Volume 36, Issue 4, Pages 593-608 (November 2009) The Evolutionarily Conserved Core Design of the Catalytic Activation Step of the Yeast Spliceosome  Patrizia Fabrizio, Julia Dannenberg, Prakash Dube, Berthold Kastner, Holger Stark, Henning Urlaub, Reinhard Lührmann  Molecular Cell  Volume 36, Issue 4, Pages 593-608 (November 2009) DOI: 10.1016/j.molcel.2009.09.040 Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 1 Conditions Used for the Isolation of Yeast Spliceosomes (A) Spliceosomal complexes are named according to the standard human nomenclature and correspond to the yeast complexes shown (Cheng and Abelson, 1987; Kim and Lin, 1996). (B) Complex B was assembled on actin WT (Figure S1) or a truncated actin substrate retaining six nucleotides downstream of the branch site UAUAAC sequence (M3-ActΔ6) and was stalled by limiting the ATP concentration in the splicing reaction (Tarn et al., 1993). Complex Bact was stalled by using M3-ActΔ6 but increasing ATP to 2.0 mM (Cheng, 1994). Complex C was stalled by using substrates with a missing or mutated 3′ss (M3-ActΔ31 and M3-ActACAC, respectively) (Rymond and Rosbash, 1985; Vijayraghavan et al., 1986). Molecular Cell 2009 36, 593-608DOI: (10.1016/j.molcel.2009.09.040) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 2 Kinetics of Splicing and Splicing Complex Formation (A and B) (A) Kinetics of in vitro splicing complex formation and (B) splicing. In lanes 1–8 of both panels, M3-Act WT is used; in lanes 9–16, M3-ActΔ6; in lanes 17–20, M3ActΔ31. (C and D) (C) Kinetics of in vitro splicing complex formation and (D) splicing using the 3′ss mutated RNA substrate M3-ActACAC. Splicing was performed at 2.0 mM ATP in yeast whole-cell extract for 0–180 min. In (A) and (C), splicing complexes were analyzed on nondenaturing gels. In (B) and (D), RNA was analyzed by denaturing PAGE. The positions of the complexes, pre-mRNA, and splicing intermediates are indicated on the right and left. (Asterisks) Unknown pre-mRNA-derived bands. Molecular Cell 2009 36, 593-608DOI: (10.1016/j.molcel.2009.09.040) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 3 Characterization of Purified B Complex (A) Profile of purified B complex (specific activity of 100 cpm/fmol) separated on a glycerol gradient. The radioactivity contained in each gradient fraction was determined by Cherenkov counting. Sedimentation coefficients were determined by analyzing the UV absorbance of a reference gradient containing prokaryotic ribosomal subunits. (B) RNA from gradient fractions 13–14 was recovered, separated by denaturing PAGE, and visualized by silver staining, autoradiography, and northern analysis. RNA identities are indicated on the right. (C) Proteins were separated by SDS-PAGE and stained with Coomassie. Molecular Cell 2009 36, 593-608DOI: (10.1016/j.molcel.2009.09.040) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 4 Electron Microscopy of Yeast Spliceosomes Overviews of negatively stained samples are shown in the left panels. Representative class averages are shown in the galleries in the middle (numbered 1 to 6), starting with the most frequently observed class, for which a schematic drawing is shown on the right. All three particles display a short protuberance that in the class averages is shown pointing downward (foot). Some structural features are labeled. Names introduced by Boehringer et al. (2004) for the human B complex are used also for the yeast B complex. A small fraction of images typical of the most frequent classes of complex Bact was also detected in the C complex preparation. Scale bars, 50 nm. Molecular Cell 2009 36, 593-608DOI: (10.1016/j.molcel.2009.09.040) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 5 The Yeast Splicing Machinery Is Less Complex Than that of Humans (Yeast) Proteins (yeast nomenclature) evolutionarily conserved between yeast and man, associated with purified yeast B, Bact, and C complexes, are placed inside of the rectangle. Proteins above the rectangle do not have a human counterpart. (Human) Proteins (human nomenclature) evolutionarily conserved between yeast and man, associated with purified human A, B, and C complexes, are placed inside of the rectangle. Proteins below the rectangle were found associated with purified human spliceosomal complexes, but the majority of them do not have a yeast counterpart (Behzadnia et al., 2007; Bessonov et al., 2008). Numbers indicate the total number of individual proteins in a particular group. (Asterisks) Proteins that do have homologs in yeast or human but were not found or found loosely associated with purified spliceosomal complexes; yeast Msl5, Npl3, Mud2, and Hub1 were found with low peptide numbers in the 20S–25S peak described above for the B complex. Cus2, Prp28, and Sad1 were not detected by MS and are included for completeness, as well as human TIA-1, which is the homolog of yeast Nam8. Proteins are grouped according to snRNP association, function, presence in a stable heteromeric complex, or association with a particular spliceosomal complex, as indicated. Molecular Cell 2009 36, 593-608DOI: (10.1016/j.molcel.2009.09.040) Copyright © 2009 Elsevier Inc. Terms and Conditions

Figure 6 Compositional Dynamics of Yeast Spliceosomes The protein composition of the yeast B, Bact, and C complexes was determined by MS. Proteins (yeast nomenclature) are grouped as described in the legend of Figure 5. The relative abundance of proteins is indicated by light (substoichiometric amounts) or dark (stoichiometric amounts) lettering and is based on the relative number of peptides sequenced (Table 1) (Supplemental Experimental Procedures). Molecular Cell 2009 36, 593-608DOI: (10.1016/j.molcel.2009.09.040) Copyright © 2009 Elsevier Inc. Terms and Conditions