Limits...
An RNA tertiary switch by modifying how helices are tethered.

Ganser LR, Mustoe AM, Al-Hashimi HM - Genome Biol. (2014)

Bottom Line: A viral tRNA-like structure has evolved a unique strategy to undergo a tertiary structure conformational switch that may help regulate viral regulation.

View Article: PubMed Central - PubMed

ABSTRACT
A viral tRNA-like structure has evolved a unique strategy to undergo a tertiary structure conformational switch that may help regulate viral regulation.

Show MeSH
Secondary structure of tRNA (a,c) and TYMV TLS (b,d) in cloverleaf (a,b) and L-shape (c,d) conformations. A, acceptor; AC, anticodon; V, variable. Red lines denote the linchpin in TLS and the corresponding junction in tRNA; dotted lines represent the interactions lost following removal of the 5’-UUAG sequence. (a) The cloverleaf diagram shows that the junction between the D- and A-stems found in tRNA is absent in TLS, but the linchpin forms an interaction in its place. (b) The L-shape fold of the TLS is stabilized by the linchpin interaction. Destabilizing this interaction allows it to extend, as shown by the arrows, whereas the closed junction of tRNA prevents this extension.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4281957&req=5

Fig1: Secondary structure of tRNA (a,c) and TYMV TLS (b,d) in cloverleaf (a,b) and L-shape (c,d) conformations. A, acceptor; AC, anticodon; V, variable. Red lines denote the linchpin in TLS and the corresponding junction in tRNA; dotted lines represent the interactions lost following removal of the 5’-UUAG sequence. (a) The cloverleaf diagram shows that the junction between the D- and A-stems found in tRNA is absent in TLS, but the linchpin forms an interaction in its place. (b) The L-shape fold of the TLS is stabilized by the linchpin interaction. Destabilizing this interaction allows it to extend, as shown by the arrows, whereas the closed junction of tRNA prevents this extension.

Mentions: Early on, it was unclear whether the TLS could indeed adopt a tRNA-like conformation because it lacked many characteristic features of canonical tRNA sequences. The TLS secondary structure determined using nuclease probing data [7] subsequently revealed how the TLS achieved a tRNA-like fold and highlighted some important differences from canonical tRNA particularly at the acceptor stem, which is the site of aminoacylation [7]. In canonical tRNA, the acceptor stem is formed by base pairing of residues in the 5’ and 3’ ends of tRNA (Figure 1a). The TLS features a truncated 5’ strand that is not involved in canonical pairing with the 3’ strand (Figure 1b). This presumably is important to free up the 5’ end to link up with the rest of the viral genome without sterically obstructing the 3’ end. The longer 3’ strand was then proposed [7] to adopt a so-called ‘pseudoknot’ - an RNA motif in which a single strand folds back on itself to form two helical stems in such a way that the strand termini are located on opposite ends of the motif. This makes it possible to create an acceptor-like stem out of the 3’-terminus that can be aminoacylated (Figure 1b).Figure 1


An RNA tertiary switch by modifying how helices are tethered.

Ganser LR, Mustoe AM, Al-Hashimi HM - Genome Biol. (2014)

Secondary structure of tRNA (a,c) and TYMV TLS (b,d) in cloverleaf (a,b) and L-shape (c,d) conformations. A, acceptor; AC, anticodon; V, variable. Red lines denote the linchpin in TLS and the corresponding junction in tRNA; dotted lines represent the interactions lost following removal of the 5’-UUAG sequence. (a) The cloverleaf diagram shows that the junction between the D- and A-stems found in tRNA is absent in TLS, but the linchpin forms an interaction in its place. (b) The L-shape fold of the TLS is stabilized by the linchpin interaction. Destabilizing this interaction allows it to extend, as shown by the arrows, whereas the closed junction of tRNA prevents this extension.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4281957&req=5

Fig1: Secondary structure of tRNA (a,c) and TYMV TLS (b,d) in cloverleaf (a,b) and L-shape (c,d) conformations. A, acceptor; AC, anticodon; V, variable. Red lines denote the linchpin in TLS and the corresponding junction in tRNA; dotted lines represent the interactions lost following removal of the 5’-UUAG sequence. (a) The cloverleaf diagram shows that the junction between the D- and A-stems found in tRNA is absent in TLS, but the linchpin forms an interaction in its place. (b) The L-shape fold of the TLS is stabilized by the linchpin interaction. Destabilizing this interaction allows it to extend, as shown by the arrows, whereas the closed junction of tRNA prevents this extension.
Mentions: Early on, it was unclear whether the TLS could indeed adopt a tRNA-like conformation because it lacked many characteristic features of canonical tRNA sequences. The TLS secondary structure determined using nuclease probing data [7] subsequently revealed how the TLS achieved a tRNA-like fold and highlighted some important differences from canonical tRNA particularly at the acceptor stem, which is the site of aminoacylation [7]. In canonical tRNA, the acceptor stem is formed by base pairing of residues in the 5’ and 3’ ends of tRNA (Figure 1a). The TLS features a truncated 5’ strand that is not involved in canonical pairing with the 3’ strand (Figure 1b). This presumably is important to free up the 5’ end to link up with the rest of the viral genome without sterically obstructing the 3’ end. The longer 3’ strand was then proposed [7] to adopt a so-called ‘pseudoknot’ - an RNA motif in which a single strand folds back on itself to form two helical stems in such a way that the strand termini are located on opposite ends of the motif. This makes it possible to create an acceptor-like stem out of the 3’-terminus that can be aminoacylated (Figure 1b).Figure 1

Bottom Line: A viral tRNA-like structure has evolved a unique strategy to undergo a tertiary structure conformational switch that may help regulate viral regulation.

View Article: PubMed Central - PubMed

ABSTRACT
A viral tRNA-like structure has evolved a unique strategy to undergo a tertiary structure conformational switch that may help regulate viral regulation.

Show MeSH