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oai:figshare.com:article/34047629 2026-10-01T17:26:09Z category_1 category_4 category_8 category_13 category_14 category_873 category_734 category_61 category_64 category_134 portal_5 item_type_1 month_year_10_2026

The RPL22 introns are predicted to assume alternate conformations. Kateřina Abrhámová (4739808) Alexandra Gredová (25157630) Karolína Navrátilová (25157633) Mohamed Boumaiza (5636147) Petr Folk (209900) Biophysics Biochemistry Microbiology Genetics Molecular Biology Chemical Sciences not elsewhere classified Biological Sciences not elsewhere classified Developmental Biology Cancer Virology intergenic regulation mediated first catalytic step 5 ’ ss div >< p additional stem loops tested splicing efficiency saccharomyces cerevisiae </ rather stalled splicing enhanced splicing inhibition intron binding using predicted stem alternate stem p structure permitted splicing b </ structural ensemble rpl22 </ ribosomal roles ribosomal proteins regulatory mechanism prevent recognition predicted features particular type others described mutagenesis identified mrna behaves later stage hybrid system fulfill non containing reporter branch point binding capacity allosteric switch (A) The RPL22 introns of Saccharomycotina yeasts contain complementary regions that suggest the formation of alternate secondary structures. The RPL22 introns of Saccharomycotina contain an absolutely conserved region of 23 nt positioned 5’ of the branch point (red), which can alternately base pair with partially complementary sequence elements located further upstream (green and blue). The homologs of RPL22A and RPL22B are grouped in the upper and lower rows of the alignment. Additional regions of complementarity are specific for the B paralogs (violet). The alignment was created using the MUSCLE algorithm <a href="https://www.ebi.ac.uk/Tools/msa/muscle/" target="_blank">https://www.ebi.ac.uk/Tools/msa/muscle/</a> and Jalview ver 2.11.2.6 was used for visualization. (B) Predicted structural ensembles of intronic RNAs of Saccharomyces cerevisiae RPL22A and RPL22B paralogs contain two major types of stem loop arrangements. Alternate structures of RPL22 introns were predicted by RNAfold [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.ref052" target="_blank">52</a>]. Pairing the conserved region (red in (A)) with the 3’complementary sequence element (3’COMP; green in (A)) leads to the formation of an inhibitory structure (denoted ‘I’), while the participation of the 5’complementary sequence element (5’COMP; blue in (A)) results in permissive structures (denoted ‘P’). Both structure types are predicted to occur in many variations and regardless of the inclusion of intron-bordering regions. The sequence range used for the modeling included 56 nt in front of the intron and 41 nt from exon 2; Minimum free energy (MFE) structures were visualized by RNAfold web server [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.ref052" target="_blank">52</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.ref053" target="_blank">53</a>] and MFE values were calculated by RNAShapes Studio [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0359197#pone.0359197.ref054" target="_blank">54</a>]. The colors correspond to the boxes in (A). The additional base pair complementarity in RPL22B (violet) is denoted as “Clamp”. 2026-10-01T17:25:45Z Image Figure 10.1371/journal.pone.0359197.g001 https://figshare.com/articles/figure/_p_The_i_RPL22_i_introns_are_predicted_to_assume_alternate_conformations_p_/34047629 CC BY 4.0