sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets

• Published in: Nucleic acids research 2008-09, Vol.36 (16), p.5290-5296
• Main Authors: García-Mayoral, María Flor, Díaz-Moreno, Irene, Hollingworth, David, Ramos, Andres
• Format: Article
• Language: English
• Subjects: Base Sequence; Binding Sites; Nuclear Magnetic Resonance, Biomolecular; Protein Binding; Protein Structure, Tertiary; RNA; RNA - chemistry; RNA - metabolism; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - metabolism
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkn509

K-homology (KH) splicing regulator protein (KSRP) is a multi-domain RNA-binding protein that regulates different steps of mRNA metabolism, from mRNA splicing to mRNA decay, interacting with a broad range of RNA sequences. To understand how KSRP recognizes its different RNA targets it is necessary to define the general rules of KSRP-RNA interaction. We describe here a complete scaffold-independent analysis of the RNA-binding potential of the four KH domains of KSRP. The analysis shows that KH3 binds to the RNA with a significantly higher affinity than the other domains and recognizes specifically a G-rich target. It also demonstrates that the other KH domains of KSRP display different sequence preferences explaining the broad range of targets recognized by the protein. Further, KSRP shows a strong negative selectivity for sequences containing several adjacent Cytosines limiting the target choice of KSRP within single-stranded RNA regions. The in-depth analysis of the RNA-binding potential of the KH domains of KSRP provides us with an understanding of the role of low sequence specificity domains in RNA recognition by multi-domain RNA-binding proteins.