells were lysed with NP-40 lysis buffer to remove cytoplasm. The nuclei were stained with 1 [mu]g/ml of either ethidium bromide or acridine-ethidium heterodimer (Molecular Probes), or with 300 ng/ml acridine orange (Sigma), for 5 min. These dyes bind DNA and their fluorescence intensity is greatly enhanced by binding to DNA. Laser induced-fluorescence imaging was performed using a Meridian ACAS550 cytometer.

RESULTS

Kinetic analysis of inhibition of DNA replication after UV 254 nm irradiation by two-dimensional gel electrophoresis

We used a two-dimensional neutral-alkaline electrophoresis technique to investigate the pattern of radioactive label incorporation into SV40 DNA after UV irradiation and to differentiate between replication and repair synthesis. It has been shown previously that SV40 replication intermediates labeled with [ 3 H]TdR can be identified by this method ( 17 , 18 ). As shown in Figure 1 A by schematic drawing and Figure 1 B by autoradiography, immediately after a 15 min pulse labeling, the nascent DNA chains of supercoiled SV40 replication intermediates (RI) could be displayed as a curve that asymptotically approached the position of mature Form I DNA in the first dimension, whereas replication intermediates containing nicks in the parental strands were represented by a curve that approached the position of Form II nicked circles (Fig. 1 C, curves RI and nicked RI respectively). When SV40 DNA was labeled for 15 min beginning at 30 min after infected cells had been irradiated with 90 J/m 2 of UV light, the intensity of replication nascent DNA curves almost disappeared and the majority of pulse label was incorporated into nicked circular Form II DNA and the late replication intermediates (indicated as arrows in Fig. 1 D). When SV40 DNA was pulse-labeled for 15 min at 60 min post-irradiation, the curves of nascent DNA disappeared even after prolonged exposure and the majority of label was found in the position of Form II nicked circular DNA and late replication intermediates (indicated as arrows in Fig. 1 E). The incorporation of radioactive label is poor due to inhibition of [ 3 H]thymidine incorporation into DNA 1 h after UV irradiation. The absence of significant number of labeled replication intermediates recovered from irradiated cells indicated that initiation of SV40 DNA replication is rapidly turned off within 30 min after UV irradiation.


Figure 1 . In vivo kinetics analysis of SV40 DNA replication after UV irradiation. Two-dimensional neutral-alkaline electrophoretic analysis of SV40 DNA after running the [ 3 H]TdR-labeled SV40 DNA in the first dimensional 1% agarose gel (top horizontal slot in A and B) and subsequently running it in the second dimensional alkaline 1.3% agarose gel (see Materials and Methods). ( A ) Schematic drawing which illustrates the different stages of replication products and the repair synthesis intermediates of SV40 DNA after UV irradiation. ( B ) Autoradiograph showing the 15 min pulse-labeled SV40 DNA from the non-irradiated cells. ( C ) The schematic drawing of (B). SV40 DNA from infected cells irradiated with 90 J/m 2 was pulse labeled for 15 min at ( D ) 30 min or at ( E ) 60 min after irradiation. Repair synthesis intermediates are subgenomic fragments under the position of Form I and Form II replication intermediate curves which are indicated by arrows. Designations in (A) are: ss circle, single-stranded circle; ss linear, single-stranded linear; RFI, replication form I. Designations in (C), (D) and (E) are ssC, single-stranded circle; ssL, single-stranded linear; RFI, replication Form I; RI, replication intermediate; Late RI, late replication intermediate. Repair synthesis intermediates are indicated by arrows.

Because [ 3 H]TdR incorporation is severely inhibited by UV irradiation in vivo , we also used an in vitro nuclear run-on assay which allows sufficient radioactive labeling to analyze further the pattern and the kinetics of electrophoretic migration in the two-dimensional gel after UV irradiation (see Materials and Methods). The DNA labeled in isolated nuclei was digested with restriction endonucleases and then displayed in a two-dimensional gel to examine the response of replication forks in different regions of SV40 DNA. In control non-irradiated sample (Fig. 2 A), three mature restriction fragments after Pst I plus Kpn I digestions appeared (indicated as a, b and c). In addition, two replication nascent DNA curves corresponding to fragments a and b were observed (indicated as RIa and RIb respectively, in Fig. 2 A). C fragment contains the termination site of replication and the nascent chains are too small to be seen in the gel. When SV40 DNA was pulse labeled at 15 min post-UV irradiation (Fig. 2 B), replication nascent DNA curves began to diminish whereas labeled DNA fragments with sizes smaller than the mature restriction fragments begin to appear under the mature fragments (indicated as arrows). At 30 min after irradiation, replication nascent DNA curves almost disappeared whereas radioactive label under the mature fragments was greatly enhanced (Fig. 2 C). No replication curves were observed at 1 h after irradiation (Fig. 2 D). These results are consistent with the findings by in vivo [ 3 H]TdR pulse labeling assay described above, and again suggest that initiation of SV40 DNA replication is rapidly shut off following UV irradiation.


Figure 2 . In vitro kinetics analysis of SV40 DNA replication after UV irradiation. Two-dimensional neutral-alkaline electrophoretic analysis of SV40 DNA labeled with [ 32 P]dCTP by in vitro nuclear run-on assay. The labeled SV40 DNA was digested with Pst I and Kpn I restriction endonucleases before electrophoresis in two-dimensional gel. ( A ) The 20 min pulse labeled SV40 DNA from the non-irradiated cell nuclei. Three mature restriction fragments are indicated as a, b and c. Two replication intermediate curves corresponding to fragments a and b are indicated as RIa and RIb respectively. Isolated nuclei were labeled with [ 32 P]dCTP for 20 min at ( B ) 15 min, ( C ) 30 min and ( D ) 60 min after exposure to 90 J/m 2 . Repair synthesis intermediates appear under the three mature fragments and are indicated by arrows. Similar inhibition was observed in cells irradiated at 15 J/m 2 .

Protein synthesis inhibitor does not alter topoisomer distribution of SV40 DNA labeled after UV irradiation-evidence for repair synthesis after UV irradiation

The results described above show that the majority of radio- activity labeled during a short pulse at 1 h or later after UV irradiation is incorporated into mature SV40 DNA and replication intermediates were not labeled. The labeled mature DNA could be derived from replication of either templates not damaged by UV irradiation or from residual DNA replication after UV irradiation. Alternatively, the mature SV40 pulse-labeled after UV irradiation could be derived from repair synthesis. To examine whether the labeling of mature DNA due to residual DNA replication or repair synthesis, we labeled SV40 DNA with [ 3 H]TdR beginning at 1 h after irradiation in the presence or absence of the protein synthesis inhibitor cycloheximide and analyzed SV40 DNA topoisomer distribution by agarose gel (Fig. 3 ). Previous studies have shown that SV40 DNA supercoiling depends on wrapping of DNA on histone cores and inhibition of protein synthesis would eliminate nucleosome assembly during replication and therefore reduces superhelical density of SV40 DNA ( 20 ). On the other hand, during repair synthesis only a small patch of DNA is involved and there is no requirement of new nucleosome formation. Therefore, inhibition of protein synthesis would not affect superhelical density in SV40 DNA undergoing repair synthesis in vivo whereas SV40 DNA superhelical density of replication products would be affected. Figure 3 shows that, in the presence of cycloheximide, labeled SV40 DNA from the control non-irradiated cells exhibited lower superhelicity than that labeled in the absence of the drug as a result of reduced number of nucleosomes (compare lane 1 with lane 2 in Fig 3 ). On the other hand, topoisomer distribution of SV40 DNA labeled from 1 to 2 h post-irradiation in the presence of cycloheximide was the same as that labeled in the absence of the drug (compare lane 3 with lane 4). These results suggest that the mature SV40 DNA labeled after semiconservative DNA replication is derived from repair synthesis rather than from residual DNA replication.


Figure 3 . UV-irradiated or non-irradiated SV40-infected cells were labeled with [ 3 H]TdR for 2 h from 24 to 26 h post-infection in the presence or absence of 10 [mu]g/ml cycloheximide. After Hirt extraction and purification, SV40 DNA was electrophoresed in a 1.2% agarose gel. The gels were stained, photographed, and processed for fluorography with 0.7 M sodium salicylate. The position of Form I and Form II DNA are indicated. Form I molecules with low superhelicity migrated slowly during electrophoresis.

Pulse-chase analysis of SV40 DNA chain elongation immediately following UV 254 nm irradiation

Since SV40 replication intermediates could still be clearly observed at 15 min post-irradiation (Fig. 2 B), this observation suggests that a certain fraction of chain elongation can proceed immediately after UV irradiation. Therefore, we studied SV40 DNA replication after irradiation by pulse-chase analysis. If chain elongation can proceed after UV irradiation, SV40 replication intermediates pulse-labeled just before UV irradiation can mature into Form I or Form II circular DNA products. On the other hand, if chain elongation is the main step inhibited after UV irradiation and initiation of replication continues unabated, then replication intermediates should accumulate in the chased sample. As shown in Figure 4 A, a significant fraction of the label was incorporated into SV40 replication intermediates during the 15 min pulse before UV irradiation. Following the 1 h chase after irradiation, no replication intermediates were observed and the majority of label was chased into Form I and II DNA molecules (Fig. 4 B). These results suggest that the majority of SV40 DNA replication intermediates labeled before UV irradiation can continue their chain elongation to form mature products.

Efficient replication of UV 254 nm-irradiated SV40 ori-based plasmids in non-irradiated cells

The results obtained by neutral-alkaline two-dimensional gel electrophoretic analysis suggest that although DNA replication is inhibited after UV irradiation, a significant fraction of chain elongation proceeds after UV irradiation. To examine whether UV-damaged templates indeed can be elongated, we transfected non-irradiated Cos-1 cells with UV-irradiated SV40-based plasmid. At 48 h after transfection, the plasmid DNA was extracted and digested with Dpn I to remove input parental DNA. The amount of progeny DNA was then examined by bacterial transformation assay or by Southern blot analysis. As shown in Table 1 , plasmid irradiated with a high dose of UV, which is used to ensure the presence of UV damages in every plasmid DNA, can still replicate as efficiently as non-irradiated plasmid. For example, at 900 J/m 2 , which generates ~40-50 dimers per plasmid ( 21 ), replication of irradiated plasmid was as efficient as that of non-irradiated plasmid when assayed at 48 h post-transfection. Similar results were obtained using Southern blot analysis (Fig. 5 ). These results show that UV irradiated plasmids can replicate efficiently if transfected cells are not irradiated and contain the initiation protein, i.e., T antigen.


Figure 4 . Pulse-chase analysis of SV40 chain elongation immediately following UV irradiation. ( A ) The SV40 DNA pulse labeled with [ 3 H]TdR for 15 min before the infected cells were irradiated with 90 J/m 2 . ( B ) The SV40 DNA after 1 h chase of irradiated cells in non-isotope medium. Positions of replication intermediate (RI) as well as single-stranded circle (ssC), single-stranded linear (ssL) and mature RFI molecules are as indicated.


Figure 5 . Southern blot analysis of the Dpn I-resistant progeny pSV2CAT plasmid after replication in Cos-1 cells for 48 h. Plasmid was irradiated with UV doses of 0, 300, 600 or 900 J/m 2 before transfection. Positions of Form I and Form II replication molecules are as indicated.

The efficient replication of irradiated plasmids in non-irradiated cells could be due to efficient repair of irradiated plasmids. To examine the repair of irradiated SV40 plasmid, we treated the transfected DNA with Mbo I to remove the unmethylated progeny plasmid DNA replicated in Cos-1 cells. The Mbo I-resistant DNA represents the input irradiated plasmid. We then tested whether these input irradiated plasmids had been repaired at various times after transfection by transforming them into recA - bacteria, which are highly UV-sensitive. The ability of a plasmid to transform recA - bacteria represents the repair of damage in the plasmid. As shown in Table 2 , the ability of input irradiated plasmids to transform HB101 increased only slightly after transfection. For example, no repair of irradiated plasmid in 1 h and only 4% of plasmid regain the ability to transform HB101 during 12 h post-UV incubation period. This result suggests that repair of input irradiated plasmid in Cos-1 contribute to a minor effect on the efficient replication observed.

Table 1 . Yield of UV-irradiated pSV2CAT plasmids after replication in Cos-1 cells, as estimated from the relative number of bacterial colonies observed after transformation by progeny plasmids
UV dose to plasmid

No. of colonies observed

Relative transformation efficiency a

(J/m 2 )

(*10 -4 )

(%)

0

213 +- 32

100

300

212 +- 21

100

600

192 +- 13

90

900

255 +- 34

100

a The progeny plasmids from cells transformed with UV-irradiated or non-irradiated plasmids were harvested by Hirt method 2 days after transfection and the same amount of Hirt extract was used to transform the indicator bacteria MC1061. Relative transformation efficiency is expressed as the ratio of the number of colonies transformed by irradiated versus non-irradiated plasmids.

If there was no significant repair of input damaged plasmids after transfection, then the efficient replication of heavily irradiated plasmids could be due to bypass of UV damage during replication. Such bypass would be expected to increase the mutation frequency in replicated DNA. To test this possibility, we employed the pBK-CMV plasmid which contains an SV40 origin and a lacZ reporter gene. The lacZ gene provides [alpha]-complementation for blue-white color selection. The plasmid was irradiated at 900 J/m 2 and transfected into Cos-1 cells. At 48 h post-transfection, the mutant frequency of progeny DNA was measured by transforming lacZ - bacteria. The mutant frequency of lacZ gene was ~5-fold higher than that of the unirradiated control. This result indicates that UV-irradiated plasmid is replicated in Cos-1 cells in an error-prone manner.

Table 2 . Transformed bacterial colonies observed after transformation of E.coli HB101 by the Mbo-1 resistant plasmid, which represents the original input irradiated plasmid, at various times after transfection of Cos-1 cells
Incubation time

Relative transformation efficiency

(h)

of unirradiated plasmid (%) a

before transfection

0.9

1

0.5

12

4

48

10

a Number of colonies transformed by plasmid irradiated at 500 J/m 2 was compared with that by unirradiated plasmid extracted after the same incubation time to determine the relative transformation efficiency.

Inhibition of SV40-based plasmid replication in cells irradiated with low dose of UV

To examine whether UV irradiation of transfected cells induces a similar effect on a non-irradiated SV40-based plasmid, we studied SV40 plasmid replication in UV-irradiated cells. Cos-1 cells were irradiated with low doses of UV before transfection and the replication of non-irradiated plasmids transfected into these cells was examined. We found that UV irradiation of cells caused a dose-dependent inhibition of transfected non-irradiated plasmid (Fig. 6 ). At 10 J/m 2 , replication of unirradiated plasmid was reduced to 38% of that in the non-irradiated control cells at 24 h post-transfection. This reduction was not due to a lower transfection efficiency of UV-irradiated cells since similar dose-dependent inhibition of plasmid yield was obtained if UV irradiation was performed after transfection (data not shown). Since this UV dose is too low to cause damage in SV40 DNA or the T antigen coding sequence in Cos-1 cells, the inhibition of SV40 plasmid replication suggests that UV irradiation induces an alteration of cellular physiology that inhibits overall DNA replication.


Figure 6 . Relative transformation efficiency by plasmids harvested from Cos-1 cells which were irradiated with various doses of UV before transfection. Plasmids were harvested at 24 h post-transfection and digested with Dpn I. The DpnI -resistant progeny DNA was used to transform the indicator bacteria to estimate the relative yield as bacterial transformation efficiency.

Rapid nuclear and chromatin changes in cells irradiated with UV 254 nm

Since the results above suggest that inhibition of DNA replication is due to a global cellular physiological change induced by UV, we examined whether any gross morphological changes were present in irradiated cells. Irradiation with 90 J/m 2 induced a rapid change in staining of cell nuclei with DNA-binding fluorescent dyes (Fig. 7 ). Immediately after UV irradiation, no alteration of chromatin staining by acridine orange was observed (Fig. 7 , compare A with B). At 30 min post-irradiation, the staining of chromatin of irradiated cell nuclei began to decline, indicating a change of nuclear structure (Fig. 7 C). At 2 h post-irradiation the average staining intensity and the average staining area of chromatin of irradiated cell nuclei was reduced to 60 and 25% of the non-irradiated cell nuclei respectively (Fig. 7 , compare A with E). The staining of nuclei recovered at 4 h post-irradiation (Fig. 7 F) indicating that the observed change in dye staining is reversible. The reduction of chromatin staining after UV irradiation parallels the inhibition of SV40 DNA replication. Similar reduction of staining was observed using ethidium bromide as probe and for the cells irradiated at 10-30 J/m 2 (data not shown).


Figure 7 . Fluorescence microscopic analysis of CV-1 cell nuclei stained with acridine orange after irradiation of cells with 90 J/m 2 . Cells were lysed with NP-40 buffer to remove cytoplasm and the nuclei were stained with 300 ng/ml of acridine orange for 5 min at ( B ) 0 min, ( C ) 30 min, ( D ) 1 h, ( E ) 2 h and ( F ) 4 h post-irradiation (see Materials and Methods). ( A ) The fluorescence staining of cell nuclei from non-irradiated CV-1 cells. Each photograph is displayed under the same magnification and color range of fluorescent staining intensity indicated as color values in (A) and (B).

DISCUSSION

In the present study we used two-dimensional neutral-alkaline gel electrophoresis technique to investigate SV40 DNA replication after UV irradiation. This technique allows us to examine the behavior of replication intermediates unambiguously. The results obtained using this analysis indicate that SV40 DNA replication is rapidly turned off after UV irradiation. This rapid inhibition of DNA replication is mainly due to the inhibition of replication initiation because the intensity of replication intermediate curves unequivocally disappear in the two-dimensional gel (Figs 1 B-E and 2 B-D). If replication initiation was not inhibited, continuing initiation would cause the stalled replication intermediates to accumulate, which was not observed in our two-dimensional gel. Our result also suggests that inhibition of SV40 DNA replication appears to be regulated by an overall inhibition of replication initiation because irradiation of host cell inhibits the replication of the non-irradiated transfected SV40 plasmid in a dose-dependent manner (Fig. 6 ). The present study demonstrates that UV irradiation inhibits mainly the initiation step of DNA replication in vivo and this inhibition is due to a micro-environment induced in the irradiated cells. This conclusion differs from previous studies of UV effect on DNA replication that elongation is the main step involved in the shut-down of DNA replication. Our study complements many other more recent investigations and points to the new concept that radiation causes immediate inhibition of replication initiation ( 5 , 22 - 25 ; see Discussion below).

Replication elongation proceeds on UV-damaged template following UV irradiation

Our data suggest that during the acute phase following UV irradiation, a significant fraction of chain elongation can proceed on UV-damaged templates. This is shown by the following experiments: (i) SV40 DNA replication intermediates defined by a short pulse with [ 3 H]TdR just before UV irradiation can be chased into mature Form I and Form II molecules (Fig. 4 ); (ii) kinetic study by in vitro nuclear run-on experiments shows a near normal SV40 DNA replication pattern immediately or at 15 min after irradiation with 90 J/m 2 of UV (Fig. 2 B) although replication is completely turned off later; (iii) heavily irradiated SV40 DNA or SV40-based plasmid replicates very efficiently after transfection into unirradiated cells (Table 1 ). The last finding is similar to results obtained by others. For example, UV-irradiated SV40-based plasmid replicates as efficiently as non-irradiated plasmid in repair-proficient human fibroblasts when assayed at 48 h post-transfection ( 26 , 27 ). In addition, studies measuring survival of transfected SV40 DNA by plaque assay using transfection with low multiplicity show that survival of SV40 DNA which contains ~32 pyrimidine dimers is reduced to only 37% of the non-irradiated control ( 28 , 29 ). Since plaque assay depends on intact early as well as late genes, it is more sensitive to UV than analysis based on DNA replication assay. Therefore, >32 pyrimidine dimers were needed to reduce DNA replication to 37%. Thus, a significant fraction of DNA replication must be able to bypass UV damage. The efficient replication of irradiated plasmid in Cos-1 cells could be due to efficient repair occurring on irradiated plasmids and/or recombination between transfected plasmid. However, there is no significant increase in the ability of input irradiated plasmid to transform HB101 during 1 h or more post-UV incubation period in our transfection assay (Table 2 ). This result suggests that efficient repair of heavily irradiated plasmid cannot account for the efficient replication we observed. In addition, a dose of 900 J/m 2 will generate ~40-50 pyrimidine dimers per plasmid ( 21 ). Poisson distribution predicts that only a minute insignificant fraction (10 -9 %) of plasmids will contain no UV damage. Thus, we consider the possibility that replication of this minute fraction or the replication-competent templates generated by recombination is quite unlikely.

Efficient bypass of UV damage during replication of DHFR domain in UV-irradiated CHO cells has been demonstrated ( 9 ). The bypass is not due to DNA recombination since no pyrimidine dimers were found in the daughter strands. The same study also cited unpublished results showing complete replication of pyrimidine dimer containing DNA in a repair-deficient CHO mutant cell line. This last observation is similar to our transfection data (Table 1 and 2 ). Hoy et al. also showed that maturation rates of DNA synthesized immediately before or after UV irradiation of CHO cells is similar ( 30 ) thus implicating that replication fork can efficiently bypass UV damages. Van Zeeland and Filon also showed that replication forks paused only briefly at pyrimidine dimers ( 31 ). Bypass of UV lesions in vitro has also been demonstrated using E.coli DNA polymerases I ( 32 ) and III ( 33 - 35 ) or in the mammalian system ( 22 , 36 , 37 ). In our in vivo experiment measuring the mutation frequency of SV40 plasmid replicated in Cos-1 cells, putatively mutagenic translesion synthesis was also observed.

Immediate inhibition of DNA replication after irradiation is mainly controlled by inhibition of replication initiation

Our observations that SV40 DNA replication was inhibited by irradiation of infected cells with UV light for a prolonged period without accumulation of stalled replication intermediates (Figs 1 and 2 ) and that irradiation of Cos-1 cells inhibited the replication of transfected, unirradiated SV40 plasmid (Fig. 6 ) suggest that immediate inhibition of DNA replication during acute phase response is mainly controlled by replication initiation. This is similar to results obtained for cells irradiated with ionizing radiation ( 23 ), in which replication of a small plasmid DNA is inhibited when cells are irradiated with a dose of X-rays too low to damage the plasmid DNA. That study suggests that immediate inhibition of DNA replication after radiation damage is regulated at the initiation levels of DNA replication, and is mediated by a trans -acting factor or factors that cause arrest of replication of undamaged small plasmid DNA in the irradiated cells. A recent study ( 24 ) of in vitro DNA replication reactions carried out by UV-irradiated HeLa cell extracts shows that their replication activity of unirradiated plasmid DNA decreases following UV irradiation. However, replication activity can be restored to these extracts by the addition of purified human single-stranded DNA binding protein, suggesting that UV-induced DNA replication arrest may be mediated through the essential component of the replication initiation complex thus implicating initiation as the regulatory step after UV irradiation. Recently, inhibition of DNA replication specifically at the level of replication initiation after ionizing irradiation has been demonstrated in the DHFR gene of a CHO cell line by two-dimensional gel replicon-mapping ( 5 ). In this technique, each class of replication intermediates traces a characteristic pattern, and fragments that contain initiation sites can be displayed as a bubble arc. When asynchronously growing cells were irradiated with X-rays, the initiation bubble arc completely disappeared within 30 min of radiation treatment and did not resume for 3-4 h. In contrast, the pattern of fragments representing the replication initiated before irradiation did not appear to change significantly in response to radiation. Our results as well as this study clearly support the idea that immediate inhibition of DNA replication after radiation is mainly controlled by replication initiation.

Global inhibition of replication may be due to a micro-environment induced in irradiated cells

The mechanism by which overall initiation of DNA replication is rapidly inhibited after radiation damage is still not understood. Some nuclear-specific signalling mechanisms involving signal transduction pathways have been invoked to explain the rapid inhibition of DNA replication after UV irradiation ( 38 , 39 ). Protein kinases have been implicated in the inhibition of replicon initiation after ionizing radiation ( 40 ). To examine the possible involvement of signal transduction pathways in the rapid inhibition of DNA replication, we studied the effect of tyrosine kinase inhibitors, genistein and tyrphostin, on SV40 plasmid replication in the UV-irradiated cells. We found no improvement of replication efficiency after blocking the tyrosine kinase signalling pathway (data not shown). Thus, the signal to inhibit DNA replication after UV is probably not significantly mediated by a tyrosine kinase pathway in our system. However, when an intracellular free radical scavenger, N -acetyl-cysteine, was added during the incubation after cells were irradiated with a UV dose of 10 J/m 2 , the SV40 plasmid replication recovered by 56%, i.e., from 43% (100%) to 67% (156%) (Table 3 ). The free radicals generated by UV irradiation may result in oxidative stress which triggers an alteration of cellular physiology. Indeed, we found rapid nuclear and chromatin changes in cells irradiated with UV (Fig. 7 ). The nuclear morphological changes may mask the recognition of replication machinery and produce a rapid mechanism for inhibition of DNA replication. This idea is also supported by a finding that DNA replication is inhibited by X-rays in chromosomal and plasmid DNA but not in mitochondrial DNA, which is located in the cytoplasm ( 25 ).

Table 3 . Yield of pSV2CAT plasmid after replication in UV-irradiated Cos-1 cells when N -acetyl-cysteine (NAC) was added during the post-irradiation incubation

Relative transformation efficiency (%)

NAC (mM)

+NAC

+UV (10 J/m 2 )

+UV +NAC a

0

100

0.1

84

43

67

a These values were adjusted after the inhibition of relative transformation efficiency by adding NAC alone.

In summary, our observations that replication of SV40 DNA was inhibited by UV irradiation of host cells and that a rapid alteration of nuclear organization was induced by UV, suggest that inhibition of DNA replication is the result of a global change in cell microenvironment after UV irradiation, and is possibly mediated by the nuclear morphology changes. However, further analysis is needed to understand the molecular mechanism involved in the regulation of DNA replication initiation after radiation damage.

ACKNOWLEDGEMENTS

This work is supported by a grant from National Science Foundation (NSC) of Republic of China. Y.-C.W. is the recipient of a postdoctoral fellowship award from NSC.

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