ATM-Mediated Transcriptional and Developmental Responses to γ-rays in Arabidopsis

Abstract

ATM (Ataxia Telangiectasia Mutated) is an essential checkpoint kinase that signals DNA double-strand breaks in eukaryotes. Its depletion causes meiotic and somatic defects in Arabidopsis and progressive motor impairment accompanied by several cell deficiencies in patients with ataxia telangiectasia (AT). To obtain a comprehensive view of the ATM pathway in plants, we performed a time-course analysis of seedling responses by combining confocal laser scanning microscopy studies of root development and genome-wide expression profiling of wild-type (WT) and homozygous ATM-deficient mutants challenged with a dose of γ-rays (IR) that is sublethal for WT plants. Early morphologic defects in meristematic stem cells indicated that AtATM, an Arabidopsis homolog of the human ATM gene, is essential for maintaining the quiescent center and controlling the differentiation of initial cells after exposure to IR. Results of several microarray experiments performed with whole seedlings and roots up to 5 h post-IR were compiled in a single table, which was used to import gene information and extract gene sets. Sequence and function homology searches; import of spatio-temporal, cell cycling, and mutant-constitutive expression characteristics; and a simplified functional classification system were used to identify novel genes in all functional classes. The hundreds of radiomodulated genes identified were not a random collection, but belonged to functional pathways such as those of the cell cycle; cell death and repair; DNA replication, repair, and recombination; and transcription; translation; and signaling, indicating the strong cell reprogramming and double-strand break abrogation functions of ATM checkpoints. Accordingly, genes in all functional classes were either down or up-regulated concomitantly with downregulation of chromatin deacetylases or upregulation of acetylases and methylases, respectively. Determining the early transcriptional indicators of prolonged S-G2 phases that coincided with cell proliferation delay, or an anticipated subsequent auxin increase, accelerated cell differentiation or death, was used to link IR-regulated hallmark functions and tissue phenotypes after IR. The transcription burst was almost exclusively AtATM-dependent or weakly AtATR-dependent, and followed two major trends of expression in atm: (i)-loss or severe attenuation and delay, and (ii)-inverse and/or stochastic, as well as specific, enabling one to distinguish IR/ATM pathway constituents. Our data provide a large resource for studies on the interaction between plant checkpoints of the cell cycle, development, hormone response, and DNA repair functions, because IR-induced transcriptional changes partially overlap with the response to environmental stress. Putative connections of ATM to stem cell maintenance pathways after IR are also discussed.

SUPPRESSOR OF GAMMA RESPONSE1 Links DNA Damage Response to Organ Regeneration

“…The transcriptional induction of ERF115 has not been previously observed in IR-response transcriptomes (Ricaud et al, 2007;Yoshiyama et al, 2009;Missirian et al, 2014), possibly due to its localized expression in a small subset of cells. Nonetheless, this discrepancy did raise the question of whether its IR induction is an artifact of the GUS or GFP fusion transgenes, rather than the native gene.…”

“…ATM (Yoshiyama et al, 2013) and inferably ATR (Furukawa et al, 2010;Yoshiyama et al, 2009) can phosphoactivate the transcription factor SOG1, as well as other proteins, in plant cells (Roitinger et al, 2015;Yoshiyama et al, 2013). Once activated, SOG1 transcriptionally induces various functional classes of DDR genes (Yoshiyama et al, 2009;Missirian et al, 2014;Ricaud et al, 2007); SOG1 induces a robust set of .100 transcripts by $4-fold within 1.5 h in response to 100 Gy IR (Culligan et al, 2006;Furukawa et al, 2010). SOG1 has a known role in transcriptionally inhibiting cell cycle progression in response to DNA damage (Preuss and Britt, 2003;Yoshiyama et al, 2009).…”

Hypersensitivity to DNA damage in plant stem cell niches

“…S3). Higher doses of zeocin caused permanent arrest of the root meristem and death of the QC and provascular cells, which has been interpreted as a consequence of premature differentiation (18) (Fig. S1).…”

“…However, accumulation of GFP fused to the destruction box of CYCB1;1 (CYCB1;1-GFP), which marks cells that are likely to be arrested in G2 phase (17,18,27), showed that the response to zeocin was widespread in the root tip ( Fig. 1D; an untreated CYCB1;1-GFP control is shown in Fig.…”

“…In plants, the best-characterized response downstream of ATM and ATR is cell cycle arrest caused by expression of the WEE1 kinase (15). After irradiation, Arabidopsis ATM also mediates the transcriptional activation of genes involved in DNA metabolism, repair, chromatin, and chromosome structure, whereas ATR has a minor role in transcriptional changes after irradiation (16)(17)(18).…”