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Plant Cell. Sep 2010; 22(9): 3020–3033.
Published online Sep 28, 2010. doi:  10.1105/tpc.110.078527
PMCID: PMC2965537

Distinct Roles of the ATR Kinase and the Mre11-Rad50-Nbs1 Complex in the Maintenance of Chromosomal Stability in Arabidopsis

Abstract

Signaling of chromosomal DNA breaks is of primary importance for initiation of repair and, thus, for global genomic stability. Although the Mre11-Rad50-Nbs1 (MRN) complex is the first sensor of double-strand breaks, its role in double-strand break (DSB) signaling is not fully understood. We report the absence of γ-ray–induced, ATM/ATR-dependent histone H2AX phosphorylation in Arabidopsis thaliana rad50 and mre11 mutants, confirming that the MRN complex is required for H2AX phosphorylation by the ATM and ATR kinases in response to irradiation-induced DSB in Arabidopsis. rad50 and mre11 mutants spontaneously activate a DNA damage response, as shown by the presence of γ-H2AX foci and activation of cell cycle arrest in nonirradiated plants. This response is ATR dependent as shown both by the absence of these spontaneous foci and by the wild-type mitotic indices of double rad50 atr and mre11 atr plants. EdU S-phase labeling and fluorescence in situ hybridization analysis using specific subtelomeric probes point to a replicative S-phase origin of this chromosome damage in the double mutants and not to telomere destabilization. Thus, the data presented here show the exclusive involvement of ATR in DNA damage signaling in MRN mutants and provide evidence for a role for ATR in the avoidance of S-phase DNA damage.

INTRODUCTION

Maintenance of genome stability is of critical importance for all cellular organisms. Cellular DNA is subject to many types of damage resulting from cellular metabolism (such as reactive radicals or stalled replication forks) or through the action of exogenous agents, such as radiation and chemical mutagens. Double-strand DNA breaks are extremely toxic lesions, potentially causing chromosomal translocations and rearrangements and ultimately cell death, senescence, or tumorigenesis (Rich et al., 2000). In response to DNA damage, cells activate complex signaling pathways that activate DNA repair, cell cycle arrest, and eventually apoptosis. These processes are based on signal transduction initiated by sensor proteins that recognize the damage and activate the transducers, which send the signal to the effector proteins (Shiloh, 2006; Cimprich and Cortez, 2008).

The major regulators of the DNA damage response are the protein kinases Ataxia telangiectasia mutated (ATM) and ATM and Rad3 related (ATR), which belong to the phosphatidyl inositol 3-kinase family (PIKKs). Each is activated in response to a different type of damage. ATR responds primarily to stalled replication forks where the generation of replication protein A–coated single-stranded DNA activates its kinase activity, while the kinase activity of ATM is enhanced in response to the presence of double-strand breaks (DSBs). DSBs are first bound by the Mre11-Rad50-Nbs1 (MRN) complex, which then recruits and activates ATM (Harper and Elledge, 2007). ATR activation in response to replicative stress, however, does not require the MRN complex (Cimprich and Cortez, 2008). Once activated, PIKKs are necessary to maintain genomic integrity by initiating multiple events, including cell cycle arrest, chromatin remodeling, repair, and eventually cell death. Phosphorylation by PIKKs of the histone variant H2AX, forming γ-H2AX, plays a key role in the recruitment and accumulation of DNA repair proteins at sites of DSB damage (Paull et al., 2000; Fernandez-Capetillo et al., 2003; Fillingham et al., 2006), and detection of this phosphorylation event using antibodies to γ-H2AX has emerged as a highly specific and sensitive molecular marker for monitoring DNA DSB damage and its repair (Kinner et al., 2008).

The MRN complex is a highly conserved complex composed of three proteins, Meiotic recombination 11 (MRE11), Radiation sensitive 50 (RAD50), and Nijmegen Breakage Syndrome 1 (NBS1; x-ray sensitive 2 [XRS2] in Saccharomyces cerevisiae), and has been shown to be involved in DNA damage repair, DNA replication, meiosis, and telomere maintenance (Czornak et al., 2008; Mimitou and Symington, 2009; Lamarche et al., 2010). The MRN complex recognizes DSBs by its ability to bind the ends of DNA, and, once bound, it unwinds (Paull and Gellert, 1999) and initiates processing of DNA ends (review in Mimitou and Symington, 2009). The interaction with NBS1 activates ATM kinase activity, resulting in phosphorylation of target proteins H2AX, Mre11, Nbs1/Xrs2, and Sae2/CtIP (for Sporulation in the absence of Spo11-2 and C-terminal binding protein-interacting protein, respectively). Interaction between Sae2/CtIP and the MRN complex activates the nuclease activity of Mre11, preparing the DNA ends and initiating resection of the 5′-ended strand for the generation of 3′ single-stranded DNA (ssDNA), which is required for the initiation of homologous recombination and subsequent activation of the ATR kinase in response to DSBs (reviewed in Mimitou and Symington, 2009; Lamarche et al., 2010).

Yeast cells mutated for any member of the MRN complex are sensitive to replication stress (D'Amours and Jackson, 2001; Shor et al., 2002), and in mammals the MRN complex has been shown to localize with proliferating cell nuclear antigene and to interact with replication protein A (RPA) during hydroxyurea (HU) treatment (Mirzoeva and Petrini, 2003; Robison et al., 2004; Olson et al., 2007). All these data suggest a key role for the MRN complex in stabilizing replication forks. Thus, ATM, ATR, and the MRN complex are all required for chromosomal integrity. However, defining their functional relationship in the maintenance of chromosomal stability has been hampered by the early lethality associated with null mutations in these genes in vertebrate cells.

By contrast, Arabidopsis thaliana plants mutated for ATR, ATM, or the MRN complex proteins are viable. atr and atm mutants are both phenotypically wild type, except for a partial sterility in the atm mutant (Garcia et al., 2003; Culligan et al., 2004). The atm mutant is sensitive to DSB-inducing agents (e.g., ionizing radiation and methyl methane sulphonate), and the atr mutant is sensitive to replication stress inducing agents (e.g., Aphidicolin or Hydroxyurea), indicating conservation of the roles of these proteins in plants. rad50 and mre11 mutants are fully sterile, indicating an essential role for RAD50 and MRE11 in meiosis (Gallego et al., 2001; Bundock and Hooykaas, 2002; Bleuyard et al., 2004). That these plants are also genetically unstable is shown by the presence of anaphase bridges in 10% of the anaphases in mitotic cells (Gallego and White, 2001; Puizina et al., 2004; Vannier et al., 2006). Fluorescent in situ hybridization (FISH) analysis of rad50 mutant cells using specific subtelomeric probes has shown that half of these chromosome fusions involve the end of a chromosome as a result of loss of telomeric repeats in the mutant plants. Concerning DNA damage signaling, the only information comes from experiments that reveal that ionizing radiation induction of γ-H2AX foci is completely dependent on ATM and ATR with a preponderant role of ATM (Friesner et al., 2005); however, no role has been described for the MRN complex.

The aim of the work presented here is to define the role of the MRN complex in the activation of the DNA damage response in plant cells. We show that the activation of both ATM and ATR kinase activities in response to γ-irradiation–induced DSBs is dependent upon the MRN complex. The essential role of the MRN complex in activation of the ATM and ATR kinases in response to DSB induction is thus conserved in plants. In the absence of RAD50 or MRE11, Arabidopsis cells activate a DNA damage response as shown by the presence of γ-H2AX foci. In these cells, phosphorylation of the histone H2AX is dependent on ATR kinase, and not ATM activity. Such spontaneous activation of γ-H2AX foci formation in the absence of MRN has not to our knowledge been previously tested in any organism. This ATR-dependent phosphorylation is strongly enriched in S-phase nuclei, and only a subset of these γ-H2AX foci are found to be associated with telomeres. Finally, plants defective in both ATR and the MRN complex show severe growth defects related to increased genomic instability. Thus, we show the exclusive involvement of ATR in DNA damage signaling in mrn mutants and provide evidence of a role for ATR in avoidance of S-phase DNA damage and assuring proper replication.

RESULTS

The MRN Complex Is Essential for Activation of the ATM and ATR Kinases in Response to Irradiation

Activation of ATM in response to γ-irradiation in vertebrate cells is dependent upon the presence of the MRN complex at the sites of DSBs. To establish whether the MRN complex is needed in plant cells for the activation of ATM and/or ATR kinases after irradiation, we performed in situ immunostaining experiments in rad50 and mre11 Arabidopsis root tip nuclei using γ-H2AX antibodies.

As expected, no foci were detected when in situ immunostaining was performed in root tip mitotic nuclei of nonirradiated wild-type or heterozygous plants (designated as wt for both in all the figures). However, in rad50 (and in mre11) mutants, 68% (and 64%) of the mitotic nuclei present γ-H2AX foci with a mean of 1.4 (or 1.3) foci per nucleus, revealing the presence of spontaneous DSBs in mutants defective in the MRN complex (Figure 1). When plants were irradiated at 25 Gy and fixed 10 min after irradiation, 100% of the nuclei from wild-type plants show γ-H2AX foci with a mean of 14 foci per nucleus, as expected from previous results (Friesner et al., 2005; Charbonnel et al., 2010). However, in irradiated rad50 mutant plants, the proportion of nuclei showing γ-H2AX foci (64%) and the number of foci per nucleus (1.2) were similar to those observed in the nonirradiated plants (1.4). Similar results were obtained after 25 Gy irradiation of mre11 mutant plants (Figure 1B). These results show that the MRN complex is required for H2AX phosphorylation in response to irradiation-induced DSBs. Given that γ-irradiation–induced γ-H2AX focus formation in Arabidopsis depends on the ATM and ATR kinases (Friesner et al., 2005), these results lead us to conclude that interaction of the complex with the irradiation-induced lesion causes activation of both ATM and ATR. Thus, as is the case in mammalian cells (Lamarche et al., 2010), the MRN complex is required for ATM- and ATR-dependent H2AX phosphorylation in response to ionizing radiation in Arabidopsis plants.

Figure 1.
The MRN Complex Is Essential for Activation of the ATM and ATR Kinases in Response to Irradiation.

H2AX Phosphorylation in rad50 and mre11 Mutant Plants Is Increased in Replicated Nuclei

We and others have previously shown that rad50 and mre11 Arabidopsis mutant plants exhibit high levels of anaphase bridges as a consequence of the repair of DSBs generated in the absence of MRN as a result of replicative stress or dysfunctional telomeres (Puizina et al., 2004; Vannier et al., 2006). As described above (Figure 1), γ-H2AX foci are detected in mitotic nuclei of unirradiated rad50 or mre11 plants. Thus, Arabidopsis plants lacking the MRN complex accumulate chromosomal instability associated with DSBs that can be visualized as γ-H2AX foci.

It is possible that the spontaneous DSBs in these mutants result from replicative stress related to the absence of the MRN complex and, if so, we should expect an enrichment of γ-H2AX foci in the S-phase or early G2-phase cells of these mutants. To test for the presence of γ-H2AX foci in replicating nuclei, root tips were incubated with the thymidine analog EdU. EdU is incorporated into chromosomal DNA during replication; thus, S-phase nuclei can be identified. Preliminary experiments to establish the length of the G2-phase showed that the first EdU-positive M-phase nuclei were detected 360 min after the addition of EdU to plantlets growing in liquid medium (S. Amiard and C.White, unpublished data; Charbonnel et al., 2010). Thus, by fixing plantlets after 60 min of incubation with EdU, we are sure that only S- and early G2-phase nuclei will be labeled. EdU detection and immunostaining of phosphorylated H2AX were then performed on these plantlets. The results in Figures 2A and 2B show that 90% (or 89% in the case of mre11) of S- or early G2-phase nuclei of rad50 mutant plants present at least one γ-H2AX focus (compared with 68% [or 64%] in M-phase figures). Furthermore, 38% of S- or early G2-phase nuclei of rad50 (and 39% of mre11) present four or more foci (compared with 12% [or 8%] in the M-phase figures; Figure 1B). These results demonstrate an enrichment of γ-H2AX foci in S- or early G2-phase nuclei of cells lacking the MRN complex, suggesting an important role for the MRN complex during replication in plant cells.

Figure 2.
H2AX Phosphorylation in rad50 and mre11 Mutant Plants Is Increased in S- and Early G2-Phase Nuclei.

In addition to problems in replication of the genome, the loss of telomeric repeats observed in the absence of RAD50 should induce a DNA damage response and H2AX phosphorylation at the unprotected telomeres. FISH of root tip nuclei with nine subtelomere-specific probes, corresponding to nine of the 10 ends of the five Arabidopsis chromosomes, was performed to verify if this is so in Arabidopsis. Approximately 14% (25/179) of the γ-H2AX foci in these nuclei colocalize with subtelomeric FISH signals, showing that unprotected chromosome ends lacking most of the telomeric repeats do activate a DNA damage response in Arabidopsis rad50 and mre11 mutants (Figure 2C).

Plant Cells Mutated in the MRN Complex Activate the ATR Kinase

The presence of γ-H2AX foci in root tip nuclei of rad50 and mre11 mutant plants suggests activation of a kinase that does not require the MRN complex. In mammalian cells, the ATR kinase is activated by RPA-associated ssDNA, which accumulates as the result of replicative stress. This type of activation of the ATR kinase by replicative stress does not require the MRN complex. To determine whether the γ-H2AX foci in rad50 mutant cells are ATR dependent, we analyzed the formation of γ-H2AX foci in double mutant rad50 atr and mre11 atr plants. Root tip nuclei from wild-type, atr, rad50, mre11, rad50 atr, and mre11 atr mutant plants were immunostained using the γ-H2AX antibodies, and the number of γ-H2AX foci were counted in mitotic cells. No foci were detected in the rad50 atr or mre11 atr nuclei (Figure 3). Thus, lesions resulting from the absence of the MRN complex activate ATR-dependent damage signaling in plant cells, and this activation does therefore not require the MRN complex.

Figure 3.
Plant Cells Mutated in the MRN Complex Activate the ATR Kinase.

To confirm these data, we tested the effect of the inhibitor Ku55933 on formation of γ-H2AX foci in rad50 mutant plants. Ku55933 (IATM) has been shown to inhibit specifically the ATM kinase in mammalian cells. (Hickson et al., 2004) We tested the ability of IATM to inhibit ATM kinase in Arabidopsis. Seeds from wild-type plants were grown in the presence of the inhibitor and irradiated at 25 Gy of γ-rays. Immunostaining of root tip nuclei showed 0.5 γ-H2AX foci/cell in plants grown in the presence of the inhibitor compared with 11 foci/cell in the control plants (Figure 4A). As expected, low levels of ATR-dependent γ-H2AX foci were still observed in 30% of nuclei. Thus, as has been shown in mammalian cells, Ku55933 specifically inhibits ATM kinase in plant cells. We next tested the effect of the inhibitor on the formation of γ-H2AX foci in rad50 mutant plants. As expected from the absence of γ-ray–induced γ-H2AX foci in the rad50 atr mutant, no effect on the number of foci was observed in these plants in the presence of the inhibitor (Figure 4B). These data thus confirm the specificity of the inhibitor for the ATM kinase in plants and that DNA lesions in the rad50 mutant cells activate the ATR kinase.

Figure 4.
ATM Independence of Spontaneous γ-H2AX Foci in rad50.

Severe Growth Defects and Increased Cell Mortality in rad50 atr and mre11 atr Mutants

Root growth was retarded to a greater extent in the rad50 atr and mre11 atr double mutant plants than in the single atr, rad50, or mre11 mutant plants. The double mutant plants also exhibited reduced leaf size and disrupted phylotaxis compared with single mutant plants, with the appearance of short floral stems with distorted floral phylotaxy being retarded more than 4 weeks in the double mutants (Figure 5). To determine whether this phenotype results from reduced cell division associated with cell cycle arrest, we quantified the number of mitotic figures in the root meristems of these plants. atr and wild-type mutant plants show similar numbers of mitotic figures per root tip; however, the number of mitoses per root tip is reduced in rad50 and mre11 mutant plants (Figure 6A). The absence of RAD50 or MRE11 thus causes retardation or arrest of the cell cycle, in accordance with the observation of γ-H2AX foci in these cells. Given that we found that ATM activation is dependent upon the presence of the MRN complex (Figure 1), it is likely that the observed cell cycle arrest in MRN-deficient plants is elicited by ATR activation. This conclusion is confirmed by the observation that there are a similar number of mitotic cells per root meristem in rad50 atr and mre11 atr mutant plants as there are in wild-type plants. Thus, in the absence of the MRN complex, plant cells accumulate DNA lesions that activate cell cycle arrest through activation of the ATR kinase signaling pathway. The growth phenotype observed in the rad50 atr and mre11 atr double mutants is thus not due to cell cycle arrest.

Figure 5.
rad50 atr or mre11 atr Mutants Present Severe Morphological Defects.
Figure 6.
Cell Cycle Regulation and Cell Death Profile in Root Tips of rad50 atr and mre11 atr Mutants.

Another possible explanation for the growth defects observed in the mrn atr double mutant plants is that cell death increases as a consequence of the accumulation of unrepaired or misrepaired DNA damage. We thus stained living plantlets with propidium iodide as a marker of cell death. Propidium iodide is excluded from living cells by the cytoplasmic membrane, and the loss of cytoplasmic membrane integrity in dead cells permits uptake of propidium iodide and nuclear staining (Curtis and Hays, 2007). rad50 and mre11 mutant plants show cell death mainly in the region around the quiescent center. By contrast, rad50 atr and mre11 atr double mutant plants have a higher number of dead cells spread throughout the meristem (Figure 6B). It has been shown that radiation-induced DSBs in root plant cells activate ATM- and ATR-dependent cell death (Friesner et al., 2005; Fulcher and Sablowski, 2009). We thus tested whether the cell death observed in rad50 atr mutant plants was ATM dependent by germinating seeds in the presence of the ATM inhibitor. No effect on cell death was observed after inhibition of the ATM kinase activity, which is in agreement with the requirement for the MRN complex in ATM signaling. These results thus show that accumulation of DNA lesions in the rad50 atr mutants causes cell death and that this, not cell cycle arrest (which is ATR dependent), is at the origin of the growth defects of these plants.

Increased DNA Fragmentation in rad50 Mutant Plants in the Absence of ATR

The MRN complex has been shown to participate in stabilizing replication forks through tethering of sister chromatids (see review in Lamarche et al., 2010). In mammalian cells, the MRN complex colocalizes with sites of BrdU incorporation during S-phase (Olson et al., 2007), and depletion of Mre11 in Xenopus laevis extracts has been shown to induce accumulation of DSBs in the absence of damage (Costanzo et al., 2001). We previously showed that rad50 mutant plants present frequent end-to-end chromosome fusions and that half of these anaphase bridges involve chromosome ends that have lost telomeric repeats (Vannier et al., 2006). We thus asked whether ATR is needed to prevent chromosome instability in plants lacking the MRN complex. Mitotic figures were analyzed from pistil cells of rad50 or rad50 atr mutant plants. As previously shown by Vannier et al. (2006), chromosome bridges were detected in 10% of mitotic anaphase cells in the rad50 mutant plants. Careful observation of the micrographs showed that approximately half of these bridges are thin and complete (classical bridges), whereas half are thick and fragmented (fragmented bridges) (Figures 7A to 7C).

Figure 7.
Increased Cytological Abnormalities and Chromosome Fragmentation in the rad50 atr Mutant.

In the rad50 atr double mutant, the number of anaphase bridges increases from 10.2% of anaphases (63/617) in rad50 plants to 33.1% (155/468) in the rad50 atr plants. Strikingly, 83.33% (125/155) of the bridges in the rad50 atr anaphase cells are fragmented bridges (44% in rad50 plants). ATR thus plays an important role in the maintenance of genomic stability in cells lacking the MRN complex.

That the observed increase in chromosome fragmentation in rad50 atr is related to a role of ATR in signaling replication fork-associated lesions generated in the absence of the MRN complex is supported by the relative enrichment of γ-H2AX foci in S-and early G2-phase nuclei of rad50 and mre11 mutants (above and Figure 2). Nevertheless, a role for ATR in preserving functional telomeres cannot be excluded. In fact, accelerated telomere shortening has been reported in atr tert mutant plants compared with tert plants (Vespa et al., 2005). If we accept this hypothesis that ATR stabilizes telomeres in cells lacking RAD50, we would expect an increase in the number of chromosome fusions involving a chromosome end in rad50 atr cells relative to rad50 cells. We performed FISH analyses in mitotic cells from rad50 and rad50 atr plants using a mixture of nine chromosome-end specific subtelomeric BAC probes (Figures 7B and 7C). Fifty-eight of 155 anaphase bridges in rad50 atr hybridize to these subtelomeric probes. Thus, 37.4% of the observed chromosome fusions include a chromosome end, less than the 55.6% detected in single rad50 mutant plants. The increase in chromosome breakage observed in rad50 atr double mutant plants is thus not due to an increase in telomere uncapping. Rather than stabilizing telomeres, ATR contributes to the signaling of stalled replication forks, in agreement with the enrichment of γ-H2AX foci in replicating rad50 and mre11 mutant cells. Interestingly, activation of DNA damage signaling is not essential for the generation of chromosome fusions.

DISCUSSION

Conservation of the Requirement for the MRN Complex in Activating ATM and ATR in Response to γ-Radiation

One of the earliest responses to radiation-induced DSBs is the phosphorylation of the histone variant H2AX. This extends from the break site into surrounding chromatin and can be detected as cytological foci by the use of the appropriate antibody. In Arabidopsis plants, it has been shown that formation of γ-H2AX foci in response to ionizing radiation damage is dependent on the kinase activity of ATM and ATR (Friesner et al., 2005). In turn, activation of ATM and ATR has been shown in mammalian cells to be dependent on the MRN complex (Carson et al., 2003; Uziel et al., 2003; Horejsi et al., 2004; Lee and Paull, 2004; Adams et al., 2006; Jazayeri et al., 2006; Myers and Cortez, 2006). We show here a complete absence of induction of γ-H2AX foci in rad50 or mre11 mutant plants by γ-irradiation, confirming that the MRN complex is required for H2AX phosphorylation by the ATM and ATR kinases in response to irradiation-induced DSBs in Arabidopsis. Thus, the essential role of the MRN complex in activation of the ATM and ATR kinases in response to DSB induction is conserved in plants.

Formation of Spontaneous γ-H2AX Foci in MRN Mutant Plants

Arabidopsis rad50 and mre11 mutants present spontaneous chromosomal instability, as gauged by the presence of dicentric chromosomes and mitotic anaphase bridges (Puizina et al., 2004; Vannier et al., 2006). In this study, we show that this instability is associated with the presence of γ-H2AX foci in mitotic figures and also that these γ-H2AX foci are enriched in nuclei of S- and early G2-phase cells. This latter observation points to an important role for the Arabidopsis MRN complex in replication and agrees with reports concerning other organisms. In mammals, the MRN complex colocalizes with replication forks (Zhao et al., 2002; Mirzoeva and Petrini, 2003) and has been shown to interact with replication protein A at the sites of stalled replication forks (Robison et al., 2004; Olson et al., 2007). In X. laevis, MRE11 prevents DSB accumulation during replication stress by promoting replication fork restart (Costanzo et al., 2001; Trenz et al., 2006). A recent report shows that the S. cerevisiae MRX complex stabilizes the association of replisome components with stalled replication forks independently of the S-phase checkpoint, and disruption of the complex provokes failure to complete DNA replication in the presence of replication stress (Tittel-Elmer et al., 2009). Telomere dysfunction provides a possible alternative explanation for the origin of spontaneous γ-H2AX foci in rad50 and mre11 mutants. We have previously shown that absence of RAD50 leads to rapid shortening of a subpopulation of telomeres (Gallego and White, 2001; Vannier et al., 2006), and we hypothesized that these uncapped telomeres could elicit a DNA damage response and H2AX phosphorylation. We confirm this here with FISH analyses using specific subtelomeric probes, showing that a proportion of the spontaneous γ-H2AX foci in rad50 plants colocalize with subtelomeric DNA. These data thus indicate that both cellular DNA replication and chromosome uncapping activate the DNA damage response in rad50 and mre11 Arabidopsis mutants.

ATR Dependence of Spontaneous γ-H2AX Foci in MRN Mutant Plants

In rad50 and mre11 mutants, we thus observe both enrichment of spontaneous γ-H2AX foci in replicating cells and also the presence of these foci at telomeres. Given the MRN dependence of ATM and ATR activation and formation of γ-H2AX foci in irradiated cells, we next asked whether these spontaneous foci arising in the absence of MRN depend upon signaling of DNA damage via the ATM and/or ATR kinases (Arabidopsis has no identifiable DNA-PKcs). To answer this question, we first used the specific ATM inhibitor (ku55933), which is frequently used in mammalian studies (Hickson et al., 2004). As this drug has not to our knowledge been used previously in plants, we first tested its efficacy in Arabidopsis plantlets. Growth in the presence of ku55933 completely abolishes irradiation-induced, ATM-dependent γ-H2AX foci in wild-type plants, thus validating the specificity of the inhibitor for ATM. The presence of this drug does not, however, affect the appearance of spontaneous γ-H2AX foci in rad50 mutant plants, suggesting that the DNA damage signaling in these mutants is ATR dependent and does not require ATM. We confirmed this by constructing rad50 atr and mre11 atr double mutants and showing that no γ-H2AX foci are detected in these plants. Thus, in contrast with the ATM-dependent H2AX phosphorylation seen after DSB induction by irradiation, ATR-mediated phosphorylation of H2AX observed in cells under replicative stress due to absence of the MRN complex is not dependent on ATM. Consistent with this observation, MRN-independent H2AX phosphorylation can occur efficiently in mammalian cells after HU or UV treatment, as demonstrated by Stiff et al. (2005) and Zhong et al. (2005). These two studies show that, following HU-induced replication arrest, MRN or ATR-deficient cells exhibit impaired G2/M cell cycle arrest, which is correlated with a defect in Chk1 phosphorylation. A third study, however, showed that the MRN complex is not indispensable for ATR-dependent phosphorylation of Chk1 in response to UV and agents that induce replication stress (Myers and Cortez, 2006). The reduction of mitotic index we observed in rad50 and mre11 root tips suggests activation of G2 arrest; however, atr rad50, atr mre11, and wild-type root tips have similar mitotic indices, showing that activation of G2-M cell cycle arrest in MRN-deficient plants is ATR dependent. Arabidopsis plants can thus activate ATR-dependent H2AX phosphorylation and cell cycle arrest in the absence of the MRN complex.

In human cells, ATR plays a role in the response to DSBs, following the action of ATM and MRN to generate RPA-coated ssDNA (Jazayeri et al., 2006; Myers and Cortez, 2006). Our detection of ATR-dependent γ-H2AX foci in mitotic cells of rad50 and mre11 mutants shows that DSBs in Arabidopsis can be processed in the absence of the MRN complex. This conclusion agrees with the recent report of a low level of ATM/MRN-independent activation of ATR in mammalian cells (Tomimatsu et al., 2009).

ATR and MRN Contributions to Genome Stability

While ATM is not essential in mice and humans, RAD50, MRE11, and ATR are essential for viability of cultured human and mouse cells and of mouse embryos (Yamaguchi-Iwai et al., 1999; Brown and Baltimore, 2000; de Klein et al., 2000). Functional analyses of the roles of these proteins in the maintenance of chromosome stability have been hampered by the lethality of null mutations. Drosophila mre11, rad50, and atm mutants die at late larval stages and show both telomeric fusions and chromosome breakage (Bi et al., 2005). By contrast, null alleles of MEI-41 (ATR ortholog) are not zygotic lethal in Drosophila melanogaster; thus, ATR appears to be nonessential (Laurencon et al., 2003). Arabidopsis plants mutated for ATR are phenotypically wild type but hypersensitive to agents that induce replication stress (Culligan et al., 2004), and we show here that double atr rad50 and atr mre11 mutant plants show severe developmental defects but are viable. Cytogenetic analyses show that rad50 atr and mre11 atr plants displayed higher chromosomal instability than either single mutant, which very probably underlies the observed developmental defects in these double mutants. This would accord with observations in Drosophila mei41 nbs1 and mei41 rad50 double mutant cells, which show higher frequencies of end-to-end chromosome fusions and chromosome breaks than the single mutants (Bi et al., 2005; Ciapponi et al., 2006). Our mitotic FISH analysis shows similar proportions of chromosome fusions involving a chromosome end in rad50 atr and rad50 mutant plants. Thus, in Arabidopsis plants, ATR does not contribute to stabilizing the telomeres but prevents chromosome breakage.

Absence of ATR thus strongly increases the number of DSBs and genomic instability in rad50 and mre11 mutant plants. These results are in agreement with data that show that ATR responds principally to problems arising at replication forks (Culligan et al., 2004; Cimprich and Cortez, 2008; Friedel et al., 2009). ATR could contribute to the activation of recombination at stalled and/or collapsed replication forks. In support of this hypothesis, ATR has been shown in human cells to phosphorylate proteins involved in the regulation of homologous recombination (Tibbetts et al., 2000). An alternative hypothesis is that ATR could promote fork stability and/or recovery of stalled forks in rad50 mutant plants, and, in support of this, a number of replisome components are substrates of the ATR kinase (Yoo et al., 2004; Liu et al., 2006; Trenz et al., 2008). A growing body of evidence suggests that human ATR and the Werner’s Syndrome helicase work together to suppress fragile replication site instability (Pichierri et al., 2003; Pirzio et al., 2008). Furthermore, it has been shown that in response to replicative stress (i.e., in the presence of HU or Aphidicolin), ATR activates the Bloom’s Syndrome helicase to restore correct fork restart and hence prevent subsequent genomic instability (Davies et al., 2004, 2007). Moreover, in various organisms, H2AX phosphorylation by ATR could contribute through recruitment of cohesin and repair factors to repair of DSBs generated in the absence of MRN (Unal et al., 2004; Lowndes and Toh, 2005; Fillingham et al., 2006; Stucki and Jackson, 2006; Kinner et al., 2008).

The accumulation of unrepaired or misrepaired DNA in the single (rad50 and mre11) and double (rad50 atr and mre11 atr) mutant plants is expected to lead to cell death and thus to developmental defects in the growing plants. Using propidium iodide staining as a marker of cell death, we found that cell death in rad50 and mre11 mutant plant roots is restricted to the meristem, while cell death in rad50 atr and mre11 atr double mutant plants spreads throughout the root. It has recently been shown that irradiation of plants with UV or γ-rays preferentially kills stem cells, and this cell death involves signaling of DNA damage through activation of both ATM and ATR kinases (Fulcher and Sablowski, 2009; Furukawa et al., 2010). While γ-irradiation–induced programmed cell death (PCD) in Arabidopsis is dependent upon ATM signaling, UV-B–induced PCD is elevated in the absence of ATM or ATR. In contrast with the ATM- and ATR-dependent PCD induced by replication stress, we describe here the death of root initials in rad50 or mre11 mutants, independently of both ATR and ATM. Thus, in the absence of RAD50, intrinsic replication stress presumably causes fork collapse and accumulation of DSB, leading to aneuploidy and/or mitotic catastrophe and, thus, the observed cell death.

In conclusion, our data show an absence of induction of γ-H2AX foci in rad50 and mre11 mutant plants by γ-irradiation, confirming that the MRN complex is required for H2AX phosphorylation by the ATM and ATR kinases in response to irradiation-induced DSBs in Arabidopsis. The essential role of the MRN complex in activation of the ATM and ATR kinases in response to DSB induction is thus conserved in plants. Spontaneous activation of γ-H2AX foci formation in the absence of MRN has not to our knowledge been tested in any organism. We show that this phosphorylation is ATR dependent and strongly enriched in S-phase nuclei, and only a subset of these γ-H2AX foci are found to be associated with telomeres. Furthermore, our detection of ATR-dependent γ-H2AX foci in mitotic cells of rad50 and mre11 mutants shows that DSB in Arabidopsis can be processed in the absence of the MRN complex. Taken together, these data suggest a key role for MRN and ATR in maintaining proper replication. In the absence of RAD50 or MRE11, cells activate ATR, presumably through ssDNA generated at stalled replication forks. Activation of the ATR kinase will then not only activate cell cycle arrest, but stabilize blocked replication forks and facilitate completion of S-phase synthesis. Failure to rescue replication forks in rad50 atr mutant plants will result in fork collapse and chromatid breakage and give rise to the appearance of dicentric chromosomes. The high degree of chromosomal instability in these plants and the resulting cell death explain their severe developmental defects (Figure 8). The embryonic lethality of rad50, mre11, and atr in mammals could well result from the critical roles of the MRN complex and ATR in maintaining proper replication as observed in Arabidopsis. The striking tolerance to these mutations, both individually and in combination, makes Arabidopsis a particularly interesting model for studies of the fundamental cellular metabolic processes that assure the replication and stability of the eukaryotic genome.

Figure 8.
Model Explaining the Role for MRN and ATR in Maintaining Proper Replication.

METHODS

Plant Material and Growth Conditions

The T-DNA insertional Arabidopsis thaliana mutants of rad50, mre11-3, and atr-2 have been described previously (Gallego et al., 2001; Culligan et al., 2004; Puizina et al., 2004). Seeds of the mre11-3 Arabidopsis line SALK_054418 and the atr-2 Arabidopsis line SALK_032841 were obtained from the Nottingham Arabidopsis Stock Centre (Scholl et al., 2000). Homozygous mutant and heterozygous plants for the RAD50 or MRE11 alleles were distinguished by phenotypic and PCR analyses, as described previously (Gallego et al., 2001; Puizina et al., 2004). The double rad50 atr or mre11 atr mutants were produced by crossing rad50 and mre11 heterozygotes with an atr homozygote using standard techniques.

Seeds were surface sterilized in 7% calcium hypochlorite for 15 min and rinsed four times with sterile water. Seeds were sown on Petri dishes containing 1× Murashige and Skoog (MS) with vitamins, MES buffer (M0255; Duchefa Biochimie) and1% sucrose (Duchefa), and solidified with 0.8% agar (Bacto-Agar; DIFCO Laboratories). Petri dishes were placed at 4°C overnight (15 h) and transferred to a growth chamber (16 h light, 8 h dark cycle) at 23°C.

Plant Treatments

To inhibit ATM kinase, Arabidopsis plants were grown in Petri dishes on solid MS medium containing 10 μM ku55933 (ATM inhibitor or IATM) (Hickson et al., 2004).

EdU detection (Vanstraelen et al., 2009) was performed as indicated by the manufacturer (Click-It EdU Alexa Fluor 594 imaging kit; Invitrogen) with modifications. For EdU (5-ethynyl-2’-deoxyuridine) incorporation, 5-d-old seedlings growing in liquid 0.5× MS medium were transferred to the same medium containing 10 μM EdU and incubated for 1 h. All the following steps were performed at room temperature. Seedlings were fixed for 15 min in 3.7% (v/v) formaldehyde in PBS, pH 7.4, rinsed twice with PBS/3% BSA, and placed in 0.5% (v/v) Triton X-100/PBS. After 20 min at room temperature, the Triton X-100/PBS was replaced with Click-It reaction solution and incubation was continued for 30 min with gentle agitation. The Click-It solution was removed, and the seedlings were rinsed in PBS/BSA and transferred to PBS.

γ-Irradiation of 5-d-old seedlings was performed with a 137Cs source (C.I.S. Bio International) at an absorbed dose of 25 Gy (1 Gy/7.2 s), and the seedlings were then fixed with 4% (v/v) paraformaldehyde, 10 or 20 min after the start of irradiation.

Cell Death Assay

Five days after germination, seedlings were placed in propidium iodide solution (5 μg/mL in water) for 1 min and rinsed three times with water. Root tips were then transferred to slides in a drop of water and covered with a cover slip for observation under the fluorescence microscope with a Zeiss filter set #43HE (adapted from Curtis and Hays, 2007).

Determination of the Mitotic Index

Roots were fixed in a solution of 4% paraformaldehyde in PBS for 45 min, washed twice in PBS/Tween 1%, incubated for 30 min in Hoechst 33258 (3 μg/mL), rinsed in PBS/Tween, and mounted under cover slips in 40% glycerol. The roots were analyzed for mitotic stages (metaphase and anaphase/telophase) using fluorescence microscopy with Zeiss filter set #49.

γ-H2AX Antibodies

Antiserum was raised and purified by Eurogentec against a phospho-specific Arabidopsis H2AX peptide following the method published by the Britt group (Friesner et al., 2005). Using a sample of antiserum kindly sent by Anne Britt, we verified that this new antiserum gives identical results in our hands to that published by Friesner et al. (Friesner et al., 2005; Charbonnel et al., 2010). We verified the number of foci at different doses and found identical results to those published by Friesner et al., with a dose of 25 Gy from a 137Cs source inducing a mean of 15 γ-H2AX foci per 4C M-phase root nucleus in wild-type plants. No or very few foci were observed in nonirradiated wild-type plants.

Five days after germination, root tips were prepared as previously described (Charbonnel et al., 2010). Briefly, root tips were fixed for 45 min in 4% paraformaldehyde in PME (50 mM PIPES, pH 6.9, 5 mM MgSO4, and 1 mM EGTA) and then washed 3 × 5 min in PME. Tips were digested for 30 min in a 1% (w/v) cellulase, 0.5% (w/v) cytohelicase, and 1% (w/v) pectolyase (from Sigma-Aldrich; Refs. C1794, C8274, and P5936) solution prepared in PME and then washed 3 × 5 min in PME. These roots were gently squashed onto slides as described (Liu et al., 1993), air dried, and stored at −80°C. Each slide was incubated overnight at 4°C with 50 to 100 μL rabbit, anti-plant γ-H2AX antiserum diluted 1:600 in fresh blocking buffer (3% BSA, 0.05% Tween 20 [Sigma–Aldrich] in 1× PBS). Slides were washed 3 × 5min in 1× PBS solution and then incubated for 2 to 3 h at room temperature in 50 to 100 μL blocking buffer consisting of Alexa 488–conjugated goat anti-rabbit (Molecular Probes, 1:1000) secondary antibodies. Finally, slides were washed 3 × 5 min in 1× PBS and mounted in Vectashield mounting medium with 4',6-diamidino-2-phenylindole (DAPI) (2 μg/mL) (Vector Laboratories).

DAPI Staining of Mitosis

As described (Caryl et al., 2000), whole inflorescences were collected and fixed, and the mitotic chromosomes of fixed flower pistils were squashed on a slide. Slides were mounted using Vectashield (Vector Laboratories) mounting medium with 1.5 mg/mL DAPI and observed by fluorescence microscopy. Images were further processed and enhanced using Adobe Photoshop software.

FISH

FISH was performed according to Mokros et al. (2006) with the modifications described by Vannier et al. (2009), using BACs from subtelomeric regions of Arabidopsis chromosomes (F6F3, F23A5, F17A22, F4P13, T20O10, F6N15, T19P19, F7J8, and K9I9), labeled either with Cy5-dUTP or Cy3-dUTP (Amersham) by standard nick translation reactions (Roche). FISH after immunostaining required a postfixation step of 30 min in 4% formaldehyde.

Microscopy and γ-H2AX Foci Analysis

Images were acquired on a Zeiss epifluorescence microscope using Axiovision software. Measurements were performed using the same software, and images were treated using Adobe Photoshop software to enhance contrast. Images stacks were captured in three dimensions (x, y, and z), and were deconvolved with the deconvolution module (theoretical PSF, iterative algorithm) of Axiovision 4.6.2 (Zeiss) software to affine γ-H2AX foci, which were counted manually. The images presented are collapsed Z-stack projections obtained using the Extended-focus module (projection method) of the Axiovision 4.6.2 software, except for immunostaining and subtelomeric FISH labeling images (Figure 2C) that correspond to the single focal plane from a deconvolved three-dimensional image.

Accession Numbers

Sequence data from this article can be found in the Arabidopsis Genome Initiative or GenBank/EMBL databases under the following accession numbers: RAD50 (locus AT2G31970; GenBank NM_128757); Mre11 (locus AT5G5426; GenBank NM_124806); ATR (locus AT5G40820; GenBank NM_123447); and ATM (locus AT3G48190; GenBank NM_114689.6).

Acknowledgments

We thank the members of the recombination group for their help and discussions. Spencer Brown and Marlene Van Straelen (Centre National de la Recherche Scientifique) are thanked for sending us the Arabidopsis EdU labeling protocol prior to publication. We thank the Etablissement Français du Sang and Dr. P. Fabrigly for access to the 137Cs irradiator. This work was partly financed by a European Union research grant (LSHG-CT-2005-018785), a French Government ANR grant (ANR-07-BLAN-0068), the Centre National de la Recherche Scientifique, the Université Blaise Pascal, the Université d’Auvergne, and the Institut National de la Santé et la Recherche Medicale. C.C. was supported by a doctoral fellowship from the Ministère de l'Education Nationale, de la Recherche et de la Technologie, and S.A. is an ANR postdoctoral fellow (ANR-07-BLAN-0068).

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