# Rearrangements within the U6 snRNA core during the transition between the two catalytic steps of splicing Eysmont K., Matylla-Kulińska K., Jaskulska A., Magnus M., Konarska M. ![figure](figure.png) General Model of the Catalytic Core Structural Rearrangements during Splicing (A) Rearrangements within the U6 core between the catalytic and inactive conformations, facilitated by Prp16. We propose that upon destabilization of the lower U6-ISL stem, the catalytic center adopts the optimal geometry for catalysis. Conversely, stabilization of pairing interactions within the lower stem promotes the Prp16-dependent transition out of the first-step conformation. (B) Consensus sequence and secondary structure diagram for U6-ISL based on the Rfam alignment. (C–E) Structural features of (C) U6-ISL, (D) U6atac-ISL, and (E) group II introns domain V. Sequences and secondary structures are shown for group representatives. (F) The free energy plot. For each representative, free energy of the lower (in blue) and upper segment (in black) is shown. The upper stem free energy shared by all U6-ISL (-12.75 kcal/mol) is shown as a black line. For group II introns, the free energies for the representative sequence (*O. iheyensis*) are shown as dots, and distributions of free energies for all (n = 92) diverse segments taken from the Rfam alignment are shown as violin plots. Statistical significance of differences between free energies was determined by the non-parametric Mann-Whitney test (p value = 7.85e-20). Free energies of destabilizing yeast lower ISL mutants (n = 18) are shown as purple dots. Alignments ------------------------------------------------------------------------------- - U6_RF00026.stockholm.sto - Intron_gpII_RF00029.stockholm.sto - U6atac_minor_RF00619.stockholm.sto R2R ------------------------------------------------------------------------------- ../../src/r2r --GSC-weighted-consensus u6-only.stk u6-only-cons.sto 3 0.97 0.9 0.75 4 0.97 0.9 0.75 0.5 0.1 R2R-1.0.5 [dhcp177-lan203] u6$ ../../src/r2r u6-only-cons.sto u6_cons.pdf PROCESSING: u6-only-cons NOTE: no #=GC R2R_LABEL line. But that's okay. <<<.<<<<.....>>>..>>>> ssContextList: [0,3;19,22) T,F,T Pair [3,4;19,19) F,F,T InternalLoop [4,5;18,19) F,F,T Pair [5,5;16,18) F,F,T InternalLoop [5,8;13,16) F,F,T Pair [8,13;13,13) F,T,T TerminalLoop ssContext [41,43;62,64] {raw [0,3;19,22) } Pair openHairpin link posFrom: 2 , [41,43;62,64] {raw [0,3;19,22) } posTo : 3 , [44,44;62,=] {raw [3,4;19,19) } default rule involvesCircularLayout==true ssContext [44,44;62,=] {raw [3,4;19,19) } InternalLoop link posFrom: 3 , [44,44;62,=] {raw [3,4;19,19) } posTo : 2 , [41,43;62,64] {raw [0,3;19,22) } default rule involvesCircularLayout==true link posFrom: 3 , [44,44;62,=] {raw [3,4;19,19) } posTo : 4 , [46,46;61,61] {raw [4,5;18,19) } default rule involvesCircularLayout==true ssContext [46,46;61,61] {raw [4,5;18,19) } Pair link posFrom: 4 , [46,46;61,61] {raw [4,5;18,19) } posTo : 3 , [44,44;62,=] {raw [3,4;19,19) } default rule involvesCircularLayout==true link posFrom: 4 , [46,46;61,61] {raw [4,5;18,19) } posTo : 17 , [47,=;59,60] {raw [5,5;16,18) } default rule involvesCircularLayout==true ssContext [47,=;59,60] {raw [5,5;16,18) } InternalLoop link posFrom: 17 , [47,=;59,60] {raw [5,5;16,18) } posTo : 4 , [46,46;61,61] {raw [4,5;18,19) } default rule involvesCircularLayout==true link posFrom: 17 , [47,=;59,60] {raw [5,5;16,18) } posTo : 5 , [47,49;55,58] {raw [5,8;13,16) } default rule involvesCircularLayout==true ssContext [47,49;55,58] {raw [5,8;13,16) } Pair link posFrom: 5 , [47,49;55,58] {raw [5,8;13,16) } posTo : 17 , [47,=;59,60] {raw [5,5;16,18) } default rule involvesCircularLayout==true link posFrom: 7 , [47,49;55,58] {raw [5,8;13,16) } posTo : 8 , [50,54;55,=] {raw [8,13;13,13) } default rule involvesCircularLayout==true ssContext [50,54;55,=] {raw [8,13;13,13) } TerminalLoop link posFrom: 8 , [50,54;55,=] {raw [8,13;13,13) } posTo : 7 , [47,49;55,58] {raw [5,8;13,16) } default rule involvesCircularLayout==true going through place_explicit's in queue got place_explicit from queue: calling PositionBackboneElement link posFrom: dummy ssContext posTo : 0 , [41,43;62,64] {raw [0,3;19,22) } priorityClass=FirstRule default rule dummy rule to position first element at: (0,0) -90 no flip got place_explicit from queue: calling PositionBackboneElement link posFrom: 2 , [41,43;62,64] {raw [0,3;19,22) } posTo : 3 , [44,44;62,=] {raw [3,4;19,19) } default rule involvesCircularLayout==true got place_explicit from queue: calling PositionBackboneElement link posFrom: 3 , [44,44;62,=] {raw [3,4;19,19) } posTo : 4 , [46,46;61,61] {raw [4,5;18,19) } default rule involvesCircularLayout==true got place_explicit from queue: calling PositionBackboneElement link posFrom: 4 , [46,46;61,61] {raw [4,5;18,19) } posTo : 17 , [47,=;59,60] {raw [5,5;16,18) } default rule involvesCircularLayout==true got place_explicit from queue: calling PositionBackboneElement link posFrom: 17 , [47,=;59,60] {raw [5,5;16,18) } posTo : 5 , [47,49;55,58] {raw [5,8;13,16) } default rule involvesCircularLayout==true got place_explicit from queue: calling PositionBackboneElement link posFrom: 7 , [47,49;55,58] {raw [5,8;13,16) } posTo : 8 , [50,54;55,=] {raw [8,13;13,13) } default rule involvesCircularLayout==true done: going through place_explicit's in queue doing place_defer (bulges) DONE PARSING: u6-only-cons Free Energy Calculations ------------------------------------------------------------------------------- - `free-energies-used-for-the-plot.csv` summary of the data mentioned belowe, used to calculate final plot - `u6 representatives free energies/u6evo-seq-ss-groups-3x3-GC.csv` free energies and sequences of U6 representatives - `yeast u6 mutants free energies/yeast u6 mutants/energies.csv` free energies and sequences of mutants of U6 ILS - `group two introns free energies/gii_dv_mini-gii3shift-upper-loop-guaa-lower-loop-guaa-flanks-GC.csv` free energies and sequences of Group II Introns - `src/calc-energy2.py` the tools used to calculate free energies Example ---------------------------------------------- Example of calculation using the script from rna-tools package (input files in `example`): $ rna_secondary_structure_prediction.py --method mcfold --file wt.fa --cstinfile gGUUguaaaACc (((((..))))) <= cst (((((..))))) -12.41 $ rna_secondary_structure_prediction.py --method mcfold --file U64c.fa --cstinfile gGcUguaaAACc (((((..))))) <= cst (((((..))))) -9.76 $ rna_secondary_structure_prediction.py --method mcfold --file A83g.fa --cstinfile gGUUguaaAgCc (((((..))))) <= cst (((((..))))) -11.3 $ rna_secondary_structure_prediction.py --method mcfold --file U64c+A83g.fa --cstinfile gGcUguaaAgCc (((((..))))) <= cst (((((..))))) -13.08