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109 The road to genome expansion is paved with good intentions: when DNA repair goes awry

The maintenance of eukaryotic genomes is ensured by three-step DNA ligation reactions employed by ATPdependent DNA ligases. However, when DNA ligases engage DNA or RNA/DNA structures with non-canonical 5′ or 3′ termini, the DNA ligase catalytic activity can paradoxically exacerbate DNA damage through a process termed “abortive ligation” which leads to toxic adducted 5′-adenylated (5′-AMP) lesions. The human Aprataxin protein (APTX, aka Hnt3 in budding yeast) is a DNA ligase “proofreader”, and catalyzes the direct reversal of AMP-modified nucleic acid to generate 5′-phosphorylated ends. However, the molecular context for deadenylation repair has remained enigmatic. To better define APTX function, we examined the importance of APTX/ Hnt3 to the RNaseH2-dependent excision repair (RER) pathway of removal of genome embedded ribonucleotides. We have demonstrated that DNA ligases undergo abortive ligation to generate adenylated 5′-ends containing a ribose characteristic of RNaseH2 incision at mono-ribonucleotides in DNA. APTX/Hnt3 efficiently repairs adenylated RNA–DNA to promote cellular survival and prevent S-phase checkpoint activation in budding yeast undergoing RER. A series of X-ray structures of human APTX/RNA–DNA/AMP/Zn complexes define a mechanism for detecting and reversing adenylation at RNA–DNA junctions. This involves A-form RNA–DNA binding, and an induced fit active site assembly controlled by APTX engagement of nicked RNA–DNA junctions. We discuss how heritable mutations in the APTX gene linked to the debilitating neurological disorder Ataxia with Oculomotor Apraxia 1 (AOA1) impact APTX protein structure and function. Altogether, the emerging results from structural, biochemical and genetic analysis of human and yeast Aprataxins leads to the hypothesis that accumulation of adenylated RNA–DNA may contribute to APTX-linked neurodegenerative disease.