On the occurrence of the T-loop RNA folding motif in large RNA molecules

Abstract

The T-loop RNA folding motif may be considered as a five-nucleotide motif composed of a U-turn flanked by a noncanonical base pair. It was recently proposed that the flanking noncanonical base pair is always a UA trans Watson-Crick/Hoogsteen base pair stacked on a Watson-Crick base pair on one side. Here we show that structural analysis of several large RNA molecules, including the recently solved crystal structure of the specificity domain of Bacillus subtilis RNase P, combined with sequence analysis, indicates a broader sequence consensus for the motif. Additionally, we show that the flanking base pair does not necessarily stack on a Watson-Crick base pair and the 3' terminus of the five-nucleotide motif is often followed by a sharp turn in the phosphate backbone rather than just a bulged base or bases.

FIGURE 1.

The T-loop motif (yellow) is formed by a U-turn (bases 2–4) flanked by a non-Watson-Crick base pair (bases 1 and 5) and is followed by a sharp turn or a bulged base or bases at its 3′ terminus. Red dots represent interactions crucial for the stability of the motif (Nagaswamy and Fox 2002). The estimation of the rate of occurrence of the particular nucleotides was based on the analysis of more than 4000 sequences. The 217–223 fragment of the S-domain of the RNase P (Krasilnikov et al. 2003) is shown as an example.

FIGURE 2.

Superposition of the T-loop motif in tRNA (PDB 1EHZ, shown in gold) and the 335–339 region of 23S rRNA (PDB 1JJ2, shown in pink). The flanking base pair is the same in both loops, but the overall structure is very different. Note that the important hydrogen bonds that serve to stabilize the U-turn cannot be made in the 335–339 region.

FIGURE 3.

T-loop motifs from different RNA molecules are structurally very similar. The fragments were superposed using the program lsqkab (CCP4; Collaborative Computational Project 4 1994). The lines at the 3′ termini show the direction of the phosphate backbone following the T-loop motif. In many instances, it is a sharp turn rather than just a bulged base or bases. The backbone may travel different paths beyond the 3′ terminus of the motif, as it is not a part of the motif, yet the motif itself is never incorporated directly into an A-helix.