A novel intron is located at position 3/4 in three tDNAs of P. aerophilum. (A) The sequences of the three tDNAs of P. aerophilum coding for tRNA-Asp (GUC) (upper line), tRNA-Glu (CUC) (middle line), and tRNA-Glu (UUC) (lower line) are shown. They extend from the putative upstream TATA promoter element (black bold) down to position 76 of the mature tRNA. Bases in uppercase letters belong to the mature tRNA, those in lowercase to the intron and mature tRNA flanking sequences. The bases making up the putative intron located between nt 3 and nt 4 of the amino acid acceptor stem, including the intronic helix h, are shown in lowercase letters (within the box labeled “intron 3/4”). The sequence elements forming the canonical splicing motif hBHBh′ (h1, H1, B1, h′1, loop, h′2, H2, B2, and h2) are shown in bold (for a definition of these elements, see text and legend to Fig. 2). Bases forming the H1 and H2 strands are bold and highlighted with gray background. Bold italics are used to indicate the complementary bases forming the h1 and h2 antiparallel strands of the helix h, and the h′1 and h′2 antiparallel strands of the helix h′. Among these three tDNAs, only one, tDNA-Glu (TTC), harbors a second intron located between nt 58 and 59 (box labeled “intron 58/59”). (B) Hypothetical 2D structure of pre-tRNA-Glu (CUC) including the splicing motif within the amino acid acceptor stem. The sequence shown here, including the cloverleaf-like structure, extends from 31 bases upstream from tRNA base 1 down to base 73 at the 3′ end of the tRNA. Plus signs are used to indicate Watson–Crick base pairing and filled circles to indicate wobble GU/UG pairings. The intron (in lowercase) is shown folded under a canonical hBHBh′ splicing motif, using the same lettering conventions as in A. The small arrows indicate the splicing positions after nt 3 and before nt 4. The path of the nucleotidic chain is symbolized with thick gray lines. Remarkably, a peculiar gccccgg sequence is present in the 5′ region of the three tRNA genes, which is an exact replica of bases 1–7 of the mature tRNA. This sequence, designated h"1 is probably part of the pre-tRNA transcript, as it is located 20 bases 3′ of the TATA element. It is shown here facing the antiparallel strand of the acceptor stem (bases 66–72, designated h"2) because it is not known whether a helix between complementary strands h"1 and h"2 can form.
