Arrangement of 3D structural motifs in ribosomal RNA

Abstract

Structural 3D motifs in RNA play an important role in the RNA stability and function. Previous studies have focused on the characterization and discovery of 3D motifs in RNA secondary and tertiary structures. However, statistical analyses of the distribution of 3D motifs along the RNA appear to be lacking. Herein, we present a novel strategy for evaluating the distribution of 3D motifs along the RNA chain and those motifs whose distributions are significantly non-random are identified. By applying it to the X-ray structure of the large ribosomal subunit from Haloarcula marismortui, helical motifs were found to cluster together along the chain and in the 3D structure, whereas the known tetraloops tend to be sequentially and spatially dispersed. That the distribution of key structural motifs such as tetraloops differ significantly from a random one suggests that our method could also be used to detect novel 3D motifs of any size in sufficiently long/large RNA structures. The motif distribution type can help in the prediction and design of 3D structures of large RNA molecules.

Figure 1.

Schematic diagrams showing the various tetraloop motifs and their hydrogen-bonding interactions, adapted from Hsiao et al. (11), Figure 3. (a) The standard tetraloop. (b) A tetraloop with a 3–2 switch where the bases of the j+2 and the j+3 residues are switched. (c) A tetraloop with insertion where a residue (in pink) is inserted between the j+1 and the j+2 residues. However, >1 residue can be inserted and if extensive enough, would produce a strand clip. (d) A tetraloop with deletion where the j+2 residue in the standard tetraloop is absent so the j+3 residue becomes the j+2 residue. Rectangles, pentagons and circles denote base, sugar and phosphate groups, respectively, while dashed lines denote characteristic hydrogen bonds.

Figure 2.

The shape histogram of a given RNA fragment. (a) The backbone atoms of a RNA fragment 1794–1797 and some of their distances to a centroid. (b) The shape histogram of a given RNA fragment represented by the frequency of an integer distance in Angstrom.

Figure 3.

Three-dimensional backbone and secondary-structures corresponding to the representative 4-mer motifs in Table 1: (a) helical motif, 178−181, (b) part of an internal loop, 1052−1055, (c) tetraloop motif, 1794−1797, (d) part of an internal loop, 209−212 and (e) part of an internal loop, 2689−2692. In the secondary structures, circles denote the residues, while filled ones denote residues comprising the 4-mer motif. Single and double lines denote one and two hydrogen bonds, respectively, dot on the line singles out non-Watson–Crick base pairs, while red lines represent base triples. Secondary structures were prepared by the program, VARNA (47).