RNP purification, components and activity.

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Hugo Wilkinson
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1 Supplementary Figure 1 RNP purification, components and activity. (a) Intein-mediated RNP production and purification. The Ll.LtrB intron RNA (red) (Exons E1 and E2 in green) and associated intron encoded protein (LtrA in yellow) were co-expressed with nisin induction. The RNP was captured and purified on chitin resin column through the chitin binding domain (CBD) that is fused to the LtrA C-terminus, released by DTT cleavage of the intein (I), and further purified by sucrose gradient sedimentation. (b) Product purity. LtrB intron RNA (902 nt) and associated LtrA protein (~70 kd) were analyzed, respectively, on a 1.2% denaturing formaldehyde agarose gel (left, lane 1, R) and on 12% denaturing SDS-PAGE gels (right, lanes 1, P), stained with Coomassie (blue) and silver (brown). Silver staining also revealed a higher molecular weight product, likely corresponding to intron RNA which stains with silver, not seen in a purified LtrA control (lanes 2). (c) RNA analysis. RNA in purified spliced RNPs (lanes 3 and 5) or extracted from the RNP (lane 4) were assayed by primer extension and the cdna analyzed on an 8% urea- PAGE gel. RNPs were either wildtype (wt) or a splicing-defective mutant of the catalytic triad (Triad). A primer, specific to the 5' end of the

2 intron (black arrow and P), was used to reveal precursor (pre-mrna) and spliced intron, from which 68-nt and 41-nt cdna products, respectively, were generated. Lane 1 corresponds to total RNA isolated from cells expressing the group II intron RNP and lane 2 to no RNA. The purified RNP resulted in predominantly a 41-nt band with a minor amount of precursor (lane 3), indicating that most of the pre-mrna had been removed. In contrast, the splicing defective Triad RNP yielded a primer extension product that corresponded exclusively to the intron-containing precursor (lane 5). (d) Activity assays with target DNA. Purified RNPs incubated with target DNA (T, 52nt) were assayed for DNA binding (left) and reverse splicing activity (right) on a 4% native- PAGE and a 10% urea-page gel, respectively. Lanes 1-3 contain no RNP, wild-type RNP and RNP from the catalytic triad mutant, respectively. Only the wt RNP, and not the catalytic mutant Triad, yielded shifted target DNA (left, black triangles). Likewise, only the wt RNP was active in reverse splicing (right) on the target DNA (IS=integration site, CS=cleavage site), producing a high molecular-weight integration product (black triangle) and the corresponding reverse splicing product (RSP) and cleavage product (CP).

3 Supplementary Figure 2 Negative-staining EM and random conical tilt reconstruction of the Ll.LtrB group II intron RNP. (a, b) One pair of electron micrographs of an untilted (a) and tilted (b) negatively stained specimen of the group II intron RNP complex. Four tilt pair particles are labeled with colored boxes, one color labeling one molecule. (c) Two-dimensional class averages of the particle images picked from micrographs of untilted specimen. Two major populated class averages are marked in cyan and lavender respectively. (d) The top row shows the RCT 3D reconstruction volumes from the tilted particle images corresponding to the two major class averages shown in (c). The bottom row shows 3D reconstructions obtained by refining the dataset merged from all the untilted and tilted particle images against the two RCT reconstruction volumes, respectively.

5 Supplementary Figure 3 Cryo-EM of the Ll.LtrB group II intron RNP and LtrA-depleted intron. (a) A representative raw micrograph of frozen-hydrated intron RNP particles generated from the 300 kv Titan Krios microscope. Few typical particles are identified by green square boxes. (b) Computed power spectrum of the micrograph in panel A. (c) Outline of the image processing steps to obtain the 3.8 Å resolution cryo-em map of the group II intron RNP complex and the 4.5 Å resolution map of the LtrA-depleted intron RNA. Reference-free 2D classification of 608,019 particle images generated ~200 2D class averages of the group II intron RNP comprising good particles free of ice contaminants and other junks. A 3D classification of the selected particles into four classes yielded three classes with strong LtrA protein occupancy that were merged as a total particle dataset of 450,296 particles and one class lacking density for the LtrA protein as a dataset of 102,522 particles. The first round of 3D auto-refinement of the merged dataset yielded a reconstruction at 4.2 Å resolution. A soft mask (shown in light grey semitransparency) around the most rigid portion of the RNP complex was used for further refinement to generate a final 3D reconstruction at 3.8 Å resolution. Local resolution maps of the 3D reconstructions without and with a soft mask during the refinement are shown on the right of the 4.2-Å and 3.8-Å resolution maps, respectively. The volumes are sliced to show the central portion of the local resolution distribution. A refinement of the LtrA-depleted intron dataset yielded a reconstruction at 4.5 Å resolution. The Euler angle distributions of particle images used for the intron RNP and the LtrA-depleted intron RNA reconstructions are shown next to corresponding EM maps. (d) Corrected gold-standard FSC curves of the final 3D reconstructions of RNP or LtrA-depleted intron RNA with or without a soft mask, respectively, after post-processing in RELION 1.3.

7 Supplementary Figure 4 Structure comparisons of the group IIA intron in the LtrA-bound state with that in the LtrA-depleted state and the group IIB intron. (a) Comparison of group IIA intron structure in LtrA-bound state (color coding of RNA domains are according to Fig. 1b) and IEP-depleted state (dark slate gray) shows a RMSD value of 2.4 Å. Regions corresponding to helices Id1 and Id3ii encompassing EBS2 and EBS1, respectively, are enlarged on upper left and right corners. (b) Comparison between tertiary structures of individual domains of the group IIA intron (this study) and group IIB intron (PDB ID: 4R0D). Domains of the group IIA intron are color coded and labeled as in Fig. 2, whereas that of the group IIB intron are shown as light grey color. Differences are displayed for each domain between the two introns. The β-β' interaction site, which is unique to group IIA intron, is boxed in red in the upper left panel. (c) Difference in relative positions of RNA helices of domain I, Id(iv) and domain IV with respect to domain V (red) between the group IIA and group IIB introns. The relative movements in group IIA intron helices are indicated by black arrows. RNA helices from group IIA and group IIB introns are shown in matching colors, except that the IIB intron helices are shown as semitransparent tubes. (d) Fourier shell correlation between atomic coordinates with the corresponding EM densities. RNP, intron-ltra complex; and DV, domain V of the intron RNA.

9 Supplementary Figure 5 Overall fitting of the initial homology model and final model of LtrA domains into the cryo-em map. (a) The fingers-palm domain initial homology model (left panel) and final model (middle panel) docked into the corresponding cryo-em density. Superposition of initial and final models (right panel) shows an RMSD value of 1.9 Å. (b) The thumb domain initial homology model (left panel) and final model (middle panel) docked into the corresponding cryo-em density. Superposition of initial and final models (right panel) shows an RMSD value of 1.6 Å. (c) The EN domain initial homology model (left panel) and final model after flipping α-helix (middle panel) docked into the corresponding cryo-em density. It should be noted that the α-helix corresponds to the DBD but was segmented with the EN domain. Superimposition of the aligned segments of the initial homology model and final EN model (right panel) shows an RMSD value of 1.7 Å. Density corresponding to the loop that connects the two-β strands was disordered and hence not modeled. (d) and (e), Overall fittings of NTD and DBD into the corresponding cryo-em masses. The 3.8 Å resolution cryo-em map (shown as semitransparent densities in matching colors) was used to model fingers-palm (a), thumb (b) and NTD (d). The dockings of EN (c) and DBD (e) domains were performed in the 5 Å resolution map (corresponding densities shown as semitransparent mass).

11 Supplementary Figure 6 Structure-based sequence alignment of the RT and EN domains. Structure based sequence alignments are performed using PROMALS3D 45. (a) Structure based sequence alignment of the RT fingers-palm domains of LtrA and Tribolium castaneum TERT (PDB: 3DU5). Secondary structures are shown with arrows for β-strands and bars for α helices. Identical residues are shaded in grey and indicated underneath with asterisks. Residues involved in TPRT in TERT and corresponding residues in LtrA are highlighted in different colors. Red, catalytic residues; Turquoise, dntp binding pocket; Green, DNA primer grip; Purple, RNA template interaction. (b) Alignment of the RT thumb domains of LtrA and Saccharomyces cerevisiae Prp8 (PDB: 3ZEF). α-helices are shown as bars, identical residues are shaded in grey and indicated underneath with asterisks. (c) Structure based sequence alignment of the EN domains from LtrA and the putative HNH endonuclease Gmet_0936 protein from Geobacter metallireducens GS-15 (PDB: 4H9D), HNH homing endonuclease I-HmuI (PDB: 1U3E), and E7 toxin (PDB: 1MZ8). Secondary structures are shown with arrows for β-strands and bars for α helices. The typical HNH motif residues are in red and four cysteine residues conserved between LtrA and Geobacter HNH endonuclease and proposed to be in additional metal ion coordination are in magenta. (d) Structure based sequence alignment of RT fingers-palm and thumb domains from LtrA, TERT, Prp8, and HIV-1 RT (PDB: 2HMI). Conserved sequence blocks RT1-RT7 in the fingerspalm domains (rectangular boxes) and the three parallel helices from Prp8 (H1-H3, boxes are in red, orange and green, as in panel b) in thumb domains in LtrA, TERT and HIV-1 RT, are defined using HIV-1 RT and Prp8 as references, respectively. Sequences in α-helices and β-strands are in red and blue, respectively. Insertions between RT sequence blocks, 2a, 4a, 5a, and 7a, and the thumb insertion ti are shown and labeled in red. Sequences of IFD-like motifs, are shaded in grey. Conserved aspartic acid residues at the RT active site are marked by red arrows. Motifs 1, 2, A, B, C, D, E (tan letters) in Tribolium castaneum TERT are in dark red boxes. Sequences that are not structurally resolved are boxed with dashed grey lines.

13 Supplementary Figure 7 Comparison of the fingers palm domain of LtrA with that of TERT and Prp8. (a) Docking of fingers-palm domain of TERT (PDB code: 3DU6; left panel) and Prp8 (PDB code: 3JB9; right panel) into the cryo-em density corresponding to the LtrA fingers-palm domain. (b) Structure superimposition of LtrA fingers-palm domains with corresponding domains from TERT (left panel) and Prp8 (right panel) show the RMSD values of 2.0 Å and 2.7 Å, respectively. (c) Rigid-body docking of TERT (left panel) and Prp8 (right panel) fingers domain onto group IIA intron shows a significant steric clash between Prp8 and intron domain Id(iii)a.

14 Supplementary Figure 8 Comparison of the thumb domain of LtrA with those of Prp8 and TERT. (a) Docking of the thumb domain of Prp8 (PDB code: 3JB9; right panel) and TERT (PDB code: 3DU6; left panel) into the cryo-em density corresponding to LtrA s thumb domain. (b) Structure superimposition of the LtrA thumb domain with corresponding domains from Prp8 (left panel) and TERT (right panel) show the RMSD values of 1.5 Å and 2.8 Å, respectively.

15 Supplementary Table 1 RMSD (Å) between LtrA RT figures/palm and thumb domains with those in TERT and Prp8 TERT Prp8 LtrA (Fingers-Palm) LtrA (Thumb)

16 Supplementary Note: Similarities of LtrA subdomains with Prp8 and TERT The docking of the atomic coordinates of the fingers-palm domains of Prp8 32 and TERT 29 into the corresponding cryo-em density of LtrA shows an overall similarity with both structures (Supplementary Fig. 7a). However, the RT domain of Prp8 is significantly larger due to the presence of several insertions in Prp8 RT, such as 4a, 5a and 7a (Fig. 3c; Supplementary Fig. 6d) that could not be accommodated by the cryo-em density (Supplementary Fig. 7a, right panel). Nevertheless, the conserved structural segments of the fingers-palm domain of LtrA superimpose well with corresponding segments from both TERT and Prp8 (Supplementary Fig. 7b; Supplementary Videos 3, 4) with RMSD values of 2.0 and 2.7 Å, respectively. Insertions 4a, 5a and 7a in the finger/palm domain of Prp8 would make a significant steric clash with the d(iii)a helix within D1 of the intron RNA (Supplementary Fig. 7c, right panel). Furthermore, both LtrA and TERT carry two conserved aspartate residues in the RT5 segment (Fig. 3c) that are involved in reverse transcription, whereas Prp8 carries only one aspartate in the homologous segment and the second aspartate is replaced by an arginine, which makes Prp8 an inactive reverse transcriptase. These observations suggest that the fingers-palm domain of TERT is most closely related to that in LtrA (Fig. 3b; Supplementary Fig. 6a). As described above, LtrA is also functionally related to the Prp8 RT of the spliceosome 3,25-28,37,38. Accordingly, we find that the thumb of LtrA possesses three parallel α- helices that more closely resemble the thumb domain of Prp8 (Figs. 3b-d; Supplementary Figs. 6b, 6d; Supplementary Video 6) than the thumb domain of TERT. Whereas coordinates of the Prp8 thumb domain 32 could be well docked into the cryo EM mass corresponding to the LtrA thumb domain (Supplementary Fig 8a, left panel), the thumb domain of TERT is much larger (Supplementary Fig. 8a, right panel) and would make a significant steric clash with the intron RNA. Our model of the thumb domain of LtrA superimposes well with coordinates of the Prp8 thumb domain (Supplementary Fig. 8b, left panel; Supplementary Video 6) with an RMSD of 1.5Å, whereas the thumb domain of LtrA only partially superimposes with the thumb domain of TERT with an RMSD of 2.8 Å (Supplementary Fig. 8b, right panel; Supplementary Table 2). The above observations further support our finding that the RT domain of LtrA carries a TERTlike fingers-palm domain and a Prp8-like thumb domain.

Supplementary Figure 1 Two distinct conformational states of the HNH domain in crystal structures. a

Supplementary Figure 1 Two distinct conformational states of the HNH domain in crystal structures. a HNH-state 1 in PDB 4OO8, in which the distance from the C atom of the HNH catalytic residue 840 to the