1. Repositioning of the Reaction Intermediate within the Catalytic Center of the Spliceosome 
Maria M. Konarska, Josep Vilardell, Charles C. Query 
Molecular Cell 
Volume 21, Issue 4, Pages (February 2006)
DOI: /j.molcel
Copyright © 2006 Elsevier Inc. Terms and Conditions

2. Figure 1
The 5′SS A3C Mutation Is Rate Limiting In Vivo for the Second Step of Splicing
(A) Two chemical steps of splicing, depicting the ACT1-CUP1 reporter pre-mRNA with intron position +3 and +4 mutations used in (C), (D), and (E). As shown in (C), A3C lariat intermediates stall prior to the second step of splicing, but additional change of U4A relieves this second step block.
(B) Schematic of RNA:RNA interactions that contribute to the first step of splicing.
(C) Splicing of A3C is limiting in vivo but improved by an additional U4A mutation. Top, primer extension analysis of RNA from cells containing ACT1-CUP1 reporters, as indicated. Primer complementary to the 3′ exon was used to reveal levels of pre-mRNA, mRNA, and lariat intermediate (indicated by icons to the left). Middle, quantitation of primer extension results presented above. For each reaction, the first step efficiency (light bars) was calculated as (M + LI) / (P + M + LI) and normalized to the first step efficiency of the wt reporter, set at 100. The second step efficiency (dark bars) was calculated as M / (M + LI) and normalized to the wt reporter second step efficiency, set at 100. Abbreviations: P, pre-mRNA; M, mRNA; and LI, lariat intermediate. Although these quantitations do not reflect absolute levels of RNA because of inherent losses due to discard pathways (see Figure S1), they nevertheless provide a useful illustration of relative differences between the tested reporters. Bottom, copper growth phenotype of the reporters used above. Comparable numbers of cells were spotted onto plates containing CuSO4, ranging from 0 to 2.0 mM. Relevant concentrations are shown, and the highest concentration on which each reporter supported growth is indicated below.
(D and E) Splicing of the A3C mutant is improved by the U6-U57A allele, worsened by the U6-U57C allele, and improved by second step suppressor prp8-161 and alleles. Primer extension analysis, quantitation, and growth on copper as in (C).
Molecular Cell  , DOI: ( /j.molcel )
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3. Figure 2
5′SS Position +4 Mutations Improve the Second Step of the A3C Mutant
(A) Schematic of ACT1-CUP1 reporter pre-mRNA, indicating intron position +3 and +4 mutations used in (B).
(B) The only combination of all 16 position +3 and +4 mutants that results in a defective second step of splicing is A3C with wt position +4 U. Top, middle, and bottom panels are as in Figure 1C. An asterisk (∗) represents reporters for which the second step efficiency is not measurable, due to low first step efficiency.
(C) The A3C mutation creates a potential Watson-Crick C:G base pair between the 5′SS and U6 snRNA, extending and stabilizing the 5′SS:U6 duplex (outlined box). Mutation of position +4 would disrupt a U:A pair, thus reducing the stability of this duplex.
Molecular Cell  , DOI: ( /j.molcel )
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4. Figure 3
The Second Step Defect of the 5′SS A3C Mutation Is Relieved by Any U6-G50 Mutation, and A3G in Combination with G50C Recapitulates This Second Step Defect
(A and C) Schematic of ACT1-CUP1 reporter pre-mRNA and U6 snRNA, indicating 5′SS position +3 and U6-G50 mutations used in (B) and (D), respectively.
(B and D) Primer extension analysis of RNA recovered from cells, quantitation, and growth on copper as in Figure 1C.
(E) The A3C mutation creates a potential Watson-Crick C:G base pair between 5′SS and U6 snRNA, extending and stabilizing the 5′SS:U6 duplex (outlined box). Mutation of U6-G50 would disrupt this C:G pair, thus reducing the stability of this duplex. A similar second step defect is recapitulated by A3G:U6-G50C.
Molecular Cell  , DOI: ( /j.molcel )
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5. Figure 4 Splicing of the A3C Mutant In Vivo Is Temperature Sensitive
Lowering of growth temperature exacerbates the A3C second step defect. Primer extension analysis of RNA from cells grown for 3 hr at the indicated temperature and quantitations, as in Figure 1C.
Molecular Cell  , DOI: ( /j.molcel )
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6. Figure 5
Disruption of Potential Base Pairing between U6 and 5′SS Position +4 or +5 Improves the Second Step for Multiple 3′SS and BS Mutants
(A and C) Schematic of ACT1-CUP1 reporter pre-mRNAs and U6 snRNA, indicating intron mutations used in (B) and (D), respectively.
(B and D) Primer extension analysis of RNA from cells, quantitation, and growth on copper as in Figure 1C. Lower gel of (D) shows primer extension analysis with an intron-specific primer, thus indicating the site of 5′SS cleavage. Quantitation in (D) represents the second step efficiency only for products having used the +1 (wt) 5′SS, normalized to wt reporter (lane 1).
(E) Disruption of 5′SS:U6-ACAGAG interactions improves the second step for BS and 3′SS mutants.
Molecular Cell  , DOI: ( /j.molcel )
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7. Figure 6
Model of Structural Rearrangements within the Spliceosome at the Time of Transition between the First and Second Steps of Splicing
(A) The first and second catalytic steps require different conformations of the spliceosome, the equilibrium between these conformations being modulated by the stability of the 5′SS:U6-ACAGAG duplex, in addition to interactions of Isy1 (Villa and Guthrie, 2005), U6 snRNA, Prp8, Prp16, and other factors (Query and Konarska, 2004). By analogy to the ribosomal decoding process, the initial signal for this conformational change may be presented by the branch structure formed in the first catalytic step. This induced-fit conformational change is facilitated by a weakened 5′SS:U6-ACAGAG duplex. Transition between first and second step conformations requires disruption of 5′SS:U6-ACAGAG pairing; thus, strong 5′SS:U6 pairing disfavors exit from the first step conformation, improving first step catalysis and inhibiting the second step; conversely, weak 5′SS:U6 pairing promotes progression into the second step conformation, improving splicing of mutant intermediates defective in this step.
(B–D) Summary of 5′SS-U6 snRNA crosslinks prior to the first catalytic step (B) (Johnson and Abelson, 2001; Chan et al., 2003; Chan and Cheng, 2005), in the first step conformation (C), (Sontheimer and Steitz, 1993; Kim and Abelson, 1996), and lariat product-U6 crosslinks after the first step (D) (Sawa and Abelson, 1992). Crosslinks in S. cerevisiae are shown by gray bolts, those in HeLa extracts by black bolts.
Molecular Cell  , DOI: ( /j.molcel )
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