ABSTRACT
The cellular response to double-strand breaks (DSBs) in DNA is a complex signalling network, mobilized by the nuclear protein kinase ataxia-telangiectasia mutated (ATM), which phosphorylates many factors in the various branches of this network. A main question is how ATM regulates DSB repair. Here, we identify the DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) as an ATM target. PNKP phosphorylates 5'-OH and dephosphorylates 3'-phosphate DNA ends that are formed at DSB termini caused by DNA-damaging agents, thereby regenerating legitimate ends for further processing. We establish that the ATM phosphorylation targets on human PNKP-Ser 114 and Ser 126-are crucial for cellular survival following DSB induction and for effective DSB repair, being essential for damage-induced enhancement of the activity of PNKP and its proper accumulation at the sites of DNA damage. These findings show a direct functional link between ATM and the DSB-repair machinery.
Subject(s)
Cell Cycle Proteins/metabolism , DNA Breaks, Double-Stranded , DNA Repair Enzymes/metabolism , DNA Repair/physiology , DNA-Binding Proteins/metabolism , Protein Serine-Threonine Kinases/metabolism , Tumor Suppressor Proteins/metabolism , Animals , Ataxia Telangiectasia Mutated Proteins , Cytotoxins/pharmacology , DNA Breaks, Double-Stranded/drug effects , DNA Repair Enzymes/genetics , HEK293 Cells , Humans , Mice , Phosphorylation/drug effects , Zinostatin/pharmacologyABSTRACT
Differential proteolytic (18)O labeling is a cost-effective but not commonly used method in the field of quantitative proteomics based on mass spectrometry (MS). In most cases, peptide identification is performed at the MS/MS level followed by peptide quantification at the MS level. In this study, identification and quantification of (18)O-labeled peptides was performed in a single step at the MS/MS level using the MASCOT 2.2 search engine, and the instrumental conditions for acquisition of ultra performance liquid chromatography electrospray MS/MS (UPLC-ESI-MS/MS) data were adapted accordingly. Using analysis of standard peptide and protein mixtures prepared by differential (16)O/(18)O labeling, under these conditions automated MS/MS data acquisition and evaluation delivered correct data. Linearity and reproducibility of this approach indicated excellent performance. In addition, the method was applied to relative quantification of protein phosphorylation in mouse brain following treatment with ionizing radiation. The analysis led to automated quantification of 342 proteins and 174 phosphorylation sites, 24 of which were up- or down-regulated by a factor of 2 or more. The majority of these phosphorylation sites were found to be located in target sequences of known protein kinases, showing the activation of kinase-regulated signaling cascades by irradiation.
