Small protein B (SmpB) is an essential component of the highly conserved tmRNA-SmpB system that has the dual function of releasing stalled ribosomes from damaged messenger RNAs and targeting incompletely synthesized protein fragments for degradation. Nuclear magnetic resonance (NMR) analysis of SmpB from Aquifex aeolicus revealed an antiparallel beta-barrel structure, with three helices packed ...

TRANSFER RNA DYNAMICS AND TRANSFER-MESSENGER RNAACCOMMODATION IN BACTERIAL RIBOSOMES AT THE SINGLE-MOLECULELEVEL byMAY DAHERDecember 2012Advisor: Dr. David RuedaMajor: Chemistry (Biochemistry)Degree: Doctor of PhilosophySingle-molecule spectroscopy, protein-induced fluorescence enhancement(PIFE), fluorescence resonance energy transfer (FRET), and several ...

Since accurate translation from mRNA to protein is critical to survival, cells have developed translational quality control systems. Bacterial ribosomes stalled on truncated mRNA are rescued by a system involving tmRNA and SmpB referred to as trans-translation. Here, we review current understanding of the mechanism of trans-translation. Based on results obtained by using directed hydroxyl radic...

Ribosome stalling is a serious issue for cell survival. In bacteria, the primary rescue system is trans-translation, performed by tmRNA and its protein partner small protein B (SmpB). Since its discovery almost 20 years ago, biochemical, genetic, and structural studies have paved the way to a better understanding of how this sophisticated process takes place at the cellular and molecular levels...

Eubacterial tmRNAs (10Sa RNAs) are unique because they function, at least in Escherichia coli, both as tRNA and mRNA (for a review, see Muto et al+, 1998)+ These ;360 6 40-nt-long RNAs are charged with alanine at their 39 ends by alanyl-tRNA synthetases or AlaRS (Komine et al+, 1994; Ushida et al+, 1994)+ Alanylation occurs thanks to the presence of the equivalent of the G3-U70 pair, the major ...

Transfer-messenger RNA (tmRNA, 10Sa RNA or ssrA) acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. The understanding at molecular level of this ubiquitous quality control system in eubacteria requires structural information. Here, we describe the purification and structural analysis of a func...