RNA/RNA interaction differences between equivalent persistent regions among trypanosomatid species. A and B illustrate differences in the contact nature in srRNA-I region 2 from T. brucei and L. donovani. This area is represented by several hydrogen bonds (yellow lines) and one standard and one nonstandard base pairing in T. brucei, while in L. donovani and T. cruzi this area is represented by three consecutive standard base pairings (Table 1; Supplemental Table S1). C and D illustrate differences in the number of segments interacting with srRNA-II region 3 from T. brucei and T. cruzi. This area associates with several nucleotides from rRNA-β, srRNA-III and srRNA-IV in the case of T. brucei, while it only contacts nucleotides from srRNA-IV in the case of T. cruzi (Table 2; Supplemental Table S2). E and F illustrate differences in srRNA-III region 3 from T. brucei and L. donovani. This region is among those with the less interacting nucleotides but one that remains constant among trypanosomatids (Table 3; Supplemental Table S3). G and H illustrate differences in the nature of interactions with srRNA-IV region 7 from T. brucei and T. cruzi. In T. brucei, 3 nt create single hydrogen bonds (yellow lines) while in T. cruzi an A-minor interaction is created with srRNA-IV A92 and the pair rRNA-β C124:G456, in addition to several hydrogen bonds (yellow lines) (Table 4; Supplemental Table S4). Numbering systems correspond to cryo-EM ribosome structures from Trypanosoma brucei (PDBID 4V8M), Leishmania donovani (PDBID 5T2A), and Trypanosoma cruzi (PDBID 5T5H), respectively.
