Group II intron structure characterizations and three-dimensional modeling

Bibliography: p. 191-205Some pages are in colour

Structural Variation and Uniformity among Tetraloop-Receptor Interactions and Other Loop-Helix Interactions in RNA Crystal Structures

<div><p>Tetraloop-receptor interactions are prevalent structural units in RNAs, and include the GAAA/11-nt and GNRA-minor groove interactions. In this study, we have compiled a set of 78 nonredundant loop-helix interactions from X-ray crystal structures, and examined them for the extent of their sequence and structural variation. Of the 78 interactions in the set, only four were classical GAAA/11-nt motifs, while over half (48) were GNRA-minor groove interactions. The GNRA-minor groove interactions were not a homogeneous set, but were divided into five subclasses. The most predominant subclass is characterized by two triple base pair interactions in the minor groove, flanked by two ribose zipper contacts. This geometry may be considered the “standard” GNRA-minor groove interaction, while the other four subclasses are alternative ways to form interfaces between a minor groove and tetraloop. The remaining 26 structures in the set of 78 have loops interacting with mostly idiosyncratic receptors. Among the entire set, a number of sequence-structure correlations can be identified, which may be used as initial hypotheses in predicting three-dimensional structures from primary sequences. Conversely, other sequence patterns are not predictive; for example, GAAA loop sequences and GG/CC receptors bind to each other with three distinct geometries. Finally, we observe an example of structural evolution in group II introns, in which loop-receptor motifs are substituted for each other while maintaining the larger three-dimensional geometry. Overall, the study gives a more complete view of RNA loop-helix interactions that exist in nature.</p> </div

The loop-helix interaction 3OFR:1493–1497 resembles the GAAA/11 nt motif in secondary structure, but assumes a distinct three-dimensional geometry.

<p>A, C) Secondary structures for 3OFR:1493–1497 (Class IV(individual)) and 1U6B:24–27 (Class I, or GAAA/11-nt). Corresponding distinctive residues are coded in yellow, orange, or green shading, or are boxed in blue. B, D) Two rotational views of the structures, with residues colored as in (A) and (C). The residues with blue backbones superpose with an RMSD of 1.35 Å between the two structures, while the two green A’s form an adenosine platform in 1U6B:24–27 but form a stack in 3OFR:1493–1497.</p

Three unique loop-helix interactions.

<p>A) Insertion of a loop nucleotide into a helix (2QBZ:100–106). B) Three splayed nucleotides interacting with a helix (1VQO:2069–2076). C) Three stacked nucleotides interacting in the minor groove, with two splayed nucleotides (3OFR:1493–1497). For all panels, blue indicates the distinctive features explained in the text.</p

Comparison of Class II Subclasses 1, 2, 3, and 4, with one representative per subclass.

<p>A) Secondary structures of four representative interactions: Subclass 1, 3IGI:90–93 (yellow); Subclass 2, 1VQO:691–694 (green); Subclass 3, 1MFQ:147–150 (orange); Subclass 4, 3OFO:159–162 (pink). Gray nucleotides are not shown in tertiary structures. B, C, D) Stereoviews of the four-structure overlay, with superposition based on backbone atoms of the four receptor nucleotides (48 atoms). In Panel D, only the tetraloop backbones are colored in order to depict differences in the tetraloop orientations.</p

Weblogo profiles for GYGA and GNAA tetraloops and their respective receptors.

<p>A, C) Secondary structures of representative GYGA- and GNAA-containing interactions. B, D) Weblogo profiles of the two types of interactions.</p

Comparison of ζ-ζ’ tetraloop-receptor structures in different lineages of group II introns.

<p>A) Class II Subclass 5 structure from 3IGI:369–372, which represents IIC introns (class C). Blue indicates receptor and tetraloop nucleotides. B) Overlay of structures in panels A and C, with superposition based on backbones of the nucleotides with solid green and yellow shading in Panels D and F. C) The GAAA/11 nt structure from 2R8S:150–153 (group I intron). White indicates receptor and tetraloop nucleotides. D-H) Secondary structures for ζ-ζ’ interactions in different lineages of group II introns (Panels D, E, G, H) or the GAAA/11 nt interaction in a group I intron (Panel F). The blue and black boxes in (D) and (F) correspond to the blue and white nucleotides in (A) and (C). The question marks in (G) and (H) indicate putative corresponding nucleotides to the green and yellow boxed nucleotides in (D) and (F), which superpose in (B).</p

GNRA tetraloop/helix interactions and GNRA tetraloop-like/helix interactions.

1<p>“Indiv” indicates an individual structure that does not form an additional level of subgrouping based on superposition. “NTL” denotes a loop that does not consist of four nucleotides (non-tetraloop).</p>2<p>“++” indicates at most minor deviations between the electron density map and the specific modeled substructure (∼8–15 nts). “+” indicates a greater degree of unmodeled positive or negative electron density.</p>3<p>The <i>E. coli</i> ribosome substructures are nearly identical to <i>Haloarcula</i>, and are omitted from the table.</p

The Class II Subclass 1.1.1/1.1.2 loop-helix interaction.

<p>(A) Secondary structure of 1.1.1/1.1.2 interactions (consensus of 11 sequences). Gray nucleotides are not shown in the three-dimensional structure. (B) Two rotational views of an overlay of 11 members of Class II/Subclass 1.1.1 (blue; mostly GYGA loops) and 1.1.2 (purple; mostly GNAA loops).</p

Three distinct three-dimensional structures formed by a GAAA tetraloop and GG/CC receptor.

<p>A, C, E) Secondary structure depictions of three structures. B, D, F) Three views of the superposition of 1VQO:1327–1330 (yellow), 3OFO:159–162 (blue) and 3OFR:124–127 (pink). In Panel F, only the backbones are colored.</p