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Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix

Rachel M. Mitton-Fry, Suzanne J. DeGregorio, Jimin Wang, Thomas A. Steitz and Joan A. Steitz

Science Vol. 330, no. 6008, pp. 1244-1247, 26 November 2010.
DOI: 10.1126/science.1195858

This week’s to the point summary and analysis by Alex Robertson:

In this paper the authors report the first known endogenous example of a U rich loop capturing and protecting a poly(A) tail sequence. Through an intramolecular clamp mechanism, the viral polyadenylated nuclear RNA (PAN RNA) contains an expression and nuclear retention element (ENE) that protects the poly(A) tail by forming a triple helix. During the lytic phase of Kaposi’s sarcoma–associated herpesvirus lifecycle, PAN RNA is produced in extremely high levels, encompassing as much as 80% of the polyadenylated RNA in a cell. This PAN RNA is 1.1kb in length, has a 5’ cap and 3’ tail, is non-coding, and has unknown function. It expresses three ENEs which have been shown to protect it from degradation as well as protect other mRNAs in cis when inserted into their sequences.

The paper presents a crystal structure of the U rich internal loop of the ENE bound to A10. The structure is a triple helix which bears a stronger resemblance to riboswitches and pseudoknots (both intramolecular) than snoRNA-rRNA complex (intermolecular). This is in contrast to their predictions based on sequence similarity. The triple helix consists of U:A-U base triples which form planes and stack up analogously to double helices. When the bases are mutated to C:A-C in one position (the poly(A) is homogeneous and can move around) the structure is disrupted, destabilizing the PAN RNA in nuclear extract. Mutating the A to a G restores function/structure by allowing the C:G-C base triple to form. Based on this and other analyses in the paper, I am convinced that their structure and interpretation of the ENE’s function are correct. They speculate that since viruses borrow strategies from their hosts, there may be similar mechanisms in host organisms.