Secondary structures of RNA elements displaying a crystallographically established (A and B) or a predicted (D) head-to-tail double T-loop module. T-loops are shown in red (first T-loop along the strand, T-loop 1) and blue (T-loop 2). The two residues preceding a T-loop are shown in orange (T-loop 1) and cyan (T-loop 2). The dotted lines show the (established of predicted) base pairs defining the core of the T-loop module (detailed in Figure 2B) and the functional platform (residues outlined with a circle). (A) B. subtilis L1 stalk (23S rRNA). The established structure and numbering are from the crystal structure of T. thermophilus 23S rRNA (pdb 1VSA) (9). (B) T. maritima RNAse P: region of the head-to-tail double T-loop module (P11–P14) (10,11). The tertiary interactions are from the crystal structure pdb 3Q1Q (12). (C) Sequence conservation encompassing the two T-loops of the structures in A, B and D: 1) L1 stalk (23S rRNA), 2) J11/12–J12/11 module of RNAse P and 3) apex of Stem I in T-box leaders. Sequence logos (highest value = 2 bits) were produced using the Weblogo interface (8) while using the following sequence alignments: 23S rRNA: primary alignments of 592 sequences from three phylogenetic domains, from the Comparative RNA Web site (13); bacterial RNAse P, class A: 340 sequences from the Ribonuclease P database (14); and T-box Stem I: alignment generated from 131 T-box sequences (‘Materials and Methods’ section). (D) B. subtilis tyrS T-box leader: apex of Stem I. Secondary structure (solid lines only) and base numbering according to (2).