APE1/Ref-1 interacts with NPM1 within nucleoli and plays a role in the rRNA quality control process.

APE1/Ref-1 (APE1), a DNA repair enzyme and a transcriptional coactivator, is a vital protein in mammals. Its role in controlling cell growth and the molecular mechanisms that fine-tune its different cellular functions are still not known. By an unbiased proteomic approach, we have identified and characterized several novel APE1 partners which, unexpectedly, include a number of proteins involved in ribosome biogenesis and RNA processing. In particular, a novel interaction between Nucleophosmin (NPM1) and APE1 was characterized. We observed that the APE1 33 N-terminal residues are required for stable interaction with the NPM1 oligomerization domain. As a consequence of the interaction with NPM1 and RNA, APE1 is localized within the nucleolus and this localization depends on cell-cycle and active rRNA transcription. NPM1 stimulates APE1 endonuclease activity on abasic dsDNA but decreases APE1 endonuclease activity on abasic ssRNA by masking the N-terminal region of APE1 required for stable RNA binding. In the APE1 knocked-down cells, pre-rRNA synthesis and rRNA processing were not affected but inability to remove 8-OHG rRNA upon oxidative stress, impaired translation, lowered intracellular protein content and decreased cell growth rate was found. Our data demonstrate that APE1 affects cell growth by directly acting on RNA quality control mechanisms, thus affecting gene expression through post-transcriptional mechanisms.