Polypyrimidine tract binding protein (PTB) is a 57 kD hnRNP protein (hnRNP I) that binds to the pyrimidine tract typically found near the 3' end of introns. Primary sequence analysis suggests that PTB contains four RNA recognition motifs (RRMs). Data from comparative structural and deletional analysis of PTB are consistent with the presence of a four reiterated domain structure. Since PTB exists in solution as a homodimer, it contains an oligomeric array of eight RRMs. Though the function of RRMs in a monomeric context has been addressed, the significance of their presence in an oligomeric context has not been investigated. To correlate structural motifs with function, we have analyzed the RNA binding properties of wild-type and deletion constructs of PTB that contain RRMs in both an oligomeric and monomeric context. These studies indicate that there is not a strong correlation between the RNA binding affinity and specificity upon oligomerization. However, the mode of RNA interaction and dimerization is linked. We have also found that the primary contributor to the free energy of PTB binding and the primary determinant for RNA binding specificity resides in RRM 3, while the primary contributor to dimer stabilization coincides with residues in RRM 2.

PTB-associated splicing factor (PSF) has been implicated in both early and late steps of pre-mRNA splicing, but its exact role in this process remains unclear. Here we show that PSF interacts with p54 nrb , a highly related protein first identified based on cross-reactivity to antibodies against the yeast second-step splicing factor Prp18. We performed RNA-binding experiments to determine the preferred RNA-binding sequences for PSF and p54 nrb , both individually and in combination. In all cases, iterative selection assays identified a purine-rich sequence located on the 39 side of U5 snRNA stem 1b. Filter-binding assays and RNA affinity selection experiments demonstrated that PSF and p54 nrb bind U5 snRNA with both the sequence and structure of stem 1b contributing to binding specificity. Sedimentation analyses show that both proteins associate with spliceosomes and with U4/U6.U5 tri-snPNP.

Polycistronic pre-mRNAs from Caenorhabditis elegans are processed by 3 end formation of the upstream mRNA and SL2-specific trans-splicing of the downstream mRNA. These processes usually occur within an ∼100-nucleotide region and are mechanistically coupled. In this paper, we report a complex in C. elegans extracts containing the 3 end formation protein CstF-64 and the SL2 snRNP. This complex, immunoprecipitated with ␣CstF-64 antibody, contains SL2 RNA, but not SL1 RNA or other U snRNAs. Using mutational analysis we have been able to uncouple SL2 snRNP function and identity. SL2 RNA with a mutation in stem/loop III is functional in vivo as a trans-splice donor, but fails to splice to SL2-accepting trans-splice sites, suggesting that it has lost its identity as an SL2 snRNP. Importantly, stem/loop III mutations prevent association of SL2 RNA with CstF-64. In contrast, a mutation in stem II that inactivates the SL2 snRNP still permits complex formation with CstF-64. Therefore, SL2 RNA stem/loop III is required for both SL2 identity and formation of a complex containing CstF-64, but not for trans-splicing. These results provide a molecular framework for the coupling of 3 end formation and trans-splicing in the processing of polycistronic pre-mRNAs from C. elegans operons. ). Polycistronic pre-mRNAs from these operons are processed into monocistronic mRNAs by cleavage and polyadenylation at the 3Ј ends of upstream gene mRNAs accompanied by trans-splicing at the 5Ј ends of downstream gene mRNAs. In general, these two processes occur within a 100-nucleotide region (Blumenthal and Steward 1997) and are mechanistically coupled (Kuersten et al. 1997).In C. elegans, 3Ј end formation is dependent on an AAUAAA signal (Kuersten et al. 1997;Liu et al. 2001). It is expected that this sequence is bound by cleavage and polyadenylation specificity factor (CPSF), as it is in mammalian cells (for reviews, see Colgan and Manley 1997;Keller and Minvielle-Sebastia 1997;Zhao et al. 1999). Presumably, C. elegans 3Ј end formation also requires cleavage stimulation factor (CstF), which binds a U-rich or GU-rich sequence downstream of the cleavage site. Homologs of each of the subunits of both mammalian CstF and CPSF are present in the C. elegans genome (C.J. Wilusz and T. Blumenthal, unpubl.).Trans-splicing generates 5Ј ends of mRNAs in trypanosomes and many animals (Murphy et al. 1986;Sutton and Boothroyd 1986;Krause and Hirsh 1987;Rajkovic et al. 1990;Tessier et al. 1991;Stover and Steele 2001;Vandenberghe et al. 2001). A spliced leader (SL) exon is donated to the 5Ј ends of mRNAs by a short RNA donor called SL RNA. The SL RNA exists as a ribonucleoprotein (RNP) particle (Thomas et al. 1988;Van Doren and Hirsh 1988;Maroney et al. 1990;Goncharov et al. 1999) that includes the Sm core proteins (Lerner and Steitz 1979). Unlike the other U snRNPs, which are capable of catalyzing repeated splicing reactions, the SL snRNP is consumed during the trans-splicing reaction.C. elegans possesses two distinct SL RNAs, SL1 RNA (Krause and Hirsh 1987) a...