Recognition of the 3′ splice site RNA by the U2AF heterodimer involves a dynamic population shift

Abstract

An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3′ splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA recognition motif domains (RRM1,2) of U2AF65 adopt closed/inactive and open/active conformations in the free form and when bound to bona fide Py-tract RNA ligands. To investigate the molecular mechanism and dynamics of 3′ splice site recognition by U2AF65 and the role of U2AF35 in the U2AF heterodimer, we have combined single-pair FRET and NMR experiments. In the absence of RNA, the RRM1,2 domain arrangement is highly dynamic on a submillisecond time scale, switching between closed and open conformations. The addition of Py-tract RNA ligands with increasing binding affinity (strength) gradually shifts the equilibrium toward an open conformation. Notably, the protein-RNA complex is rigid in the presence of a strong Py-tract but exhibits internal motion with weak Py-tracts. Surprisingly, the presence of U2AF35, whose UHM domain interacts with U2AF65 RRM1, increases the population of the open arrangement of U2AF65 RRM1,2 in the absence and presence of a weak Py-tract. These data indicate that the U2AF heterodimer promotes spliceosome assembly by a dynamic population shift toward the open conformation of U2AF65 to facilitate the recognition of weak Py-tracts at the 3′ splice site. The structure and RNA binding of the heterodimer was unaffected by cancer-linked myelodysplastic syndrome mutants.uring gene expression, the removal of introns is essential for translation of mature mRNA. The splicing process involves a large number of splicing factors for the correct recognition of introns (1). Whereas U1 snRNP contacts the 5′ splice site, recognition of the 3′ splice site involves binding of SF1/BBP to the branch point sequence (BPS) (2-5) and binding of the U2 auxiliary factor (U2AF) heterodimer to the poly-pyrimidine-tract (Py-tract) that precedes the AG dinucleotide at the intron/exon junction. Binding of U2AF to the 3′ splice site during the early steps of spliceosome assembly recruits the U2 snRNP (6-9). The strength, i.e., splicing efficiency, of a 3′ splice site requires recognition of the BPS, Py-tract, and the AG dinucleotide. However, of these three RNA elements, the Py-tract exhibits the largest degree of variability, and thus, weak to strong splice sites are primarily classified depending on the composition of the Py-tract (7, 10).U2AF is a heterodimer consisting of a large (U2AF65) and a small (U2AF35) subunit. U2AF65 harbors two canonical RNA recognition motifs (RRM1,2) and an atypical C-terminal RRM domain, called the U2AF homology motif (UHM). U2AF35 has one RRM (which acts as an UHM), flanked N-and C-terminally by two CCCH-type zinc finger motifs, respectively (Fig. S1A) (9, 11, 12). The U2AF heterodimer is formed by recognition of a peptide motif, cal...

Effects of Fluorophore Attachment on Protein Conformation and Dynamics Studied by spFRET and NMR Spectroscopy

“…undergoes a conformational transition during its transit time through the confocal volume [32] . As shown recently, the free U2AF65 protein exhibits dynamics as observed from the deviation from the static FRET line, while U2AF65 bound to RNA is significantly more rigid (Figure S8) [22] . Comparing these two-dimensional histograms of U2AF65 labeled with different acceptor fluorophores, we observe a significantly higher population of the closed state when the protein is labeled with Atto532/Cy5 or with Atto532/Atto647N than with Atto532/Alexa647.…”

“…A high FRET state (FRET efficiency 80%) is observed for the free form of U2AF65 for all the different combinations of fluorophores (Figure 1B , left ). This FRET state corresponds to a population of molecules dynamically switching between a closed and an open conformation [22] . When bound to RNA, U2AF65 adopts an open conformation, which is visible with a FRET efficiency of ~45% for all combinations of fluorophores (Figure 1B, right ).…”

Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs

“…Major U2AF2 conformations in the absence of RNA include “closed” and “open” structures that have been characterized by NMR, small-angle X-ray scattering, and single molecule Förster resonance energy transfer 13–16 . The “open” U2AF2 conformation is selectively stabilized by RNA binding and has been characterized at high resolution by X-ray crystallography 15 .…”

RNA and Proteins: Mutual Respect

“…von Voithenberg et al . 35 showed that RRM1 and RRM2 undergo dynamic exchange between a closed or open orientation at equilibrium ( Figure 2). In the closed state, RRM1 and RRM2 do not bind RNA, but when the conformation is open, a polypyrimidine tract can bind.…”