Figure 1.

The four pseudouridylation guide RNAs: Afu-4, Afu-46, Afu-52, and Afu-190 from A. fulgidus. (A) Potential base-pairing interaction with 16S or 23S rRNA involving each pseudouridylation pocket. The predicted site of pseudouridylation is denoted by an arrow, and its location within the cognate rRNA is indicated by numbering. Its distance from the ACA/AGA- (or H-) box (usually between 14 and 16 nt) is indicated also. The snmRNA sequence in a 5′-to-3′ orientation is shown in the upper strand, with the apical part of the long hairpin domain schematized by a solid line. (B) Verification of predicted pseudouridylation sites in A. fulgidus rRNA by primer extension. Total cellular RNA samples submitted or not to CMC modification (lanes R and N, respectively) were analyzed by primer extension using ³²P-labeled primers complementary to an appropriate segment of 16S or 23S rRNA. Predicted sites are denoted by arrowheads, additional pseudouridines thus far without a known cognate H/ACA guide are denoted by arrows, and cDNA sizes (in nt) are indicated in the margin.