Poster abstracts

Poster number 15 submitted by May Daher Farhat

Structural characterization of the TLD Domain of tmRNA in complex with SmpB

May Daher (Chemistry, Wayne State University), David Rueda (Chemistry, Wayne State University)

Abstract:
Truncated mRNAs missing a stop codon cause synthesis of defective proteins and trap
ribosomes at the end of their incomplete message. Stalled ribosomes can cause 2 major
problems: the defective unfinished protein can be toxic for the cell, and the pool of
ribosomes available for translation is depleted. In bacteria, both problems can be solved
by a rescue process called trans-translation, which employs transfer-messenger RNA
(tmRNA) and its cofactor the small protein B (SmpB). Previous studies have shown the
importance of tmRNA during gene expression and for virulence in many pathogenic
bacteria, making it an attractive target for antimicrobial drug discovery. However, key
aspects of this mechanism are still not fully understood.
Here, we have used fluorescence anisotropy and fluorescence resonance energy transfer
to characterize the strucuture of the tmRNA-SmpB complex. Our results show that SmpB
binds the TLD domain of tmRNA tightly and specifically. However, we did not observe
any conformational change in the global structure of the tmRNA in complex with SmpB.
Furthermore, the distance between the acceptor stem and the irregular helix of the
tmRNA-SmpB complex is ~ 5 Å shorter than in regular tRNA, in contradiction with a
previously proposed hypothesis based on a recent crystal structure. This result suggests
that tmRNA-SmpB complex maybe compact enough to fit freely into the A site of the
ribosome.

Keywords: tmRNA, SmpB, structural Characterization