A multiple-method approach reveals a declining amount of chloroplast DNA during development in Arabidopsis
© Rowan et al; licensee BioMed Central Ltd. 2009
Received: 12 April 2008
Accepted: 07 January 2009
Published: 07 January 2009
A decline in chloroplast DNA (cpDNA) during leaf maturity has been reported previously for eight plant species, including Arabidopsis thaliana. Recent studies, however, concluded that the amount of cpDNA during leaf development in Arabidopsis remained constant.
To evaluate alternative hypotheses for these two contradictory observations, we examined cpDNA in Arabidopsis shoot tissues at different times during development using several methods: staining leaf sections as well as individual isolated chloroplasts with 4',6-diamidino-2-phenylindole (DAPI), real-time quantitative PCR with DNA prepared from total tissue as well as from isolated chloroplasts, fluorescence microscopy of ethidium-stained DNA molecules prepared in gel from isolated plastids, and blot-hybridization of restriction-digested total tissue DNA. We observed a developmental decline of about two- to three-fold in mean DNA per chloroplast and two- to five-fold in the fraction of cellular DNA represented by chloroplast DNA.
Since the two- to five-fold reduction in cpDNA content could not be attributed to an artifact of chloroplast isolation, we conclude that DNA within Arabidopsis chloroplasts is degraded in vivo as leaves mature.
The chloroplast genomes of higher plants range in size from 120 to 160 kb and encode fewer than 100 proteins, most of which function in photosynthesis [1, 2]. Fluorescence microscopy using the DNA fluorochrome 4',6-diamidino-2-phenylindole (DAPI) reveals a condensed form of the chloroplast DNA (cpDNA), the nucleoid, that varies in size, number, and location during early leaf development [3, 4]. Replication of cpDNA in meristematic cells leads to an increase during leaf development in the amount of cpDNA per chloroplast and per leaf cell and the fraction of total cellular DNA present as cpDNA [5, 6]. For Arabidopsis, the number of genomes per plastid in the first leaf increases about 15-fold (from ~40 to 600) during the period from 3 to 7 days after germination . As leaf cells expand and mature, the amount of cpDNA declines in Arabidopsis  (We made an error in the Abstract of  when we stated that the decline in cpDNA amount proceeds "until most of the leaves contain little or no DNA". The decline in cpDNA amount proceeds until most of the chloroplasts contain little or no detectable DNA), barley, spinach, pea, rice, maize, Medicago truncatula, and tobacco [9–14]. The reduction in cpDNA has been attributed to either cpDNA degradation and/or to dilution of a constant amount of cpDNA by chloroplast division following the cessation of cpDNA replication, depending on the species.
Recent studies report a constant amount of cpDNA during leaf development in Arabidopsis and tobacco, as determined by blot-hybridization of restriction-digested DNA  and also by real-time quantitative PCR (qPCR) for Arabidopsis . These authors proposed that the decline in DNA per plastid observed for Arabidopsis  resulted from an artifact associated with the isolation of plastids before quantification of cpDNA. If the amount of DNA per chloroplast were actually constant during this period of leaf expansion, then Arabidopsis and tobacco would be atypical among the plants for which such data have been reported, and would not serve as good models for certain aspects of chloroplast development. Thus, it seemed necessary to revisit this contentious issue.
We previously reported that the amount of DNA per chloroplast declined only during the expansion of older (but not young) leaves in tobacco . We concluded that tobacco exhibited the greatest degree of cpDNA preservation during leaf development among the eight plants investigated. In the present study, we assess the amount and molecular integrity of cpDNA for Arabidopsis by several methods: DAPI-staining of leaf sections as well as individual isolated chloroplasts, qPCR with DNA prepared from total tissue as well as from isolated chloroplasts, fluorescence microscopy of ethidium-stained DNA molecules prepared in gel from isolated plastids, and blot-hybridization of restriction-digested total tissue DNA. With each of these methods, we find a reduction during development in the amount of DNA per chloroplast and the fraction of cellular DNA represented by cpDNA. This reduction cannot be attributed solely to DNA dilution caused by chloroplast division. Since the data demonstrate that the loss of DNA from plastids during leaf development does not result from an artifact of plastid isolation, we conclude that DNA is degraded in vivo as Arabidopsis plastids mature.
Decline in cpDNA content is not an artifact of chloroplast isolation
We conclude that the reduction in DAPI-DNA fluorescence observed in isolated chloroplasts occurs in planta and not as a consequence of the isolation process. The same conclusion was reached for analogous data for maize .
Changes in structural form of individual cpDNA molecules during leaf development
DNA in chloroplasts of some plant species is initially present as complex, branched linear molecules that become progressively simpler and smaller as leaves develop [10, 12]. We previously observed that complex forms were generally present in younger leaves of Arabidopsis  and absent from older leaves. It is possible that chloroplasts do not exhibit detectable DAPI-DNA staining because cpDNA is present as dispersed small molecules incapable of generating a strong signal. In this and the following section, we further characterize the changes in structure of cpDNA molecules during Arabidopsis leaf development in order to examine this possibility.
Additional file 1: Moving pictures of a Class I cpDNA molecule. EtBr-stained cpDNA embedded in agarose was subjected to an electric field (anode is to the left) and images were recorded every 20 s for 420 s. After 320 s, the electric field was reversed (anode is to the right). (MOV 4 MB)
Assessment of plastid DNA content by fluorescence microscopy and real-time quantitative PCR (qPCR)
If the reduction of DAPI-DNA fluorescence in chloroplasts during development occurs because of a reduction in cpDNA molecular size rather than a reduction in cpDNA amount, we would expect different results when estimating the DNA content per plastid using DAPI-DNA fluorescence compared with a method that does not rely on fluorescence microscopy. In one method, we measured the DAPI-DNA fluorescence and calculated the number of genomes per plastid using Vaccinia virus particles as a standard [10, 12], and we used qPCR in the other method. For qPCR, the amount of DNA obtained from a known quantity of plastids was determined using a standard curve of cpDNA amounts.
The mean genome copy number per plastid for the immature tissue was 57 ± 5 determined by DAPI-DNA fluorescence and 77 ± 7 determined by qPCR (Figure 6B). Mean genome copy number per plastid for the mature tissue was 25 ± 3 by DAPI-DNA fluorescence and 24 ± 2 by qPCR. The two methods gave similar values for the mean genome content, and a reduction in DNA content per plastid between the immature and mature tissues was observed in both cases. Thus, the reduction in DAPI-DNA fluorescence is attributed to a reduction in cpDNA amount, rather than solely a reduction in molecular size.
Changes in cpDNA amount determined by blot-hybridization
Relative number of plastid genomes (plastomes), chloroplasts per cell, and frequency of cell types
We have now compared the amount of cpDNA present at the level of individual chloroplasts, as well at the whole tissue level. In order to assess how the amount of cpDNA varies with development at the cellular level, we employed qPCR to assess the plastome copy number relative to nuclear genome copy number and obtain a ratio of these two DNAs. If all the cells are diploid and a single copy nuclear gene is used, multiplying this ratio by 2 gives the number of plastid genomes (plastomes) per cell. For Arabidopsis however, ploidy level varies from cell to cell and also varies during development [18, 19].
Frequencies of nuclear ploidy classes and mean nuclear DNA content during development.
Percent of nuclei
69.4 ± 1.1
28.3 ± 0.4
2.2 ± 0.7
2.7 ± 0.1
25.3 ± 1.4
40.8 ± 0.8
30.1 ± 1.2
3.9 ± 1.2
5.2 ± 0.1
45.5 ± 0.6
36.3 ± 0.2
14.4 ± 0.2
3.8 ± 0.4
4.2 ± 0.2
19.3 ± 1.1
23.2 ± 1.7
31.2 ± 3.1
26.3 ± 3.4
7.8 ± 0.5
21.5 ± 3.4
27.4 ± 2.5
20.8 ± 11.1
18.1 ± 3.2
12.2 ± 4.0
10.0 ± 1
22.8 ± 1.9
26.2 ± 1.8
17.5 ± 0.7
21.7 ± 2.1
11.8 ± 1.0
10.2 ± 0.5
The ratio of plastome copy number to nuclear genome copy number was assessed using the chloroplast psbA gene and both a multiple-copy nuclear gene (18S rRNA, Figure 8B) and a single copy nuclear gene (ROC1, Figure 8C). Using real-time PCR with the single copy nuclear gene ROC1, the number of 18S copies per haploid nuclear genome was determined to be 568 ± 158, which is similar to the 700 ± 60 value reported previously . The ratio of chloroplast to nuclear DNA is higher for immature tissues (samples 1–3) compared with older tissues (samples 4–6), regardless of whether a single copy or multiple copy gene was used for the nuclear DNA. Taking into account the number of copies of 18S per haploid nuclear genome and the average ploidy of the cells (Table 1), we calculated the number of plastomes per cell (Figure 8D). We similarly calculated the number of plastomes per cell for data collected using the ROC1 gene (Figure 8E). In both cases, the number of plastomes per cell was lowest in the youngest tissue (255 ± 13 for 18S and 301 ± 22 for ROC1). The rest of the tissues varied between 465 ± 22 and 894 ± 65 plastomes per cell without any obvious developmental trend. Zoschke et al.  similarly observed (using qPCR to determine the ratio of several plastid genes to the nuclear 18S gene) that the number of plastomes per cell varies from 1000 to 1500 without developmental correlation. A conclusion that seems to follow from these results is that the cpDNA content per cell does not decline during development, as it does for individual chloroplasts (Figures 1, 2, 3, 4, 5 and 6) and the fraction of total DNA represented by cpDNA (Figures 7 and 8B, C). This conclusion requires that the stability of cpDNA is the same among cells irrespective of nuclear ploidy level, a matter discussed below.
Number of chloroplasts per cell during development.
Chloroplasts per cell
Number of cells analyzed
25.6 ± 1.9a
39.1 ± 3.3b
48.4 ± 7.5b
Frequency of cell types observed in cytological sections of young and mature leaf tissue.
# of cells
As leaves develop, profound changes occur in every measurable property of the plastid, including size, color, anatomy, physiological function, biochemical composition, and gene expression. For six species of flowering plants, a decrease in plastid genome copy number during leaf maturation shows that cpDNA can be added to this list. Measurements of cpDNA per plastid showed that Arabidopsis and tobacco were similar to the other six. But in other reports on tobacco and Arabidopsis, it was concluded that the amount of cpDNA remained constant as leaves matured. As discussed below, however, one report relied on non-quantitative data to reach a quantitative conclusion regarding cpDNA, and the other relied on the assumption that the computation of cpDNA per cell using qPCR and flow cytometry is an accurate representation. Furthermore, in both of these reports, only one method was used to assess cpDNA amount during development. Our data, obtained by multiple methods, show that Arabidopsis is typical with respect to cpDNA loss during leaf development.
We have evaluated alternative hypotheses for the decline in cpDNA amount during development in Arabidopsis. Li et al.  and Zoschke et al.  proposed that the reduction in cpDNA content reported for mature leaves is an artifact that results from the loss of cpDNA during chloroplast isolation. Our present data, however, contradict this proposal because we find a decline in cpDNA for chloroplasts within cells as observed in leaf sections. Furthermore, Kato et al.  found that plastids of white sectors of the yellow variegated2 mutant contain more DNA than those of green sectors, as evidenced by staining leaf sections and protoplasts with DAPI and Hoechst dyes. The data presented by these authors were also obtained for plastids within cells and suggest that DNA content declines during plastid differentiation in vivo.
Under a second hypothesis, the reduced DAPI fluorescence of mature chloroplasts is not due to a reduction in DNA amount, but is due to a reduction in the size of cpDNA molecules. Although our moving pictures do show that cpDNA molecules become smaller and more fragmented during development (Figure 5), DNA content of chloroplasts measured by both DAPI fluorescence and by qPCR was about two- to three-fold higher in immature tissues than in mature tissues (Figure 6), consistent with the two- to seven-fold change in cpDNA reported previously for a broader developmental range of tissues . Thus, low levels of DAPI fluorescence in mature chloroplasts accurately reflect low DNA contents. Furthermore, examination of individual chloroplasts by DAPI-staining reveals the range of DNA contents among plastids, as well as the DNA distribution within the plastid and plastid size, parameters that cannot be assessed by qPCR.
A reduction in the amount of DNA present in an individual chloroplast can result from either cpDNA degradation or dilution during chloroplast division [9, 11, 17]. A third hypothesis, therefore, is that the observed decline in cpDNA content occurs only because of dilution. We observed a reduction in cpDNA amount between intermediate and mature stages of plant development without an increase in the number of chloroplasts per cell over this period. Thus, division alone cannot explain the low level of DNA present in mature chloroplasts.
We found that the proportion of total cellular DNA represented by cpDNA declines during development, using blot-hybridization as the method of assay (Figure 7). Li et al.  concluded that cpDNA levels remained constant throughout development in Arabidopsis (as determined by inspection, but not quantification, of some of their blot-hybridization signals). However, these authors neglected to discuss the data presented in their Figure 3b (lanes 2 and 3), which showed a seemingly greater amount of cpDNA in a young leaf than a mature leaf. In addition, they did not use a nuclear DNA probe in blot-hybridization in order to determine whether equal amounts of DNA were loaded in the lanes to be compared, further confounding the qualitative interpretation of hybridization signals. Lastly, the developmental age of the tissue was not clearly defined. We show that cpDNA amount does remain constant after the decline has occurred (even in senescent leaves; Figures 1 and 2). It is possible that the tissues showing no apparent change in signal have already passed the stage during which cpDNA levels decline. Li et al.  also concluded that cpDNA remains constant during tobacco leaf development using visual inspection of blot-hybridization signals from cpDNA and ''promiscuous'' cpDNA in the nucleus. We found that DNA per tobacco chloroplast increases during early leaf development and then decreases, but does not reach undetectable levels . Since Li et al.  did not specify the age of their tobacco plants, we cannot determine whether their data conflict with ours for tobacco. Since for both tobacco and Arabidopsis, the well was not included in the image of the blot-hybridization, the extent of restriction digestion cannot be assessed. For Arabidopsis, however, our quantitative data (Figure 7) show that cpDNA declines during leaf development when the blot-hybridization assay is used, in agreement with inspection of lanes 2 and 3 of Figure 3b of Li et al. , and the lack of hybridization in the well indicates a complete restriction digest.
We found that the ratio of chloroplast-to-nuclear DNA (determined by qPCR) in young tissues was two- to three-fold higher than in mature tissues. A two- to three-fold reduction of this ratio was also reported by Zoschke et al (; see their Figure 2b). We used the ratio of chloroplast-to-nuclear DNA to calculate the number of plastomes per cell based on the mean nuclear ploidy (determined by flow cytometry). The calculated number of plastomes per cell did not appear to vary substantially during development. This result apparently contradicts our data showing a decline in cpDNA during development. We now evaluate the assumptions in the method used to calculate plastomes per cell in order to resolve this contradiction.
A reduction in the ratio of chloroplast-to-nuclear DNA can result from either an increase in nuclear DNA (a ploidy level increase) or a decrease in cpDNA. It is clear that the amount of nuclear DNA increases during development (Table 1; Figure 8A). We did not observe a slight decrease in mean nuclear ploidy at late stages of leaf development, as was reported by Zoschke et al. . Mean ploidy at these stages was reduced only 20–25% and the authors found an overall trend of increasing ploidy with leaf age. This increase does not occur uniformly among all cells, however, as evidenced by the increase in the proportion of cells in the highest ploidy classes at the later stages of leaf development (Table 1). Thus, some cells experience more rounds of endoreduplication than others. In addition, the decrease in cpDNA content may not occur uniformly among cells. Chloroplasts exhibit both a larger range in DNA content and a higher mean DNA content in seedling shoots and intermediate-aged leaves than in mature leaves (Figure 6). However, many of the chloroplasts from the immature tissues contain a similarly low amount of DNA as chloroplasts from mature leaves (in immature samples, the mean cpDNA content is high because some chloroplasts contain a lot of DNA, more than 100 genome equivalents). Thus it is likely that a substantial proportion of chloroplasts have already undergone a reduction in DNA even at an immature stage, indicating that not all cells initiate the reduction process at the same time. Furthermore, in some cells the cpDNA content may not change during development. For the leaves of wheat, Miyamura et al.  reported that the DNA content of non-photosynthetic plastids remains low, never approaching the high levels seen in developing chloroplasts. Thus, cells containing non-photosynthetic plastids, such as those found in the epidermis  and vasculature, may undergo endoreduplication, but may not contribute to the changes in DNA content observed for plastids obtained from leaves. Such cells comprise about half of the cells in Arabidopsis leaves (Table 3).
When calculating the number of plastomes per cell, we can only measure the change in nuclear DNA amount (by flow cytometry) and the change in the chloroplast-to-nuclear DNA ratio (by qPCR) for the whole population of cells (shaded boxes in Figure 9). The fold increase in ploidy for the whole population is similar to the fold decrease in chloroplast-to-nuclear DNA ratio. One interpretation of these results is that the decrease in the chloroplast-to-nuclear ratio occurs only because the nuclear DNA copy number is increasing and that cpDNA amount does not decline during development. However, this interpretation is contradicted by our data for individual chloroplasts, considering that chloroplasts are not dividing during this time (Figures 1, 2, 3, 4, 5, 6 and Table 2). Furthermore, if the calculated number of plastomes per cell were correct, then chloroplasts from intermediate-aged leaves would be expected to have an average of only 16 genomes per chloroplast (612 plastomes per cell [Figure 8] divided by 39 plastids per cell [Table 2]), which is also contradicted by our measured values (58 genomes per plastid, Figure 6 legend). Another interpretation is that all cells do not participate equally in endoreduplication and cpDNA reduction. Under this interpretation, a reduction in the chloroplast-to-nuclear DNA ratio is due to an increase in nuclear DNA only for some cells (Type 1) and is due to a decrease in cpDNA for others (Type 2). Type 1 cells make a large contribution to the net increase in mean ploidy and a much smaller contribution to the net reduction in cpDNA because these cells contain a small amount of cpDNA. Type 2 cells do not contribute to the net increase in ploidy, but contribute greatly to the net reduction in the chloroplast-to-nuclear DNA ratio. Thus, the net increase in nuclear ploidy of about two- to three-fold approximates the net decrease in the chloroplast-to-nuclear DNA ratio. The calculation of plastomes per cell is based on only these two parameters, giving the impression that there is no change (left portion of the bottom box under "plastomes per cell" in Figure 9), and this interpretation is consistent with all of our data. If it were possible to analyze the change in nuclear ploidy and the chloroplast-to-nuclear DNA ratio for individual cells, a net decrease in plastomes per cell would be evident (right portion of the bottom box under "plastomes/cell" in Figure 9) because a change in the chloroplast-to-nuclear DNA ratio could be directly ascribed to a change in either chloroplast or nuclear DNA amount for a given cell.
We find that the amount of cpDNA declines during development of Arabidopsis leaves and that cpDNA is degraded in vivo. This conclusion is supported by each of the several methods we employed, with each elucidating a different aspect of that decline. Examination of DNA at the level of individual plastids shows changes in the average amount of cpDNA, its location within the plastid, and the range of DNA content among plastids. Visualizing individual cpDNA molecules reveals the change in their size, complexity, and structure. These data are consistent with our previous conclusion  that whereas the average DNA content per plastid declines only several-fold, the DNA of individual plastids can decline to undetectable levels. Calculation of plastomes per cell by combining data obtained from qPCR and flow cytometry can be used to assess cpDNA change per cell for tissues with a nuclear DNA content that is constant during development. For maize, a species without endoreduplication in shoot tissues, we found that qPCR-based calculation of plastomes per cell reflected the same decline in cpDNA amount obtained with individual plastids . For species like Arabidopsis with a high degree of endoreduplication, however, the calculation can be misleading because the cpDNA for an average cell is computed from data obtained from a mix of different cell types and would not accurately reflect cell-to-cell variation . If all cells do not participate equally in endoreduplication and decline of cpDNA, this method cannot be used to determine whether the amount of DNA per chloroplast is changing during development. To avoid confounding variables such as endoreduplication, plastomes per cell can also be calculated using methods that do not rely on nuclear DNA. Individual chloroplasts from intermediate-aged leaves of Arabidopsis contain 58 genomes on average (Figure 6 legend). As there are about 39 chloroplasts per cell (Table 2), this gives 2262 plastomes per cell. In comparison, there are 1152 – 1200 plastomes per cell in mature tissues. In summary, we have demonstrated that the amount of DNA per chloroplast declines in vivo during development in Arabidopsis, at least for the environmental conditions and tissues examined. Whether cpDNA per cell declines depends on the method used to calculate the amount of cpDNA per cell.
Seeds of Arabidopsis thaliana (Col.) were sown in soil and held at 4°C for at least 72 h to promote uniform germination. Plants were grown in a growth chamber at 19°C with 16/8 h light/dark cycles at 100 microeinsteins m-2 s-1 (Figure 5, intermediate and mature samples) or in a greenhouse with temperatures that ranged from 15 – 23°C and a 16/8 h light cycle maintained year-round (Figures 1, 2, 3, 4, 5, 6, 7, 8). Tissue samples consisting of leaves that are less than 30% of their maximum length are described as "young". Tissue samples consisting of leaves 30–70% of their maximum length or seedling shoots are described as "intermediate". Under our growth conditions, the first and second rosette leaves typically reach a maximum length of 10 mm; thus a first or second rosette leaf that is 2 mm long is 20% of its maximum size. However, a 2 mm long eighth rosette leaf (which reaches an average maximum size of 24 mm) is only 8% of its maximum size. Both young and intermediate leaves are described as "immature". Fully expanded leaves are described as "mature". Leaves that are fully expanded and starting to yellow are described as "senescent".
Isolation of chloroplasts and protoplasts and preparation of leaf sections
To minimize microbial contamination, plant tissue was soaked in 0.5% sarksoyl for 3–5 min and rinsed thoroughly before isolating chloroplasts following the high salt protocol that does not include treatment with DNase [12, 25]. Chloroplasts were washed and resuspended in sorbitol dilution buffer (SDB; 0.33 M sorbitol, 20 mM HEPES, 2 mM EDTA, 1 mM MgCl2, 0.1% bovine serum albumin [BSA] adjusted to pH 7.6) and layered over 70% Percoll in SDB. After centrifugation at 12,000 × g for 10 min at 4°C, the chloroplasts were removed from atop the Percoll and washed twice in SDB and fixed in 0.8% glutaraldehyde in SDB before further analysis. Isolated chloroplasts were used for the data presented in Figures 5 and 6. Leaves were sectioned by hand and immediately fixed in 0.8% glutaraldehyde in SDB. For determination of cell type frequency, leaves were fixed in 0.8% glutaraldehyde overnight, dehydrated using a graded ethanol series, and infiltrated with Technovit 7100 plastic resin (Heraeus Kulzer, Wehrheim, Germany). The tissue was then embedded and polymerized in Technovit 7100, and a Leica RM-6145 mictrotome (Wetzlar, Germany) was used to prepare 8-μm-thick sections.
For isolation of protoplasts, plant tissue was sliced into approximately 1 mm2 pieces and incubated in 0.2% BSA, 1.7% cellulase, 1.7% cellulysin, 0.026% pectolyase, 2 mM CaCl2, 10 mM MES-KOH pH 5.5, 0.55 M mannitol at 30°C for 20 min. Tissue pieces were washed twice for 5 min in 2 mM CaCl2, 10 mM MES-KOH pH 5.5, 0.57 M mannitol and placed into 5 mM CaCl2, 2 mM MgCl2, 10 mM MES-KOH pH 5.5, 0.22 M mannitol to allow protoplasts to be released from the tissue.
Fluorescence and light microscopy of chloroplasts, protoplasts and leaf sections
Fixed leaf sections and isolated chloroplasts were adjusted to 1–2 μg/ml DAPI, and 1% β-mercaptoethanol in SDB. Imaging of chloroplasts and leaf sections was performed as described previously . The contrast has been enhanced using Open lab™ image capture software uniformly among all fluorescence images presented in Figures 1 and 3 to improve visibility of nucleoids with weak DAPI-DNA fluorescence. The relative fluorescence intensity (Rfl) of DAPI-stained chloroplasts was measured as described previously [8, 12, 23]. Rfl was determined similarly for glutaraldehyde-fixed, DAPI-stained Vaccinia virus particles. The number of chloroplast genome equivalents per plastid was calculated using the equation: chloroplast genome equivalents = 1.33V (where V = the DAPI-DNA Rfl of the plastid divided by the mean Rfl of Vaccinia virus particles). The value 1.33 is a constant that accounts for the differences between the size and base composition between the Arabidopsis chloroplast genome and the Vaccinia virus genome and was determined as (% AT content of Vaccinia virus genome/% AT content of Arabidopsis chloroplast genome) × (number of bp of Vaccinia virus genome/number of bp of Arabidopsis chloroplast genome), where % AT for Vaccinia (Copenhagen strain) is 66.6, % AT for Arabidopsis cpDNA is 64%, number of bp for Vaccinia DNA is 197,361 and number of bp for Arabidopsis cpDNA is 154,361. Brightfield images of the chloroplasts were recorded and used to measure plastid area. Plastids of protoplasts were counted by observation of the chlorophyll autofluorescence. A Student's T test was used to determine whether population means exhibited a statistically significant difference.
Preparation of chloroplast DNA for visualization by fluorescence microscopy
Chloroplasts were embedded in agarose, and lysed overnight at 48°C in 1 M NaCl, 5 mM EDTA, 1% sarkosyl and 200 μg/mL proteinase K. Agarose-embedded cpDNA was stained with 0.1 μg/mL ethidium bromide and visualized as described . For Additional File 1, an electric field of 10–12 V/cm in 1× TBE (90 mM Tris-borate, 2 mM EDTA) was employed.
Real-time quantitative PCR
Chloroplasts were counted using an eosinophil counting slide (Spiers-Levy, Blue Bell, PA). Lysis of a known concentration of chloroplasts was performed as described . Amounts of cpDNA ranging from 5 fg/μL to 50 pg/μL were used to generate a standard curve for determining the concentration of cpDNA present in the chloroplast lysates. Standards were diluted in the same solution as used for the lysates to provide identical reaction conditions for standards and unknowns. The forward primer 5' TTGCGGTCAATAAGGTAGGG 3' and reverse primer 5' TAGAGAATTTGTGCGCTTGG 3' were used to amplify a 189-bp fragment including part of the psbA gene and an intergenic region. Amplification of 1 μL chloroplast DNA was carried out using the iQ™ SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA). Following an initial denaturation at 94°C for 3 min, 45 cycles of 15 s denaturation at 94°C, 15 s annealing at 57°C, and 20 s extension at 72°C were performed and amplification of the reactions monitored using the Chromo 4 real-time detection system (Bio-Rad Laboratories). A melting curve from 65°C to 95°C was used to confirm the presence of single products. Data were analyzed using the Opticon Monitor 3 software (Bio-Rad Laboratories), and the amount of DNA in each of the unknown samples was determined in fg/μL. One fg represents approximately 6.3 copies of the chloroplast genome. The number of copies of the chloroplast genome per μL was calculated from the number of fg/μL divided by the number of chloroplasts per μL to obtain the number of copies of the chloroplast genome per chloroplast. Twelve replicates of each sample were analyzed. Control reactions with no template resulted in no amplification of the cpDNA fragment.
For relative quantification of chloroplast genomes per nuclear genome, the Nucleon Phytopure DNA isolation kit (GE Healthcare, Piscataway, NJ) was used to prepare total DNA from plants at the stages of development indicated in Figure 8. The forward primer 5'AGAGACGCGAAAGCGAAAG3' and reverse primer 5'CTGGAGGAGCAGCAATGAA3' were used to amplify a 156-bp portion of the chloroplast psbA gene. The forward primer 5'CCCCTACTTAACCGGTGGTC3' and reverse primer 5'GAAGCGGCGAATATCTCACA3' were used to amplify a 113-bp region of the Arabidopsis nuclear DNA encompassing a 5' portion of the nuclear ROC1 gene and an upstream intergenic region. The forward primer 5'AAACGGCTACCACATCCAAG3' and reverse primer 5' ACTCGAAAGAGCCCGGTATT 3' were used to amplify a 101-bp portion of the 18S rRNA gene. Amplification and detection were carried out as described above, except only 40 cycles were used. Reactions contained 0.3 – 0.8 ng of template DNA. All primer sets had an efficiency of at least 90%. The copy number of cpDNA relative to nuclear DNA was calculated using the 2-ΔCTmethod [27, 28]. Six to twelve replicates of each sample were analyzed. Control reactions with no template resulted in no amplification.
Blot-hybridization of restriction-digested DNA
Total DNA was isolated using the Nucleon Phytopure DNA isolation kit and quantified using the Quant-It™ DNA High Sensitivity Kit (Invitrogen, Carlsbad, CA) and a Victor3 V plate reader (Perkin Elmer, Waltham, MA). 108 ng of total DNA was digested with SpeI, separated by gel electrophoresis, and transferred onto a N+ nylon membrane. An 854-bp fragment of the chloroplast petA gene and a 1050-bp fragment of the nuclear DRT100 gene were labeled with alkaline phosphatase using the AlkPhos Direct Labeling Reagents, and hybridization was detected using the CDP-Star Detection Reagent (GE Healthcare, Piscataway, NJ). The hybridization signals were quantified using NIH Image J software. Lanes on the image of the blot were selected and the software plotted the intensity of the signal down the lane. A sharp peak was observed at the location of the band. The area under this peak was calculated using the instructions provided on the Image J website http://rsbweb.nih.gov/ij/docs/menus/analyze.html. The peak with the largest area was given a value of 100, and all other peak areas were expressed relative to that value. These values are shown below the lanes in Figure 7. Serial dilutions of undigested DNA ranging from ~0.3 ng to 10 ng were prepared, spotted onto an N+ nylon membrane, alkali denatured, neutralized and hybridized with the petA probe. Signals were quantified as described above. A two-fold difference in DNA content gave approximately a two-fold difference in signal intensity when measured at an appropriate exposure time.
Flow cytometric determination of nuclear ploidy
Plant tissue was chopped with a razor blade in chopping buffer (CB; 15 mM HEPES, 1 mM EDTA, 80 mM KCl, 20 mM NaCl, 300 mM sucrose, 0.2% Triton-X, 0.5 mM spermine, 0.1% β-mercaptoethanol) for 1–2 min and filtered through a 30-μM-pore filter. The filtrate was centrifuged at 500 × g for 7 min. Chicken erythrocyte nuclei (BioSure, Grass Valley, CA) were added to each pellet of nuclei to provide a size standard (2.5 pg) and resuspended in CB with 50 μg/mL propidium iodide and 50 μg/mL RNase A. The ploidy level of nuclei was determined using a Becton Dickinson FACScan flow cytometer. Data were acquired and analyzed using CellQuest software. The mean ploidy level was determined using a weighted average based on the number of nuclei in each ploidy class divided by the total number of nuclei analyzed. C = [(2*N2C) + (4*N4C) + (8*N8C) ...]/(N2C + N4C + N8C...). C is the mean ploidy and N is the number of nuclei in the ploidy class indicated by the subscript.
We thank Jerry Davison and Veronica DiStilio for assistance with flow cytometry, Elizabeth van Volkenburgh for advice and materials for the protoplasting procedure, and Keiko Torii and Lynn Pillitteri for help preparing plastic-embedded leaf sections. This investigation was supported in part by Public Health Service National Research Award T32 GM07270 from the National Institute of General Medical Sciences.
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