Biophysical studies of an expanded RNA recognition motif from the Bruno protein

RNA recognition motifs (RRMs) are a ubiquitous class of proteins which bind RNA in a sequence-specific fashion, often with high affinity. The mechanisms through which this single protein domain recognizes diverse RNA sequences is not fully understood. High-resolution three-dimensional structures are particularly important in understanding the structural features required for RNA recognition and binding. This work presents the structure of an expanded RRM domain from the Drosophila melanogaster Bruno protein. The Bruno protein is involved in establishing proper body patterning during development. This is accomplished through the translational repression of several mRNAs, in particular, the oskar mRNA. Previous work has identified an expanded RRM domain within the Bruno protein. This RRM requires an additional forty amino acids prior to the start of the canonical RRM domain for high affinity RNA binding. The protein was found to contain a canonical RRM domain comprised of four anti-parallel [beta] strands and two [alpha] helices. The RRM is preceded by a ten amino acid loop that interacts with [alpha]₁ and [beta]₂, while the remaining amino acids are flexible in solution. Interestingly, the deletion of these residues does not alter the fold or stability of the RRM domain. Thus, these additional residues must be involved in RNA binding, as they are not required for structure. From these studies, the Bruno RRM represents a new example of protein features required for recognition and high affinity binding of RNA.