Nucleophosmin binds G-quadruplex regions at ribosomal DNA

Nucleophosmin (NPM1) is an abundant phospho-protein that plays a key role in ribosome biogenesis. NPM1 binds nucleic acids and has intrinsic RNAase and chaperone activities. Although mainly localized at nucleoli, NPM1 continuously shuttles between the nucleus and the cytoplasm to fullfill its functions. The gene encoding NPM1 is mutated in 50–60% of normal kariotype acute myeloid leukemia (AML) patients. A distinctive feature of NPM1 mutants is their stable and aberrant localization in the cytoplasm of leukemic cells. All mutations lead to critical changes at the NPM1 C-terminus: i) loss of tryptophan residues 288 and 290 (or 290 alone), which destabilizes the C-terminal domain; ii) generation of a new NES motif, which reinforces the nuclear export of NPM1 protein. Both alterations are critical for perturbing NPM1 mutant traffic and for the underlying aberrant accumulation of NPM1 in the cytoplasm of leukemic cells. Nucleoli are complex structures assembled around tandem arrays of rDNA genes and here we investigate the structural determinants of NPM1 nucleolar localization. We show that a domain encompassing the last 70 residues of the protein (NPM1-C70) binds with high affinity oligonucleotide sequences with G-quadruplex structure found at the non-coding strand of ribosomal DNA. Importantly the most common leukemic NPM1 variant C-terminal domain is unfolded and completely loses this activity. This is the consequence of G-quadruplex binding domain destabilization, since mutations aimed at refolding the leukemic variant also result in rescuing the G-quadruplex binding activity and nucleolar localization. In conclusion this work establishes the structural bases for understanding NPM1 nucleolar localization and its impairment by AML-associated mutations.