A transient α-helix in the N-terminal RNA recognition motif of polypyrimidine tract binding protein senses RNA secondary structure

Author:

Maris Christophe1,Jayne Sandrine1ORCID,Damberger Fred F1ORCID,Beusch Irene1ORCID,Dorn Georg1,Ravindranathan Sapna2,Allain Frédéric H-T1ORCID

Affiliation:

1. Department of Biology, ETH Zurich, 8093 Zürich, Switzerland

2. Central NMR facility, National Chemical Laboratory, Pune 411008 India

Abstract

Abstract The polypyrimidine tract binding protein (PTB) is a multi-domain protein involved in alternative splicing, mRNA localization, stabilization, polyadenylation and translation initiation from internal ribosome entry sites (IRES). In this latter process, PTB promotes viral translation by interacting extensively with complex structured regions in the 5′-untranslated regions of viral RNAs at pyrimidine-rich targets located in single strand and hairpin regions. To better understand how PTB recognizes structured elements in RNA targets, we solved the solution structure of the N-terminal RNA recognition motif (RRM) in complex with an RNA hairpin embedding the loop sequence UCUUU, which is frequently found in IRESs of the picornovirus family. Surprisingly, a new three-turn α3 helix C-terminal to the RRM, folds upon binding the RNA hairpin. Although α3 does not mediate any contacts to the RNA, it acts as a sensor of RNA secondary structure, suggesting a role for RRM1 in detecting pyrimidine tracts in the context of structured RNA. Moreover, the degree of helix formation depends on the RNA loop sequence. Finally, we show that the α3 helix region, which is highly conserved in vertebrates, is crucial for PTB function in enhancing Encephalomyocarditis virus IRES activity.

Funder

Swiss National Science Foundation

Publisher

Oxford University Press (OUP)

Subject

Genetics

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