Molecular basis of RNA recognition by the human alternative splicing factor Fox-1.
The Fox-1 protein regulates alternative splicing of tissue-specific exons by binding to GCAUG elements. Here, we report the solution structure of the Fox-1 RNA binding domain (RBD) in complex with UGCAUGU. The last three nucleotides, UGU, are recognized in a canonical way by the four-stranded beta-sheet of the RBD. In contrast, the first four nucleotides, UGCA, are bound by two loops of the protein in an unprecedented manner. Nucleotides U1, G2, and C3 are wrapped around a single phenylalanine, while G2 and A4 form a base-pair. This novel RNA binding site is independent from the beta-sheet binding interface. Surface plasmon resonance analyses were used to quantify the energetic contributions of electrostatic and hydrogen bond interactions to complex formation and support our structural findings. These results demonstrate the unusual molecular mechanism of sequence-specific RNA recognition by Fox-1, which is exceptional in its high affinity for a defined but short sequence element.
Auweter
Sigrid D
SD
Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
Fasan
Rudi
R
Reymond
Luc
L
Underwood
Jason G
JG
Black
Douglas L
DL
Pitsch
Stefan
S
Allain
Frédéric H-T
FH
D017398:Alternative Splicing; D001483:Base Sequence; D006801:Humans; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D000072260:RNA Splicing Factors; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020349:Surface Plasmon Resonance
C455479:RBFOX1 protein, human; D000072260:RNA Splicing Factors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins