ATM protein kinase: the linchpin of cellular defenses to stress

Abstract

ATM is the most significant molecule involved in monitoring the genomic integrity of the cell. Any damage done to DNA relentlessly challenges the cellular machinery involved in recognition, processing and repair of these insults. ATM kinase is activated early to detect and signal lesions in DNA, arrest the cell cycle, establish DNA repair signaling and faithfully restore the damaged chromatin. ATM activation plays an important role as a barrier to tumorigenesis, metabolic syndrome and neurodegeneration. Therefore, studies of ATM-dependent DNA damage signaling pathways hold promise for treatment of a variety of debilitating diseases through the development of new therapeutics capable of modulating cellular responses to stress. In this review, we have tried to untangle the complex web of ATM signaling pathways with the purpose of pinpointing multiple roles of ATM underlying the complex phenotypes observed in AT patients.

Fig. 1

ATM kinase structure and post-translational modifications. A schematic representation of ATM protein structure. Kinase, FAT, FATC, and PRD (yellow) domains are shown in the C-terminus; HEAT (Huntingtin, Elongation factor 3, alpha subunit of PP2A and TOR1), TPR (tetratricopeptide), ARM (Armadillo), and PFT (protein farnesyl transferase) repeats are shown in the N-terminus schematically in dark green and magenta. Protein interaction motifs of ATM are also shown: TAN (Tel1/ATM N-terminal) motif (dark blue), N-terminal substrate-binding site (Subs); putative leucine zipper (red) and proline-rich motif (dark purple) (see text for details); An emerging complexity in post-translational modifications of ATM is demonstrated. ATM autophosphorylation and phosphorylation (P), Acetylation (Ac), and cysteine modification (C*) sites are shown. All these sites play a role in ATM kinase activation. The exact number of phosphotyrosine (pY) sites or identities of tyrosine kinases capable to phosphorylate these sites in ATM remain elusive at present (see text). Possible, but yet unidentified post-translational modifications (?PTM) of ATM kinase are also shown

Fig. 2

MRN complex and recognition of DNA double-strand break. a Schematic representation of the domain structures of MRE11, RAD50 and NBS1. FHA (fork-head associated) and BRCT (BRCA1 C- terminal) domains are shown in the Nbs1 N-terminus; MRE11-interacting motifs (MIM) and ATM-interacting domains (FXF/Y) are located at the C-terminus. MRE11 has N-terminal nuclease domain and two DNA-binding domains. NBS1-interacting motif is also located in the N-terminus. In RAD50, two Walker A and B motifs (ABC ATPase) are shown at the N- and C-termini. Adjacent MRE11-interacting motifs (MIM) are also depicted. The rest of the molecule is long coiled-coil domains containing zinc-hook motif (CXXC) in the middle. b Positioning of MRN–ATM complex at the site of DNA break. MRN complex recognizes DNA breaks in chromatin via DNA-binding motifs in MRE11 and RAD50. DNA-end tethering activity of MRN complex is mediated by RAD50 coiled coil “hooks” (see text). NBS1 is important for recruitment of ATM kinase to the site of the break through its C-terminal ATM-interacting motif. In the absence of determined ATM X-ray structure, the overall geometry of the complex at the site of the break remains hypothetical. ATM activation is possible in the absence of MRN complex (see text), however, molecular mechanisms of this process remain to be elucidated

Fig. 3

Cross-talk between ATM, ATR, and DNA-PK kinases at the sites of DNA double-strand breaks. Identified phosphorylation sites of phosphatidylinositol (PI) 3-kinase-like kinases (PIKKs) and their targeting subunits are shown. Functional significance of many phosphorylation sites is not known. It is not yet clear if all trans-phosphorylation signaling events exist between ATM, ATR, and DNA-PK kinases [49, 152] (see text). Activity of individual PIKK complexes can be modulated by signaling inputs from other kinases [155, 157] (e.g., CDKs and CK2). While ATM-dependent phosphorylation of MRN complex occurs in vivo [82, 87], phosphorylation of Ku70/80 by DNA-PK can be demonstrated in vitro, but does not have functional significance in vivo. ATR-dependent ATRIP phosphorylation was demonstrated both in vitro and in vivo, however, it does not play a role in DNA damage signaling

Fig. 4

Events happening at or around DNA double-strand breaks (DSBs) in chromatin. The recruitment of protein complexes and modifications in the chromatin area surrounding DNA breaks are shown. Activation of ATM kinase depends on series of phosphorylation and acetylation events as wells as its recruitment to the site of the break via interaction with MRN complex. Non-covalent modification of ATM kinase by poly-ADP-ribose polymers (PAR) also plays a role. Early events include ATP-dependent chromatin relaxation, recruitment of HP1β, exposure of histone H3 methylation sites and recruitment of histone acetyltransferase TIP60. The hierarchy of events or cross-talk between signaling pathways has not yet been established (see text). Acetylation of ATM by TIP60 is important for subsequent autophosphorylation and activation steps. Activated ATM phosphorylates histone H2AX and triggers a cascade of further histone modifications and recruitment of DNA damage response proteins. Phosphorylated histone H2AX (γH2AX) recruits MDC1, which in turn is phosphorylated by ATM. This event leads to recruitment of ubiquitin ligase RNF8, which in cooperation with UBC13 ubiquitinates H2AX. Recruitment of second ubiqutin ligase RNF168 is important for growth of ubiquitin chains. Acetylation of H2AX by TIP60 is important for its ubiquitination by UBC13. Exposure of histone H3/H4 methylation sites also leads to recruitment of 53BP1 to the sites of DNA DSBs and its subsequent phosphorylation by ATM

Fig. 5

Cytoplasmic and oxidative stress signaling pathways mediated by ATM. Selected pathways of ATM-dependent signaling in cytoplasm are shown. Various extra- and intra-cellular stimuli resulting in ROS production lead to ATM kinase activation independently of DNA damage signaling pathway (see text). ROS activate ATM kinase in the cytoplasm through oxidation of cysteine residues resulting in formation of catalytically active dimer. Sequestration of inhibitory phosphatases (PP2A-C) to caveolin-enriched lipid rafts in the membrane might also play a role in the ATM activation process. ATM signals through LKB1 and AMPK kinases to suppress activity of the mTORC1 kinase complex and activates autophagy. ATM is also involved in AMPK-dependent mitochondrial biogenesis pathway. ATM activation by oxidative stress leads to dissociation of SMAR1 (scaffold/matrix-associated region1-binding protein)-AKR1a4 (NADPH-dependent aldehyde reductase) complex and SMAR1 translocation into nucleus. ATM is activated in response to insulin and phosphorylates 4E-BP1 (eIF-4E-binding protein 1) influencing translation initiation signaling. DNA-damage induced activation of NF-κB pathway is mediated by ATM shuttling to cytoplasm and through association with NEMO/IKKγ. ATM recruitment to membranes through TRAF6 interaction activates the kinase complex of TAK1-TAB1-TAB2/(TAB3). TAK1 kinase complex activates IKK–NF-κB signaling