**3.7 ATM/ATR dependent regulation of DNA repair**

A central regulator of the fate of damaged cells between apoptosis or cell cycle arrest and DNA repair in animals is the tumor-suppressing p53, sometimes dubbed the "guardian of the genome". This transcription factor controls not only cell cycle genes like p21 and apoptosis factors like PUMA, NOXA, and BAX but also various components of major DNA repair pathways such as CSB, DDB2 and XPC (NER); FANCC (DNA crosslink repair) and MSH2, MLH1, and PMS2 (mismatch repair) (Gatz and Wiesmuller, 2006; Brady and Attardi, 2010). There is also evidence that it has a more direct role in BER, interacting with APE1 and OGG1 and thereby enhancing the excision of oxidized DNA bases (Gatz and Wiesmuller, 2006; Vigneron and Vousden, 2010). Additionally p53 seems to recognize and bind directly to certain DNA structures e.g. Holliday junctions and mismatches where it represses the

Recognition and Repair Pathways of Damaged DNA in Higher Plants 215

can and should be considered as excellent and viable alternatives to investigate the fundamentals of DNA repair processes. Tolerance towards mutations and abiotic stresses along with the relative ease of upkeep and propagation of the research organisms are two

Due to their inability to elude many constantly damaging influences, plants need to utilize efficient ways to cope with these stresses. One strategy plants seem to have adopted to manage the higher demands on DNA repair is redundancy. For instance, genes of every pathway discussed here were found to be duplicated in Arabidopsis or rice (Singh et al., 2010). Additionally the existence of both 8-oxo-guanine glycosylases, OGG1, as well as MutM/Fpg in Arabidopsis demonstrate functional redundancy of independent, alternative repair pathways, which may have originated from the incorporation of chloroplast and mitochondrial genes into the nuclear genome (Boesch et al., 2009; Singh et al., 2010; Rowan

Probably because of these gene duplications, functional redundancies, and more efficient or alternative pathways in comparison to animals, plants often have greater flexibilities in how they can respond to and potentially tolerate damaged DNA and mutations. For example a homozygous mutant in ATR kinase, which would be lethal in mammals, can in plants be investigated for the impact on DNA repair, control of apoptosis or gene expression profiles. In order to see the global effects of genotoxic stressors on a model organism, the subjects need to be exposed to different degrees of damaging agents. Here, plants are ideal models because of their sessile nature. They can be cultivated under very steady and reproducible conditions, while stress exposure is highly controlled. In addition, from an ethical point of view, plants can be taken to the edge of survival with very harsh treatments such as high levels of UV-light or toxin applications that for some may be not comfortable to perform on

In comparison to animals, plants are low cost organisms that only require minimal monitoring along with water and occasionally fertilizer. Small plants like the moss *Physcomitrella patens* or *Arabidopsis thaliana* can be cultivated to great numbers within in a few square feet while by comparison animals require adequate space and regular food, water, and cleaning. While mutant lines are readily available for many animal and plant systems, shipment and propagation of plant resources can be quite straightforward. Seeds can be harvested for immediate propagation of the next generation or stored long-term, even at room temperature, before use months or even years later. Sending seed material to colleagues around the world is technically simple since no special transport accommodations need to be made. Generating transgenic *Arabidopsis* lines using *Agrobacterium* infection is a standard lab procedure, and allows for rapid complementation of mutant lines to verify protein functionality and observation of response and recovery. Also generation time of Arabidopsis plants is very short with just two months from seed to

In addition to using plants as basic models to understand DNA repair processes, there are also practical reasons why this area of research urgently needs to be expanded. With the increase in food shortages for increasing populations, the recognition of environmental toxins and the growing evidence of impending and occurring climate changes across the world, it becomes critical to rapidly develop plants that can better cope with environmental stress. As such, stress tolerant crop plants generated either by genetic engineering or classical breeding will become increasingly important resources to guarantee stable food

supplies to the human population in an expected changing environment.

factors that we will briefly discuss in this final section of the review.

et al., 2010).

animals.

seed.

activities of HR and NHEJ (Bakalkin et al., 1994; Subramanian and Griffith, 2005; Gatz and Wiesmuller, 2006).

Activation of p53 after DNA damaging conditions is achieved by phosphorylation by the checkpoint kinases ATAXIA TELANGIECTASIA MUTATED (ATM) and ATAXIA TELANGIECTASIA AND RAD3 RELATED (ATR) (Canman et al., 1998; Tibbetts et al., 1999). While recent studies imply that ATM is a sensor for the redox state of the cell, it is mainly known to be activated by the above-mentioned DSB sensing MRN-complex (Bakkenist and Kastan, 2003; Falck et al., 2005; Kruger and Ralser, 2011; Perry and Tainer, 2011). ATR, on the other hand, is recruited to RPA-coated UV-induced lesions by the ATR INTERACTING PROTEIN (ATRIP) (Wright et al., 1998; Cortez et al., 2001; Ball and Cortez, 2005; Warmerdam et al., 2010). Once activated both kinases phosphorylate p53 and the effector kinases CHK1 and CHK2 regulating cell cycle and DNA repair (Brady and Attardi, 2010).

Curiously no plant homologues of p53 have been identified in any of the model organisms. This is probably linked to the absence of the core apoptotic machinery as we know it from animals. In contrast most of the DNA repair targets of p53, as well as ATM and ATR, are very well conserved in plants. Where loss of one of the checkpoint kinases in animals is lethal, the existence of viable *atr* and *atm* mutant plants in Arabidopsis make it an ideal model for their investigation. Both are involved in the response to ionizing radiation (IR) and necessary for the IR-induced transcription activation of many genes participating in DNA repair, cell cycle control, transcription, and replication (Culligan et al., 2006; Ricaud et al., 2007; Yoshiyama et al., 2009; Furukawa et al., 2010).

This raises the question if there is a factor that is functioning as a p53 analog mediating the DNA damage response between ATM/ATR and the downstream repair factors. An answer to that could be SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1). Though unrelated to p53 and unique to plants, this transcription factor, discovered in a screen for suppressor mutants of the -irradiation induced cell cycle arrest of Arabidopsis *uvh1* seeds, is necessary for the activation of genes downstream of both ATM and ATR in response to -irradiation (Preuss and Britt, 2003; Yoshiyama et al., 2009; Furukawa et al., 2010). SOG1, ATM, and ATR were also found to trigger plant programmed cell death (PCD) in root meristems after - or UV-B irradiation, a mechanism that was recently shown to be distinct from animal apoptosis (Fulcher and Sablowski, 2009; Furukawa et al., 2010). Hence, SOG1 is a good candidate to control repair processes in a p53-like fashion, at least by activating transcription of the plant homologues of factors like DDB2, MSH2 and XPC in response to UV and IR stresses.

Current research indicates that plants and animals share roughly similar repair pathways. But for some repair proteins that have been described in animals no homologues have been found in plants, as yet. However, with ongoing research, it seems plausible that plant counterparts will be identified that can substitute for missing animal orthologs as it appears to be the case with p53 and SOG1.
