Proc. Nati Acad. Sci. USA Vol. 80, pp. 1347-1351, March 1983 Cell Biology

Dynamics of pyrimidine deoxynucleoside triphosphate pools in relationship to DNA synthesis in 3T6 mouse fibroblasts (nucleoside incorporation/compartmentation/amethopterin block) BjORN NICANDER AND PETER REICHARD Medical Nobel Institute, Department of Biochemistry I, Karolinska Institutet, Box 60400, S-104 01 Stockholm, Sweden Contributed by Peter A. Reichard, November 18, 1982

ABSTRACT The 3H-labeled nucleosides cytidine, deoxycyti- tivity into DNA to this value (1, 2). Such a procedure becomes dine, and thymidine are rapidly incorporated into DNA via dCTP imperative when one wishes to distinguish between effects of or dTTP pools. Between 30 and 60 minafter addition of tracer different manipulations-e. g., pharmacological interference- amounts ofa labeled nucleoside to the medium ofrapidly growing on precursor synthesis and DNA replication. Knowing the spe- 3T6 cells, dNTPpools attained a constant specific activity resulting cific activity of a dNTP under steady-state conditions may in from a steady-state equilibrium between incorporation of nucleo- addition permit determination of absolute rather than relative side, de novo synthesis, and linear incorporation of isotope into rates of DNA synthesis. DNA. Removal oflabeled deoxycytidine or thymidine depleted the The of dNTP pools ofisotope within a few minutes and incorporation into possibility compartmentation of dNTP pools poses DNA stopped. When de novo synthesis ofdTTP was blocked with additionalicomplications (3). Fractionation ofcells in nonaque- amethopterin, the intracellular dTTP pool rapidly reached the ous media led to -the suggestion of separate cytoplasmic and. specific activity of thymidine of' the medium and isotope-incor- nuclear dNTP pools in Chinese hamster ovary cells (4). Kinetic poration into DNA then measured absolute rates of DNA synthe- experiment with HeLa cells were interpreted to indicate pref- sis. In experiments with and without. amethopterin, we found no erential incorporation of labeled thymidine into DNA via a kinetic evidence for the existence ofmore than one dTTP pool and dTTP pool that was not in equilibrium with dTTP formed de the decay ofthe pool suggested that all dTTP served as precursor novo (5). The suggested channeling of DNA precursors via a ofDNA. In contrast, experiments with deoxycytidine and cytidine postulated multienzyme "replitase" also leads to compartmen- suggested the presence of separate dCTP'pools with preferential tation of dNTPs (6). DNA synthesis from the pool labeled from cytidine. The aim ofthe present work was to relate the synthesis and breakdown ofpyrimidine dNTP pools to DNA synthesis in 3T6 Incorporation ofradioactive thymidine or, less frequently, other cells. When dTTP was labeled by using thymidine and de novo labeled nucleosides into DNA is often used to measure the rate synthesis was blocked with amethopterin, the specific activity of DNA synthesis. With thymidine and other deoxynucleo- ofthe pool rapidly approached that ofthe radioactive thymidine' sides, incorporation involves a series of phosphorylation steps in the medium, permitting determination of absolute rates of leading directly to dNTPs; with ribonucleosides, reduction of DNA synthesis. In parallel experiments, we measured incor- the ribose moiety is required in addition. dNTPs are also formed poration of labeled thymidine, deoxycytidine, or cytidine into de novo from small molecules. These interrelationships for the DNA and dNTP pools in the absence of amethopterin. From nucleosides thymidine, deoxycytidine, and cytidine are out- dataobtained under steady-state conditionswith thymidine and lined below. cytidine, we could calculate rates of DNA synthesis very close to those obtained with thymidine in the presence ofamethop- Thymidine Deoxycytidine Cytidine terin, while the results with labeled deoxycytidine gave much lower values. These experiments suggest that, under steady- dTMP +- dUMP +- dCMP CMP state conditions, DNA in 3T6 cells is synthesized from dTTP I 1 I I and dCTP pools in rapid equilibrium with labeled thymidine dTDP de novo dCDP - CDP or cytidine. On the other hand, isotope from deoxycytidine ap- I synthesis I T pears to be preferentially incorporated into a dCTP pool that, dTTP dCTP de novo is not used directly for DNA synthesis. We also found that the synthesis decay ofthe labeled dTTPpoolclosely matched the rate ofDNA \DNA / synthesis; Clearly, incorporation of a labeled nucleoside into DNA de- MATERIALS AND METHODS pends on other factors in addition to the rate of the final poly- Materials. [5-3H]Cytidine, [5-3H]deoxycytidine, and [meth- merization of dNTPs. yl-3H]thymidine with specific activities of 20-30 Ci/mmol (1 In spite of this, incorporation of thymidine has been used Ci = 3.7 GBq) and 3H- and a-32P-labeled dNTPs were obtained widely, and often successfully, to monitor relative rates ofDNA from Amersham. Care was taken to use the radioactive com- synthesis, neglecting possible errors introduced by changes in pounds shortly after delivery or to redetermine their specific specific radioactivities ofdTTP. A safer, but more cumbersome, activity by HPLC. approach would be to measure the specific activity of the im- Incorporation of 3H-Labeled Nucleosides into Cells. 3T6 mediate precursor dNTP and relate incorporation of radioac- mouse fibroblasts (105 cells) were explanted onto 5-cm dishes and grown for 44-48 hr at 37°C in 5 ml of Dulbecco's modified The publication costs ofthis article were defrayed in part by page charge Eagle's medium/10% inactivated horse serum to a density of payment. This article must therefore be hereby marked "advtertise- ment" in accordance with 18 U. S. C. §1734 solely to indicate this fact. Abbreviation: HAT, hypoxanthine/amethopterin/thymidine. 1347 Downloaded by guest on September 29, 2021 1348 Cell Biology: Nicander and Reichard Proc. Natl. Acad..Sci. USA 80 (1983) 0.6-1.0 X 106 cells. Three hours before addition.ofisotope, the rate. The observed specific activity ofagiven dNTP is the result medium was reduced to 2.5 ml and buffered with 1 M Hepes ofa balance between phosphorylation ofthe labeled nucleoside (pH 7.4) (final concentration, 25 ,uM). In experiments measur- and de novo synthesis. The rate of DNA synthesis can be cal- ing the decay of dNTPs, the cells' were transferred in a warm culated from -the incorporation at 60-120 min. After that time (370C) room from the incubator to tightly sealed boxes.contain- (arrow in Fig. 1), radioactive medium was replaced with pre- ing 5% C02/95% air atmosphere and all further manipulations warmed conditioned medium containing 0.3 A&M unlabeled in the warm room outside the boxes were as brief as possible. nucleoside. With [3H]thymidine and [3H]deoxycytidine, this A 3H1-labeled nucleoside without dilution was added to the resulted in rapid depletion ofthe intracellular acid-soluble ra- medium to afinal concentration ofabout 0.33uM and incubation dioactivity, indicating rapid -turnover of the dNTP pools, with was continued for the indicated times. To measure the decay half-lives of-about 5 min. With [3H]cytidine, about 90% ofthe of label, medium was removed by aspiration and immediately acid-soluble radioactivity waspresentasCTPand, aftermedium replaced with 2.5 ml ofconditioned medium (from parallel cul- change, isotope continued to flow from this pool into the much tures without isotope) containing 0.3 ,uM unlabeled nucleoside. smaller dCTP pool. In this case, we could therefore not deter- Incubations were terminated and isotope incorporation into mine the turnover of the dCTP pool. DNA was determined as described (7) except that 2 ml of cold Decay ofdNTP Pools. A more careful analysis ofthe events 60% methanol (8) was used in place ofHCI04. The mixture was during the first 10 amin of the decay of dTTP and dCTP pools centrifuged at 22,000 x g for 45 min, the supernatant was evap- labeled by using thymidine or deoxycytidine, respectively, was orated to dryness at reduced pressure, and the residue so ob- made in a second experiment. In Fig. 2 the logarithms of the tained was dissolved in 0.2 ml of 10 mM Tris buffer (pH 7.0) specific activities ofthe two dNTPpools are plotted as afunction and used for the determination of dNTPs (8, 9) and their specif- oftime. The linearity ofthe firstpart ofthe curves suggests that, ic activity (refs. 1, 2; unpublished data). during this part of the experiment, the reaction followed first- All values in the figures and tables are normalized to 106 cells. order kinetics with half-lives of5.5 (dTTP) and 6'(dCTP) min. From these values and the pool sizes for dTTP (80 pmol) and dCTP (115 pmol), one can calculate that the initial decay of ra- RESULTS dioactivity corresponded to turnover rates of 10 and 13 pmol/ Attainment of Steady-State Conditions. Tracer amounts of min per 106 cells, respectively. highly 3H-labeled thymidine, deoxycytidine, and cytidine were Thymidine Incorporation Measures the True Rate ofDNA added to separate sets ofcultures ofrapidly growing 3T6 cells. Synthesis. Rates ofDNAsynthesis duringbriefexperiments can After 60 min at 370C, equilibrium was attained in each case (Fig. be computed from the incorporation of isotope into DNA and 1). The total acid-soluble radioactivity, as well as the specific the specific activity ofa dNTP pool labeled under steady-state activity ofthe labeled dNTP pools, had reached a plateau value conditions as described in Fig. 1. This approach assumes that and isotope incorporation into DNA was occurring at a linear the measured value for the dNTP pool represents the specific activity of the immediate precursor for DNA synthesis. How- ever, a given dNTP may be present in more than one pool and have a different specific activity in each. If then DNA is syn- + 16 thesizedpreferentially from only one such pool-derived, e.g., by de novo synthesis via reduction ofribonucleotides-the spe- -14 cific activity ofa given dNTP pool labeled by using thymidine or deoxycytidine via the salvage pathway may not represent the 12 relevant value for measurement of the rate of DNA synthesis. We investigated this question by an experiment in which the de novo pathway was blocked and the cells were forced to syn-

an tn c1J i 152 X i 'U 41.- u %-f I I 4 12 9 ip,} +~~~~+z + + '+ I-100 46 -1 10 .'0 '4 2 'Cyfdine I 60 120 mi FIG. 2. Decay of radioactivity of!dNTP pools labeled with thymi- dine ordeoxycytidime. 3T6 cells were grown in radioactive medium for FIG. 1. Time course df incorporation of labeled nucleoside into AO min, mediumwaschanged, andsampleswere removedforanalysis acid-soluble nucledtide (+ +) and DNA (e---4). -of acid.soluble pools. Downloaded by guest on September 29, 2021 Cell Biology: Nicander and Reichard Proc. Natl. Acad. Sci. USA 80 (1983) 1349 thesize DNA from dTTP obtained exclusively via the salvage Table 1. Effect of HAT medium on dTTP pools and rate of pathway from added radioactive thymidine. For this purpose, DNA synthesis amethopterin was included in the culture medium (10) and the DNA synthesis cells were supplied with exogenous hypoxanthine and thymi- dTTP Radioactivity dTMP dine (HAT medium). Such cells, as well as -parallel cultures in 1oo incorporated, incorporated, were and the normal medium, pulsed with [3H]thymidine Medium pmol cpm/pmol cpm/min amount ofradioactivity incorporated into DNA and the specific pmol/min activity ofthe dTTP pool were determined at various times after Normal 90 5,900 77,000 13 addition of the radioactive nucleoside. Two separate experi- HAT 1 150 280 3,400 12 ments with HAT medium were made: (i) HAT medium was HAT 2 172 220 3,000 14 present from the start of the culture-i.e., for 48 hr before ad- dition of [3H]thymidine (HAT 1)-and (ii) HAT medium was sults ofthree such experiments are summarized in Table 2. In introduced into the culture medium, only 2 hr before addition each case, several sets of cultures were pulsed with tracer of isotope (HAT 2). After 48 hr, the HAT 1 cultures (1 X 106 amounts of nucleoside and the linear incorporation of isotope cells per dish) had reached almost exactly the same density as into DNA and the specific-activities ofthe correspondingdNTP the control cells (0.8 x 106 cells per dish), showing that the pools were determined, similar to the experiment described in growth rates were similar. Fig. 1 (experiment 2 of Table 2 is in effect identical to the Incorporation of isotope into DNA (Fig. 3) was linear 30-90 one described in Fig. 1). min after addition of [3H]thymidine in both normal and HAT In each experiment, the rate of DNA synthesis computed cultures [where the enlarged dTTP pools (see Table 1) might the of was much delay equilibration with [3H]thymidine]. The amount of radio- from incorporation [3H]deoxycytidine less than the rate calculated from incorporation ofthymidine or cytidine. activity incorporated per unit time was about 20-fold higher in This indicates that the specific activity of the dCTP pool labeled the control cultures. However, as shown in Table 1, this dif- by using deoxycytidine was not identical to the specific activity ference is matched by a corresponding difference in the specific activities of the dTTP pools. The latter values had already pla- of dCTP used for DNA replication. With [3H]cytidine, how- teaued by the 30-min time point; the values given in Table 1 ever, the computed rates of DNA synthesis were similar to represent averages from four determinations between 30 and those found with [3H]thymidine. Taken together, our data indi- 90 min. All three cultures synthesized DNA at identical rates cate compartmentation of the dCTP pool. (expressed as pmol of dTMP incorporated). In the two HAT This question was further investigated by measuring the ef- experiments, the specific activities of the dTTP pools were al- fect of HAT medium on the incorporation of deoxycytidine into most identical to the specific activity of the [3H]thymidine of DNA. HAT increases the size of the dTTP pool (Table 1), which the medium. In contrast, the specific activity of the dTTP pool inhibits the reduction of CDP (11) and decreases the size of the ofthe control culture was only 39% ofthe specific activity ofthe dCTP pool to one-fourth (data not shown). Because deoxycy- precursor thymidine, demonstrating dilution by endogenous tidine kinase is feedback inhibited by dCTP (12), HAT medium dTTP synthesis. facilitated the entry of labeled deoxycytidine into the dCTP In conclusion, this experiment showed that the true rate of pool, resulting in an almost 6-fold increase in its specific activity DNA synthesis of 3T6' cells can be calculated from the' incor- and' an even greater increase in incorporation of isotope into poration of labeled thymidine' into DNA, provided that. the DNA (Table 3). The rate of DNA synthesis calculated from de- specific activity ofthe dTTP pool is determined under steady- oxycytidine incorporation in the presence of HAT was equal to state conditions. the rate calculated from thymidine (Table 3). DNA Synthesis from [3H]Deoxycytidine and [3H]Cytidine. Comparison of dNTP Pool Turnover and Rate of DNA Syn- Can the rate ofDNA synthesis be similarity computed from the thesis. The data in Fig. 2 and experiment 1 of Table 2 derive incorporation ofdeoxycytidine or cytidine? To decide this ques- from the same sets of cultures and permit direct correlation of tion, the incorporation ofthese nucleosides into DNA was com- the decay of the radioactive dNTP pools with the rate of DNA pared with the incorporation of thymidine in parallel sets of synthesis. cultures. Thymidine incorporation then gave the correct rate With dTTP, the decay [(10 pmol/min)/106 cells] closely of DNA synthesis with which the rates computed from the in- matchedthe rate of DNA synthesis (11 pmol/min per 106cells), corporation of other nucleosides could be compared. The re- indicating that, under steady-state conditions, all dTTP is used for DNA replication. This conclusion is further strengthened by our finding that little' or no radioactivity was excreted into (+. I E E 3. the medium during the decay period (data not shown). With

Ad 2 ~ ~ ~ ~ ,~ Table 2. Rates of DNA synthesis as determined from specific W- activities of dNTP pools labeled by' using thymidine, I' x l. I Z) E 1- deoxycytidine, or cytidine Specific activity Labeled dNMP z a Radioactive of dNTP, in DNA, 30 60 90 Exp. nucleoside cpm/pmol pmol/min min 1 Thymidine 6,800 11 Deoxycytidine 390 4 FIG. 3. Effect of HAT medium on incorporation of [3H]thymidine 2 Thymidine 3,900 14 into DNA. Labeled thymidine was added to cultures in normal medium Deoxycytidine 580 6 (e) or in medium to which HAT medium had been added 2 (x) or 48 (+) hr earlier. The specific activity of thymidine in normal medium Cytidine 380 16 3 Deoxycytidine 950 5 (0.3 AuM) was 15,200 cpm/pmol and thatin HAT medium (16.3 AM) was 286 cpm/pmol. Cytidine 770 12 Downloaded by guest on September 29, 2021 1350 Cell Biology: Nicander and Reichard Proc. Natl. Acad. Sci.'USA 80 (1983) Table 3. Effect of HAT medium on apparent rate of DNA culate a turnover ofdTTP that closely matched the incorpora- synthesis as determined by incorporation of deoxycytidine tion of dTMP into DNA calculated from the incorporation of or thymidine radioactivity under steady-state labeling conditions. The stoi- Labeled dNMP chiometry between the amount of radioactivity leaving the dNTP pool, in DNA, dTTP.pool and the amount ofradioactivity entering DNA sup- System cpm/pmol pmol/min ports the existence ofa single dTTP pool, exclusively involved Deoxycytidine 380 4 in DNA synthesis. Our data do of course not exclude the ex- Deoxycytidine/HAT -2,200 11 istence of minor separate dTTP pools-e.g., in mitochondria Thymidine 3,700 12 (17)-or of several major pools in rapid equilibrium with each Thymidine/HAT 380 11 other. The dCTP pool behaved differently. When the poolcand DNA HAT was added to the medium 2 hr before addition of isotope. were labeled by using deoxycytidine, calculated rates of DNA synthesis were lower than rates calculated from incorporation dCTP labeled by using deoxycytidine, the decay (13 pmol) of thymidine. On the other hand, cytidine labeling gave values clearly exceeds the computed rate of DNA synthesis (4 pmol). similar to those obtained with thymidine. In these comparisons, one must include the reported thymidine/deoxycytidine ratio of 1.3 for mouse DNA (18). Deoxycytidine incorporation thus DISCUSSION underestimated the rate of DNA synthesis while cytidine in- We have for some time been interested in the interrelationship corporation gave slightly high values. This suggests that deoxy- between the synthesis of deoxyribonucleotides and their utili- cytidine and cytidine introduce isotope into separate dCTP pools zation for DNA replication (13). We have carried out measure- and that the pool labeled by using cytidine wagmore directly ments of dNTP pool sizes under various conditions of cell related to DNA synthesis. These pools need not necessarily be growth and shown that there are large increases in the sizes of present in the same cell and we cannot exclude the possibility all four pools during the transition of cells from G1 to S phase that deoxycytidine preferentially labeled dCTP present in cells (14, 15). In particular, the size of the dCTP pool appeared to not involved in DNA synthesis while cytidine labeled dCTP in show considerable correlation with the percentage of cells in cells in S phase. It is more likely, however, that both nucleosides S phase. were mainly incorporated into cells in S phase. Cytidine then With the present experiments, we begin to analyze the dy- labeled adCTP pool directly connected with DNA synthesis while namics ofpyrimidine dNTP turnover. We used cultures ofrap- deoxycytidine.labeled a second pool that reached equilibrium idly growing 3T6 mouse fibroblasts with a generation time of with the first one slowly. This explanation is favored by the stim- about 12 hr. From autoradiography with [ H]thymidine, we ulation of deoxycytidine incorporation by HAT medium (Table estimate that, during our experiments, about 70% of the cells 3), an effect that can be ascribed to the contraction of the first were in different stages of S phase. Even though the hetero- dCTP pool formed by the reduction of CDP coupled to an in- geneity of the cell population poses problems in the interpre- crease of isotope incorporation from deoxycytidine into the sec- tation of our results, we believe that most of the effects de- ond dCTP pool. scribed here relate to interrelationships between pyrimidine Earlier results (4) suggested that the dCTP pool is compart- dNTP pools and DNA synthesis in S-phase cells. mentalized between the cytoplasm and the cell nucleus while dCTP and dTTP pools of 3T6 cells were labeled by addition the dTTP pool is exclusively in the nucleus. -Our present data of radioactive nucleosides to-,the growth medium. Earlier work could- relate to this result: the nuclear dNTPs then represent by Plagemann et al. (16) has shown a rapid transport of labeled the proximal precursor pools and are labeled from thymidine nucleosides from the medium into cultured cells followed by and cytidine while deoxycytidine preferentially labels the cy- rate-limiting phosphorylation steps as outlined in the Intro- toplasmic dCTP pool. duction. The trace amounts of nucleosides used in our exper- The existence ofmore than one dCTP pool makes it difficult iments caused minimal perturbation of the sizes of the dNTP to analyze the decay of isotope from dCTP labeled by using pools, not measurable by our method. After an initial lagperiod, deoxycytidine. dCTP also serves as a substrate for dTMP for- the specific activities of the dNTP pools attained constant values mation via deamination of dCMP to dUMP (see the Introduc- and isotope incorporation into DNA became linear. From data tion). During this reaction sequence, all isotope is lost to the obtained during this steady-state period, we could calculate a medium because both.deoxycytidine and cytidine were labeled rate of DNA synthesis, expressed as pmol of dNMP incorpo- in the 5' position of the pyrimidine ring. Further work is re- rated, assuming that the determined specific activity of the dNTP quired to clarify this situation. the pool was identical with the specific activity of substrate of This work was supported by grants from the Swedish Medical Re- the polymerase. search Council, Magn. Bergvall's Stiftelse, and the Medical Faculty of This assumption was validated for the dTTP pool by an ex- the Karolinska Institutc. periment in which the pool was labeled with thymidine under two sets of conditions: (i) tracer amounts of labeled thymidine 1. Stimac, E., Housman, D. & Huberman, J. A. (1977)J. Mol. Biol. and excess labeled in HAT medium. In the second 115, 485-511. (ii) thymidine 2. Hellgren, D., Nilsson, S. & Reichard, P. (1979) Biochem. Bio- case; the radioactivity ofthe intracellulardTTPpool approached phys. Res. Commun. 88, 16-22. the specific activity of the external thymidine after 30 min and 3. Mathews, C. K., North, T. W. & Reddy, G. P. V. (1979) Adv. represented the specific activity of the substrate of the poly- Enzyme Regul. 17, 133-156. merase. Rates of DNA synthesis calculated from the two parallel 4. Skoog, L. & Bjursell, G. (1974) J. Biol. Chem. 249, 6434-6438. sets of cultures were identical, showing that the experiment 5. Kuebbing, D. & Werner, R. (1975) Proc. Natl. Acad. Sci. USA 72, with the trace amount oflabeled also lead to the cor- 3333-3336. thymidine 6. Reddy, G. P. V. & Pardee, A. B. (1980) Proc. Natl. Acad. Sci. USA rect value. 77, 3312-3316. The turnover rate of the dTTP pool was determined after 7. Akerblom, L., Pontis, E. & Reichard, P. (1982) J. Biol. Chem. replacement of radioactive medium with medium containing 257, 6776-6782. unlabeled thymidine. From the decay of isotope, we could cal- 8. Skoog, L. (1970) Eur. J. Biochem. 17, 202-208. Downloaded by guest on September 29, 2021 Cell Biology: Nicander and Reichard Proc. Nati. Acad. Sci. USA 80 (1983) 1351

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