Point mutations distal to the processing site affect Drosophila pre-5 S RNA processing: long range cooperation and a breathing model

Drosophila pre-5 S RNA, which consists of five conserved stem-loop domains and a 15-nucleotide 3' tail, is 3'-end processed to 120 nucleotide mature 5 S RNA before ribosome assembly. Large deletions in stems II and III, all of stems IV and V, and loop C prohibit Drosophila 5 S RNA processing; deletion of stem rv and half of V. does not (Preiser, P. R., and Levinger, L. (1991a) J. Biol. Chem. 266, 7509-7516). Several point mutations in stem I reduce, while certain neighboring sequence changes stimulate, processing Levinger, L., Vasisht, V., Greene, V., and Arjun, I. (1992) J. Biol. Chem. 267, 23683-23687). Herein we extend this 5 S RNA fine structure analysis to regions farther from the processing site. Most point mutations in loop B, stem III, and loop C severely inhibit processing. One loop C substitution stimulates processing; when combined with stimulatory sequence changes in stem I and loop A, these dispersed mutations improve processing manyfold, perhaps by stabilizing a required conformation or strengthening a protein-binding site. Central stem II sequence changes inhibit processing; several adjacent sequence substitutions which weaken base pairing improve processing. Combining these results with earlier work from stem I and loop A, we hypothesize that slight reduction in base pairing may improve groove access of polypeptide chains to essential contact positions