Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Issue 12 (16th May 2014)

• Record Type: Journal Article
• Authors: Daubner, Gerrit M.; Brümmer, Anneke; Tocchini, Cristina; Gerhardy, Stefan; Ciosk, Rafal; Zavolan, Mihaela; Allain, Frédéric H.-T.
• Is Part Of: Nucleic acids research. Volume 42:Issue 12(2014)
• Page Start: 8092
• Page End: 8105
• Publication Date: 2014-05-16
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gku445
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract : The STAR family comprises ribonucleic acid (RNA)-binding proteins that play key roles in RNA-regulatory processes. RNA recognition is achieved by a KH domain with an additional α-helix (QUA2) that seems to extend the RNA-binding surface to six nucleotides for SF1 ( Homo sapiens ) and seven nucleotides for GLD-1 ( Caenorhabditis elegans ). To understand the structural basis of this probable difference in specificity, we determined the solution structure of GLD-1 KH-QUA2 with the complete consensus sequence identified in the tra-2 gene. Compared to SF1, the GLD-1 KH-QUA2 interface adopts a different conformation resulting indeed in an additional sequence-specific binding pocket for a uracil at the 5′end. The functional relevance of this binding pocket is emphasized by our bioinformatics analysis showing that GLD-1 binding sites with this 5′end uracil are more predictive for the functional response of the messenger RNAs to gld-1 knockout. We further reveal the importance of the KH-QUA2 interface in vitro and that its alteration in vivo affects the level of translational repression dependent on the sequence of the GLD-1 binding motif. In conclusion, we demonstrate that the QUA2 domain distinguishes GLD-1 from other members of the STAR family and contributes more generally to the modulation of RNA-binding affinity and specificity of KH domain containing proteins.