K-turn motifs in spatial RNA coding - PubMed (original) (raw)
Review
K-turn motifs in spatial RNA coding
Henri Tiedge. RNA Biol. 2006 Oct.
Abstract
Three-dimensional architectural motifs are increasingly recognized as determinants of RNA functionality. We submit that such motifs can encode spatial information. RNAs are targeted to subcellular localities in many eukaryotic cell types, and especially in neuronal and glial cells, RNAs can be transported over long distances to their final destination sites. Such RNAs contain cis-acting long-range targeting elements, and recent evidence suggests that kink-turn motifs within such elements may act as spatial codes to direct transport. Kink-turns are complex RNA motifs that feature double- and single-stranded components and introduce a signature three-dimensional structure into helical stems. We propose that the overall architectural design as well as the individual character--as specified by nucleotide identity and arrangement--of kink-turn motifs can serve as RNA targeting determinants.
Figures
Figure 1
The classic KT motif. K-turns were first described in human U4 snRNA and in Haloarcula marismortui rRNAs. In this illustration, the KT motif is exemplified by KT U4 in the C/D Box of U4 snRNA (A–C) and by KT-7 in 23S rRNA. The deduced classic consensus is shown in (C). (A) Tertiary structure with the C-stem seen towards the front right, the NC-stem towards the rear left. Salient intramolecular interactions are indicated, with A-minor interactions symbolized by a horizontal bidirectional arrow (see also below). (B) Secondary structure, C-stem facing towards the bottom. Illustration reprinted from Hardin and Batey, with permission from Elsevier. The following intramolecular interactions are universal to classic K-turns. (U4 numbering is used.) Of the tandem sheared G•A pairs, G32•A44 is non-planar. A44 also engages in stacking interactions with both A33 and A30, as a result forming cross-strand triple adenosine stacks., Thus, A30 stacks onto and thereby caps the NC-stem, and A29 stacks onto and caps the C-stem. These stacking interactions are critical for the 3D architecture of the motif. Also contributing to motif conformation is a type I A-minor interaction. In this tri-nucleotide motif, the O2′ atom and the “soft” N1-C2-N3 edge of an adenosine (which itself is typically part of a sheared G•A pair) fit into the minor groove of a receptor G-C WC base pair. In the case of U4 sRNA, this interaction is realized by A33 fitting into the minor groove of the G45-C28 pair. The A-minor motif is supported by trans-SE/SE interactions between A33 and G45. Trans-SE/SE interactions are also maintained between A29 and A44, or their equivalents in other classic K-turns. The specificity of these multiple intramolecular interactions form the basis for the unique 3D architecture. U31 bulges out, i.e. is extruded and does not interact with the other nucleotides of the motif. It is located at the apex of the 120° kink in the helical backbone. (C) KT motifs are aligned with their C-stems (G-C pairs) to the left, NC-stems (G•A pairs) to the right of the asymmetric internal loop. In the classic K-turn of the consensus type, nucleotides other than the ones shown are rarely tolerated in the positions indicated, except that distal G-C base pairs (i.e. those at the flanks of the motif) may occur in either the G-C or the C-G orientation. º denotes the transitional position between the NC-stem and the resumption of A-form helical structure by G-C WC base pairs; this position may be occupied by an intervening base pair, by an unpaired residue, or not at all. R, purine; N, any nucleotide. Blue, canonical G-C pairs of the C-stem; red, non-canonical G•A pairs of the NC-stem; orange, nominally unpaired internal loop nucleotides engaged in stacking interactions; yellow, extruded nucleotide.
Figure 2
Classic KT motifs in targeted neural mRNAs. See Figure 1 for color coding and motif alignment. Note that the internal loop nucleotide adjacent to the C-stem is consistently A, the long strand intervening nucleotide consistently G. These nucleotides may be specific to targeting KT motifs and are therefore referred to as targeting character nucleotides. For neural mRNAs, GenBank/EMBL/DDBJ accession numbers and nucleotide numbers are given. KT motifs are typically located in the 3′ UTRs except for KT GlyRα which is located at the 3′ end of the open reading frame. A modified version of DNAMAN software (Lynnon Corporation, Vaudreuil-Dorion, Quebec, Canada) was used to query RNAs for KT motifs. Query parameters were written such that searches were limited to classic KT motifs of the consensus type.
Figure 3
Classic K-turn motif in the 3′ UTR of MBP mRNA (KT MBP). The relationship between KT MBP, A2RE and A2RE11 is shown on top. Mutational analysis of A2RE1132 revealed differential effects of nucleotide replacement on hnRNP A2 binding. The exchange of nucleotides in the KT long strand that are essential for integrity and/or identity of the motif (shown in green) results in drastically diminished or entirely abolished binding to hnRNP A2. In contrast, C2U and C3G mutations result in only moderately diminished binding. For A2RE and A2RE11, nucleotides outside the KT motif long strand are shown in gray. A2RE11 numbering is used for mutants.
Figure 4
KT BC1 and KT BC200 belong to the KT-58 subgroup of the classic K-turn family, featuring a more symmetric internal loop structure., In KT motifs of this subgroup, the C-stem G-C pair that is adjacent to the internal loop can also be represented as orange internal loop nucleotides as they are likely to participate in stacking. Analogously, the internal loop G/C nucleotides that are adjacent to the C-stem in KT BC1 can also be represented as a blue standard WC pair as they are likely to engage in canonical base pairing. The G·U pair in KT BC1 may be either of the wobble WC type or of the sheared trans-H/SE type., Note that the geometry of the GA core is inverted in KT BC1, probably an indication that the motif assumes the reverse K-turn conformation. The minimal K-turn motif is shown for comparison.
Figure 5
Embedding of KT motifs in stem-loop structures. (A) KT BC1, (B) KT Mζ, (C) KT MBP. In this illustration, base pairings are represented as follows: = (G-C WC); - (A-U WC); · (wobble WC); • (non-canonical). K-turns are boxed and are identified using the same color coding as above. In KT BC1, the internal loop G-C nucleotides that are adjacent to the C-stem can also be represented as a standard WC pair in blue; see Figure 4. In addition to KT motifs, the stem-loop structures feature other non-helical elements that may be functionally relevant, among them unpaired nucleotides and internal loops (gray nucleotides in the MBP stem loop, C) that display features of C-loop motifs.
References
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