U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing

Hilliker, Angela K.; Mefford, Melissa A.; Staley, Jonathan P.

doi:10.1101/gad.1536107

Cited by 106 publications

(137 citation statements)

References 64 publications

(136 reference statements)

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“…Parts of the primary sequence and secondary structure of yeast U2 snRNA are shown. Two competing structures (Hilliker et al, 2007;Perriman and Ares, 2007), stem-loop IIa (top) and stem IIc (bottom), are schematically represented. The base-pairing interactions between the U2 branch site recognition region and the pre-mRNA branch site are also schematically shown.…”

Section: Discussionmentioning

confidence: 99%

“…Mechanistically, how do induced pseudouridines affect premRNA splicing? Recently, the Ares and Staley labs proposed a model reliant on the fact that U2 toggles between two mutually exclusive structures, stem-loop IIa and stem IIc, during splicing (Hilliker et al, 2007;Perriman and Ares, 2007) (Fig. 7).…”

Section: Pseudouridine Differs From Its Counterpart Uridine In Severalmentioning

confidence: 99%

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Pseudouridines in spliceosomal snRNAs

2011

Protein Cell

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Spliceosomal RNAs are a family of small nuclear RNAs (snRNAs) that are essential for pre-mRNA splicing. All vertebrate spliceosomal snRNAs are extensively pseudouridylated after transcription. Pseudouridines in spliceosomal snRNAs are generally clustered in regions that are functionally important during splicing. Many of these modified nucleotides are conserved across species lines. Recent studies have demonstrated that spliceosomal snRNA pseudouridylation is catalyzed by two different mechanisms: an RNA-dependent mechanism and an RNA-independent mechanism. The functions of the pseudouridines in spliceosomal snRNAs (U2 snRNA in particular) have also been extensively studied. Experimental data indicate that virtually all pseudouridines in U2 snRNA are functionally important. Besides the currently known pseudouridines (constitutive modifications), recent work has also indicated that pseudouridylation can be induced at novel positions under stress conditions, thus strongly suggesting that pseudouridylation is also a regulatory modification.

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Section: Discussionmentioning

confidence: 99%

Section: Pseudouridine Differs From Its Counterpart Uridine In Severalmentioning

confidence: 99%

Pseudouridines in spliceosomal snRNAs

2011

Protein Cell

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“…Finally, Prp22p, which promotes release of the mRNA after exon ligation (15,16), discriminates against mutated consensus sites before exon ligation (11). Fidelity is also promoted by the sequestration of suboptimal substrates through equilibration between distinct spliceosomal states (17)(18)(19).…”

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confidence: 99%

Spliceosome discards intermediates via the DEAH box ATPase Prp43p

Mayas

Maita²,

Semlow

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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To promote fidelity in nuclear pre-mRNA splicing, the spliceosome rejects and discards suboptimal substrates that have engaged the spliceosome. Whereas DExD/H box ATPases have been implicated in rejecting suboptimal substrates, the mechanism for discarding suboptimal substrates has remained obscure. Corroborating evidence that suboptimal, mutated lariat intermediates can be exported to the cytoplasm for turnover, we have found that the ribosome can translate mutated lariat intermediates. By glycerol gradient analysis, we have found that the spliceosome can dissociate mutated lariat intermediates in vivo in a manner that requires the DEAH box ATPase Prp43p. Through an in vitro assay, we demonstrate that Prp43p promotes the discard of suboptimal and optimal 5′ exon and lariat intermediates indiscriminately. Finally, we demonstrate a requirement for Prp43p in repressing splicing at a cryptic splice site. We propose a model for the fidelity of exon ligation in which the DEAH box ATPase Prp22p slows the flow of suboptimal intermediates through exon ligation and Prp43p generally promotes discard of intermediates, thereby establishing a pathway for turnover of stalled intermediates. Because Prp43p also promotes spliceosome disassembly after exon ligation, this work establishes a parallel between the discard of suboptimal intermediates and the dissociation of a genuine excised intron product.RNA helicase | RNA processing | small nuclear RNA | ribonucleoprotein particle | Saccharomyces cerevisiae I n nuclear pre-mRNA splicing, the excision of introns is catalyzed by the spliceosome, a ribonucleoprotein machine comprising five snRNAs and ∼80 conserved proteins (for reviews, see ref. 1 and references therein). This machine assembles de novo on each pre-mRNA substrate and must rearrange its components throughout the splicing cycle through the activity of at least eight DExD/H box ATPases (2). The protein and RNA components of the spliceosome recognize the conserved elements of the intron at the 5′ splice site, the branch site, and the 3′ splice site. The RNA and possibly protein components also play key roles in catalyzing splicing, which occurs by two transesterification reactions (1). In the first reaction, the branch site adenosine attacks the 5′ splice site, generating a free 5′ exon and a lariat intermediate. In the second reaction, the 5′ exon attacks the 3′ splice site, excising the intron and ligating the exons. To establish specificity in splicing, the spliceosome discriminates optimal from suboptimal substrates.The specific pathway that discriminates against a suboptimal substrate depends on the extent to which a substrate is suboptimal. A grossly suboptimal substrate will fail to bind the spliceosome. Although such pre-mRNAs can be degraded in the nucleus (3), they can also be exported and then degraded in the cytoplasm (4-8). In contrast, optimal substrates are specifically retained in the nucleus to favor splicing (9).A nearly optimal substrate engages the spliceosome, necessitating more sophisticated fidelity ...

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“…13,24,65 Using protein-free snRNAs, Yuan and colleagues 29 used a FRETbased assay that took advantage of the increase in the luminescence other in the folded, active structure of the U6/U2 complex found in the activated spliceosomes, perhaps in an arrangement similar to the one found in group II introns. 12,14 While several studies indicate that the transition from the first step of splicing to the second involves a conformational change, 54,[57][58][59] it is likely that the same three domains of U6 are involved in catalysis of both steps of splicing. Mutagenesis studies have suggested a critical role for all three regions in both the first and second steps of splicing.…”

Section: The Three Dimensional Positioning Of Snrnas In the Active Sitementioning

confidence: 99%

“…While the active site elements undergo a minor remodeling between the two steps of splicing, several other RNA-RNA interactions including snRNA-substrate interactions seem to be significantly rearranged during the catalytic cycle of the spliceosome. [57][58][59][60][61] …”

Section: The Three Dimensional Positioning Of Snrnas In the Active Sitementioning

confidence: 99%