Journal of Experimental Botany, Vol. 54, No. 383, pp. 699±706, February 2003 DOI: 10.1093/jxb/erg079 RESEARCH PAPER Genes encoding two essential DNA replication activation proteins, Cdc6 and Mcm3, exhibit very different patterns of expression in the tobacco BY-2 cell cycle Gerardas Dambrauskas1,4, Stephen J. Aves1, John A. Bryant1,3, Dennis Francis2 and Hilary J. Rogers2 1 2 School of Biological Sciences, Washington Singer Laboratories, University of Exeter, Exeter EX4 4QG, UK School of Biosciences, Cardiff University, PO Box 915, Cardiff CF10 3TL, UK Received 4 July 2002; Accepted 14 October 2002 Abstract Very little is known about the expression patterns in plants of genes that encode proteins involved in the initiation of DNA replication. Partial cDNA sequences that encode Cdc6 and Mcm3 in tobacco have been isolated. The sequences were used as probes in northern blots which suggested that, in the cell cycle of synchronized tobacco BY-2 cells, expression of CDC6 is con®ned to late G1 and S-phase whereas the expression of MCM3 is not con®ned to any particular cell cycle phase. These data were con®rmed and extended by real-time PCR measurements of mRNA abundance through the cell cycle. CDC6 exhibits a very clear peak of expression in S-phase whereas MCM3, expressed at a much lower level than CDC6, is not cell-cycle-regulated. These patterns of cell cycle gene expression resemble those found in the ®ssion yeast Schizosaccharomyces pombe rather than those in budding yeast or mammalian cells. Key words: BY-2, Cdc6, cell cycle, DNA replication, Mcm3, tobacco. Introduction The initiation of DNA replication at eukaryotic origins of replication is a complex multi-step process (reviewed in Bryant et al., 2001). In summary, origins marked by the origin±recognition complex are recognized and bound by the `loading factors' Cdt1 and Cdc6. This permits the binding of the MCM (mini-chromosome maintenance) complexes, leading to the expulsion of the loading factors. 3 4 The helicase activity of the MCM complexes initiates the unwinding of the double helix leading to the formation of a replication bubble and the establishment of two replication forks. Binding of the primase-polymerase-a loading factor, Cdc45, then occurs, followed by loading on to the template of the primase-polymerase-a complex itself. This multi-step process involves proteins that are required transiently at each origin, such as Cdt1, Cdc6 and Cdc45, and proteins required throughout replication of the complete replicon, such as the MCM proteins (Labib and Dif¯ey, 2001) and primase-polymerase-a (required not only for the initiation of the leading strand but also for the initiation of each Okazaki fragment). In common with most other proteins involved in plant DNA replication, very little is known about expression patterns of the genes encoding these important proteins during the cell cycle. Sabelli et al. (1996) suggested, on the basis of the distribution of mRNA as detected by in situ hybridization, that the expression of MCM3 in maize roots was restricted to only a part of the cell cycle, but it was not possible to ascertain which phase that was. For CDC6, however, there are clear data from Arabidopsis thaliana cell cultures showing that expression is limited to late G1 and S-phase (de Jager et al., 2001; Castellano et al., 2001). In other eukaryotes, two general patterns of gene expression have been observed. In budding yeast, Saccharomyces cerevisiae, a very high proportion of the genes involved in DNA replication are expressed only in S-phase (or in late G1 plus S-phase) under the control of the MCB (MluI cell cycle box) elements in their promoters (Johnston and Lowndes, 1992; Koch and Nasmyth, 1994). A very similar pattern occurs in Metazoa, although some of the genes, such as those encoding replicative enzymes, are To whom correspondence should be addressed. Fax: +44 (0)1392 264668. E-mail: [email protected] Present address: Department of Biochemistry, North Carolina State University, Raleigh, NC 27695, USA. Journal of Experimental Botany, Vol. 54, No. 383 ã Society for Experimental Biology 2003; all rights reserved 700 Dambrauskas et al. expressed at signi®cant levels outside S-phase, but are further up-regulated in S-phase (Yamaguchi et al., 1996; Zhao and Chang, 1997; Huikeshoven and Cotterill, 1999). In ®ssion yeast, Schizosaccharomyces pombe, by contrast, the expression of only a few DNA replication genes is con®ned to S-phase. These include cdt1, cdc18 (homologous to CDC6 of S. cerevisiae), cdc22 (large subunit of ribonucleotide reductase) and cig2 (a B-type cyclin) (Gordon and Fantes, 1986; Fernandez Sarabia et al., 1993; Kelly et al.,1993; Connolly and Beach, 1994; ObaraIshihara and Okayama, 1994; Hofmann and Beach, 1994). Other DNA replication genes that have been investigated in S. pombe, including those encoding the initiating DNA polymerase and the MCM proteins, fail to show a peak of expression at any particular cell cycle phase. Using an easily synchronizable cell line should help to resolve the timing of expression of regulatory genes of S-phase in the plant cell cycle. Therefore, the expression of genes encoding replication initiation proteins in tobacco (Nicotiana tabacum) BY-2 cells is studied here. For this study, two genes, CDC6 and MCM3 that show different expression patterns in S. pombe but similar patterns in S. cerevisiae and in Metazoa, were selected initially. Expression of these genes in synchronized cultures, using two different techniques for mRNA assay, has been rigorously investigated. The results clearly show that the expression of tobacco CDC6 is con®ned to late G1 and S-phase, whereas the expression of MCM3 occurs throughout the cell cycle. Materials and methods Maintenance and synchrony of tobacco BY-2 cells The tobacco BY-2 cell line (derived from Nicotiana tabacum cv. Bright Yellow-2) was maintained as described by Nagata et al. (1992). The cells were synchronized by a 24 h incubation of stationary phase cells (7 d since previous subculture) in a medium containing 5 mg ml±1 aphidicolin (Herbert et al., 2001). The cells were released from the aphidicolin block by thorough washing in BY-2 medium and then transferred into 100 ml fresh medium. The mitotic index was determined by staining nuclei with 0.1 mg ml±1 bis-benzamide tri-hydrochloride, Hoechst 33258, solution (Sigma) in the presence of 2% Triton X-100 and examining them under UV light (365 nm) with a Nikon EFD-3 microscope. Preparation of probes for northern hybridization N. tabacum complementary DNA (cDNA) was made as described below (see Reverse transcription) and probes were generated from the cDNA by PCR. Primers for MCM3 were based on the pea (Pisum sativum) homologue (Accession no. AJ012750). Primers for CDC6 were based on the A. thaliana homologue (Accession no. AJ293020). Primers for GAPdH were based on the tobacco cytosolic glyceraldehyde-3-phosphate dehydrogenase sequence (Accession no. M14419). The primers are listed in Table 1. Thirty cycles of PCR were performed from cDNA at 95 °C for 2 min, 55±65 °C (depending on the primers used) for 30 s and 72 °C for 1 min. The products were cloned into pGEMâ-T Easy Vector (Promega) and sequenced. The probe (196 bp) for A. thaliana histone H4 was a gift from Dr Nicole Chaubet-Gigot (Strasbourg). Table 1. Primers used for ampli®cation of sequences from cDNA Target Sequence (5¢ to 3¢) MCM3 MCM3 CDC6 CDC6 GAPdH GAPdH CTG CGT CTG GTC AGC TCC CAA GAA CTG TCA GCA AGA ACC ATT GCC CCA GGG TGT CCA GGA ACT GGA AGT GCG CTC CTG CAG ACA CAT AGA GCC T GCT GCT GAC TTG AAG GGT GGT GCC CCC CAT TCA TTG TCA TAC CAC GAC RNA extraction and Northern blots Total RNA was isolated from BY-2 cells using TRI ReagentÔ (Sigma) following the manufacturer's protocol. RNA samples (30 mg) were separated on 1% agarose formaldehyde gel and transferred onto Nylon 66-Blotting membrane (Fluka). The probes were labelled with 32P using Ready-To-Go DNA Labelling Beads (Amersham Biosciences) and hybridized in Northern MaxÔ hybridization solution (Ambion) overnight at 42 °C. The membrane was washed with 13 SSPE, 0.1% SDS for 10 min at 42 °C followed by two washes with 0.53 SSPE 0.1% SDS for 10 min at room temperature. The membrane was exposed to X-ray ®lm (Fuji) with an intensifying screen. Reverse transcription Complementary DNA was synthesized in a 50 ml reaction volume. A sample of total RNA (10 mg) was incubated at 65 °C for 5 min with 500 ng of oligo-dT primer (Sigma), then cooled for 10 min to 22 °C to allow oligo-dT to anneal to the poly(A) tail of mRNA. 5 ml of 103 ®rst strand buffer (Stratagene), 40 units of RNase Inhibitor (Sigma), dNTPs to 200 mM, and 80 units of M-MuLV reverse transcriptase (Stratagene) were added to the reaction mix which was incubated at 37 °C for 1 h. To inactivate reverse transcriptase the reaction was incubated at 90 °C for 5 min. The cDNA was then ready for real-time PCR. Primers used for real-time PCR The primers were based on the N. tabacum MCM3, CDC6, H4, and GAPdH sequences previously characterized (see above). The speci®city of the ampli®ed products was veri®ed by gel electrophoresis and sequencing prior to use in real-time PCR reactions. The primers for real-time PCR are shown in Table 2. Real-time quantitative PCR Quantitative PCR was performed with the real-time PCR system, LightCyclerÔ (Roche Diagnostics, Mannheim, Germany), using SYBRâ Green I double strand DNA binding dye. The ampli®cation of a target with the primers listed in Table 2 was carried out in a total volume of 5 ml containing 1 pmol of each primer, 5 mM MgCl2, 1 ml LightCyclerÔ DNA Master SYBRâ Green I (containing 1.25 units of Taq polymerase, 103 Taq buffer (500 mM KCl, 100 mM TrisHCl, pH 8.3), dNTPs each at 2 mM, 103 SYBRâ Green I; Roche Diagnostics) and 100 ng of cDNA prepared as described above. The ampli®cation protocol comprised four phases: (i) denaturation of the template DNA, (ii) ampli®cation of the target DNA, (iii) melting curve analysis for product identi®cation, and (iv) cooling the rotor and the thermal chamber. The initial template denaturation was at 95 °C for 30 s, followed by 40 three-step cycles of template denaturation at 95 °C with a 0 s hold, primer annealing at 63 °C for 7 s and extension at 72 °C for 17 s. Fluorescence data were collected after each extension step. Melting curve analysis was performed by heating the template at 95 °C with a 0 s hold, then cooling to 65 °C with a 15 s hold and ®nally raising to 95 °C with a 0.1 °C s±1 Cdc6 and Mcm3 in the tobacco BY-2 cell cycle 701 Table 2. N. tabacum primers used for the real-time PCR LightCyclerÔ system Target Amplicon length Sequence (5¢®3¢) Tm (°C) GAPdH GAPdH MCM3 MCM3 Histone H4 Histone H4 CDC6 CDC6 452 452 550 550 320 320 320 320 GCA CTA CCA ACT GCC TTG CAC CT GGC AAT TCC AGC CTT GGC ATC G CTG CGT CTG GTC AGC TCC CAA GAA C CTG TCA GCA AGA ACC ATT GCC CCA GC GGC ACA GGA AGG TTC TGA GGG ATA ACA TAA CCG CCG AAA CCG TAG AGA GTC C GAG AAG CAG CAG CCA GCA GGC ACG GCA CAT AGT TCC AAT GCT TGA GGC 64.2 64.0 67.9 68.0 66.5 66.3 69.6 62.7 temperature transition rate while continuously monitoring the ¯uorescence. All other phases were performed with a 20 °C s±1 transition rate. Fluorescence was analysed using LightCyclerÔ Analysis Software. The crossing point for each reaction was determined using the Second Derivative Maximum algorithm and manual baseline adjustment. Concentrations of standards were determined by measuring the A260. Reporter gene construction and plant cell transformation The cauli¯ower mosaic virus 35S promoter (CaMV35S) was removed from the uidA reporter gene plasmid pCAMBIA1305.2 (CAMBIA, Canberra, Australia) by digestion with EcoRI and NcoI. The A. thaliana MCM3 promoter was ampli®ed using standard PCR procedures. The forward primer introduced an EcoR1 restriction site and the reverse primer introduced an Nco1 restriction site. Forward primer: 5¢-CCTTTTGAATTCTCT GCCCTATCG-3¢. Reverse primer: 5¢-TTACCATGGTTCTTAACAAAATCTGGGTTC-3¢. The ampli®ed promoter was subcloned into the pGEMâ-T Easy vector (Promega), checked by sequencing, then excised by digestion with EcoRI and NcoI and cloned into the pCAMBIA1305.2 vector upstream of the uidA (gus) reporter gene to create an MCM3promoter-uidA fusion. The plasmid was introduced into Agrobacterium tumefaciens LBA 4404 and used to transform tobacco BY-2 cells, essentially as described by An (1987). Hygromycin-resistant calli were pooled and reintroduced into suspension culture. The transgenic cell suspension was maintained by subculturing 5 ml of stationary-phase cells into 95 ml of fresh medium supplemented with timentin (ticarcillin/potassium clavulanate) (250 mg ml±1) and hygromycin (100 mg ml±1). After two rounds of subculture, timentin was omitted from the medium. Results CDC6 and MCM3 in tobacco In order to generate homologous probes for northern blotting, speci®c fragments of the tobacco CDC6 (Accession no. AJ298071) and MCM3 (Accession no. AY077639) cDNAs were ampli®ed by PCR, cloned and sequenced. Alignments with homologous predicted protein sequences from other plants (Fig. 1) show a high degree of identity between species for Mcm3: over the regions analysed Nicotiana tabacum Mcm3 is 81% identical with Mcm3 of Arabidopsis thaliana, 79% with Pisum sativum, and 81% with Zea mays. From the limited data available Cdc6 appears to be less conserved, showing only a 66% identity between the corresponding proteins in N. tabacum and A. thaliana (Fig. 1). Expression of CDC6 and MCM3 in the tobacco cell cycle To determine the cell cycle expression patterns of tobacco CDC6 and MCM3, RNA samples from tobacco BY-2 cells synchronized by aphidicolin block and release were analysed. Mitotic indices determined at 1 h time intervals after release from the block indicated a high degree of synchrony (Fig. 2a) and this was con®rmed by probing northern blots with the S-phase marker histone H4 (Fig. 2b). The length of the S-phase observed in these experiments was c. 3.5 h, similar to that reported for BY-2 cells in other recent publications (Sorrell et al., 1999; Herbert et al., 2001). An obvious phase-related expression pattern of CDC6 was observed, with the peak levels of mRNA occurring in S-phase, after which expression declined so as to be undetectable by northern hybridization by late G2/early M-phase (Fig. 2b). By contrast, the expression of MCM3 did not show any cell cycle-related pattern: there were ¯uctuations in the amounts of mRNA detected by northern hybridization (Figs 2b, 3), but these did not show any clear correlation with cell cycle phase and indeed varied between different experiments. These variations were ascribed to dif®culties in detecting scarce mRNAs (see below) using northern hybridization, although a high loading of total RNA (30 mg) was used. Similar patterns of expression for CDC6 and MCM3 were observed in cells that had been subjected to a double-block regime (aphidicolin and propyzamide) (data not shown). Real-time PCR analysis of CDC6 and MCM3 mRNA in the tobacco cell cycle In order to con®rm and extend the results obtained by northern hybridization a further series of experiments was carried out in which estimates of relative mRNA abundances were made by quantitative RT-PCR using the LightCyclerÔ system. The concentration of glyceraldehyde 3-phosphate dehydrogenase (GAPdH) mRNA in each sample was determined to correct for differences in the amount of RNA (northern analysis did not reveal any ¯uctuations of GAPdH expression during the cell cycle: Fig. 2b). The expression of histone H4 was again used as a marker for S-phase (Fig. 4). Some histone H4 expression was detected at all time points but the obvious peak of 702 Dambrauskas et al. Fig. 1. (a) Alignment of tobacco Mcm3 predicted protein sequence (Nt, accession no. AAL76090) with the corresponding sequences from pea (Ps,: CAA10166), Arabidopsis (At: CAA03887), and maize (Zm: AAD48087). (b) Alignment of tobacco Cdc6 predicted protein sequence (Nt Accession no: CAC18552) with Arabidopsis Cdc6b (At: CAC83650). expression during the ®rst 2±3 h after release from the aphidicolin block clearly indicated that the bulk of cells were in S-phase during that period. Comparison of the expression patterns of CDC6 and MCM3 again revealed clear differences: MCM3 did not show a phase-related peak of expression whereas the expression of CDC6 was strongly correlated with S-phase (Fig. 4). These data clearly con®rm the conclusions from the Northern hybridization data and also show that, during S-phase, the CDC6 message is three to four times more abundant than the MCM3 message. Reporter gene expression driven by the MCM3 promoter Synchronized cells that had been transformed with the uid-A (gus) gene under the control of the Arabidopsis thaliana MCM3 promoter provided further con®rmation of the expression pattern of MCM3. Figure 5 shows an RTPCR analysis of gus mRNA through the cell cycle: there is no phase-related peak of expression, in strong contrast to the expression pattern of the resident histone H4 gene. Discussion The cloning and characterization of speci®c fragments of CDC6 and MCM3 from tobacco add to the very small number of plants from which these sequences have been isolated and extends previous work from this group on MCM3 in pea (Accession no. AJ012750; Bryant et al., 2001). These results are the ®rst to show expression patterns in the tobacco cell cycle of genes directly involved in DNA replication and clearly indicate that the two genes studied here exhibit very different patterns of expression. The expression of CDC6, encoding one of the MCM loading factors, in BY-2 cells is similar to that of RNR2 (ribonucleotide reductase small subunit) in being strongly correlated with DNA replication (Philipps et al., 1995; Cdc6 and Mcm3 in the tobacco BY-2 cell cycle 703 Fig. 2. Expression within the tobacco BY-2 cell cycle of MCM3, CDC6 and histone H4. (a) Time-course of tobacco BY-2 mitotic index after release from the aphidicolin block. (b) Detection by northern hybridization of mRNAs encoding Cdc6, Mcm3, histone H4, and GAPdH throughout the cell cycle after release from the aphidicolin block. Cell cycle phases were determined as previously described (Herbert et al., 2001). Chaboute et al., 1998). In this respect, it resembles the expression pattern of CDC6 homologues in nearly all other eukaryotes in which it has been investigated, including S. pombe (Kelly et al., 1993) and Metazoa (Hateboer et al., 1998; Yan et al., 1998). These results are also similar to those very recently obtained with cultured cells of Arabidopsis thaliana (de Jager et al., 2001; Castellano et al., 2001). Indeed, the patterns of expression of both CDC6 and histone H4 after release from the aphidicolin block in A. thaliana resemble very closely those reported here for tobacco, albeit that the data presented here for tobacco provide a more detailed analysis than that carried out with A. thaliana. Ramos et al. (2001), however, report that CDC6 is apparently strongly expressed in cultured A. thaliana roots treated with oryzalin (a mitotic metaphase inhibitor), but is not expressed in roots treated with hydroxyurea which were presumed to be held in S-phase. However, allocation to cell cycle phase may have been problematic because it is noted that histone H4 was expressed as strongly in roots held in M-phase as in control roots that had not been blocked at any cell cycle phase. The likelihood is therefore, based on results from tobacco (this paper) and A. thaliana cell cultures (de Jager et al., 2001; Castellano et al., 2001), that CDC6 expression occurs in late G1 and in S-phase. In animals, the expression or up-regulation of genes in late G1 and in S-phase is dependent on transcription factors of the E2F family (Zhao and Chang, 1997; Fig. 3. Relative expression within the tobacco BY-2 cell cycle of MCM3, CDC6 and histone H4 analysed by northern hybridization. Data were normalized against the expression of GAPdH, a housekeeping gene. Hateboer et al., 1998; Leone et al., 1998; Yan et al., 1998). Thus E2F transcription factors are the functional equivalents of the DSC1 transcription factors in S. cerevisiae that recognize the MCB elements. Regulation by E2F transcription factors has now been shown for a limited number of plant genes, including a CDC6 of A. thaliana (de Jager et al., 2001; Castellano et al., 2001) and the tobacco genes 704 Dambrauskas et al. Fig. 5. RT-PCR detection of gus expression driven by the Arabidopsis thaliana MCM3 promoter in aphidicolin synchronized tobacco BY-2 cells. Histone H4 expression was used to indicate S-phase. GAPdH is presented as the loading control. Fig. 4. Relative expression within the tobacco BY-2 cell cycle of MCM3, CDC6 and histone H4 analysed by real-time PCR. Data were normalized against the expression of GAPdH, a housekeeping gene. Error bars represent the range of values between two replicates within an individual experiment. encoding the small subunit of ribonucleotide reductase (Chaboute et al., 1998) and PCNA (Egelkrout et al., 2001; Kosugi and Ohashi, 2002). The expression pattern of MCM3, in showing no clear phase-related peaks, resembles that of mcm3 in S. pombe, but contrasts with that in S. cerevisiae and in mammals where there is a peak of expression in S-phase (see Introduction). It is thus interesting that the promoter of the MCM3 gene in A. thaliana contains two E2F transcription factor recognition sites (see accession no. AJ000058) and that this promoter drives the expression of a reporter gene in tobacco cells in a similar cell cycle phase-independent manner to that observed with the resident MCM3 gene. Thus possession of E2F recognition sites within a promoter is not enough to confer a late G1-S expression pattern. However, it is noted that, in a similar series of experiments recently reported by Stevens et al. (2002), the A.thaliana MCM3 promoter did confer on the gus gene a clear pattern of expression in G1-S of the tobacco BY-2 cell cycle. These authors further concluded that the two E2F binding sites were both involved in regulating this pattern of expression. The reason for this difference between the results of Stevens et al. and those presented here is not clear. However, in their paper no analysis of expression of the resident MCM3 gene in BY-2 cells was presented, whereas the conclusions reached by the present authors are based on extensive and repeated analysis of the expression of the tobacco MCM3 gene. In relation to research on MCM3 in other plants, Sabelli et al. (1999) were unable to detect Zea mays MCM3 mRNA by northern hybridization whereas in this laboratory a 2.7 kb message has been detected in tobacco (this paper) and a 2.9 kb message has been detected in pea (Moore, 1999; Bryant et al., 2001). Sabelli et al. (1999) ascribe their failure to an inability to incorporate suf®cient radiolabel into the probe, but it is just as probable that the problem resides in the low abundance of the mRNA (see Results). However, Sabelli et al. (1996) had earlier Cdc6 and Mcm3 in the tobacco BY-2 cell cycle 705 reported that in situ hybridization of MCM3 mRNA showed an uneven distribution in Z. mays root meristems, consistent with expression being con®ned to cells in particular, but unidenti®ed phases of the cell cycle. The data obtained with cultured tobacco cells presented here clearly do not support this suggestion, although the possibility of differences between dicots and monocots is acknowledged. Thus far, the limited data available for plants suggest greater similarity to S. pombe in which few genes other than cdt1 and cdc18 (=CDC6) show G1-S phase-speci®c cell cycle expression (see Introduction), than to S. cerevisiae and to Metazoa in which many DNA replication genes show S-phase-related peaks of expression. The signi®cance of these expression patterns for plant development is not clear. 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