FC0070
Nucleophosmin (NPM1)  -  DNA G-quadruplex c-Myc promoter

Biological function
Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a number of functions in ribosome biogenesis and export, cell cycle control, and response to stress stimuli.

Domain organization/sequence features
NPM1 C-terminal domain binds G-quadruplex regions at ribosomal DNA and at gene promoters, including the well characterized sequence from the nuclease-hypersensitive element III region of the c-MYC promoter.

Structural evidence
NPM1 terminal folds into three-helix bundle and is equipped by a lysine-rich unstructured tail, which has been shown to be necessary for high affinity recognition. The C-terminal domain of NPM1 is able to recognize both DNA and RNA in a sequence- independent manner, it was recently shown that the affinity may significantly vary depending on the nucleic acid conformation.

Biochemical evidence
The c-MYC-derived oligo Pu24I is recognized with different affinities by NPM1 C-terminal constructs differing for the presence of an unstructured flanking tail. 225-294 segment has a K_D of 11μM, while that of the 243-294 segment is 102 μM. The region differentiating the two constructs (residues 225–242) is completely unstructured and this fuzzy region remains unstructured after binding. Two concomitant Lys to Ala substitutions (Lys²²⁹-Lys²³⁰) in the unstructured segment of NPM1-C70 result in a dramatic decrease of global affinity.

Structure/Mechanism
The unstructured tail plays a double role in the reaction mechanism. On the one hand, it facilitates the formation of an encounter complex through long range electrostatic interactions; on the other hand, it directly contacts the G-quadruplex scaffold through multiple and transient electrostatic interactions, significantly enlarging the contact surface. NPM1 was shown to bind G-quadruplex regions at ribosomal DNA both in vitro and in vivo.

Mechanism category
Tethering

Posttranslational modification
Both acetylation and phosphorylation may interfere with NPM1 nucleic acid binding and play a role in NPM1 activity and trafficking throughout the cell cycle. Lys²²⁹ and Lys²³⁰ that are among the lysines acetylated by p300 and deacetylated by SIRT1. A number of putative phosphorylation sites are also present in the tail, including Ser²²⁷, Thr²³⁴, Thr²³⁷, and Ser²⁴²; among these, the phosphorylations of Ser²²⁷ by PKC and of Thr²³⁴-Thr²³⁷ by the Cdk1/cyclinB complex were experimentally validated.

Significance
Fuzzy segment flanking the interacting domain may provide a larger platform for long range electrostatic interactions or even transient physical contacts to fine-tune binding. Furthermore, this fuzzy region can be modified by post-translational modifications, driving regulatory changes.

Medical relevance
The NPM1 gene, overexpressed in a number of solid tumors, has been proposed as a marker for colon, gastric, ovarian, and prostate carcinomas. NPM1 is also frequently modified in hematopoietic tumors. For instance, in both lymphoid and myeloid disorders, NPM1 chromosomal translocations lead to the production of several oncogenic fusion proteins. NPM1 is the most frequently mutated gene in acute myeloid leukemia; mutations map to the C-terminal domain of the protein and cause its denaturation and aberrant cytoplasmic translocation.

Further reading
20858903, 24952945