The Plasticity of a Translation Arrest Motif Yields Insights into Nascent Polypeptide Recognition inside the Ribosome Tunnel

Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Molecular cell (Impact Factor: 14.02). 05/2009; 34(2):201-11. DOI: 10.1016/j.molcel.2009.04.002
Source: PubMed


The recognition of a C-terminal motif in E. coli SecM ((150)FXXXXWIXXXXGIRAGP(166)) inside the ribosome tunnel causes translation arrest, but the mechanism of recognition is unknown. Whereas single mutations in this motif impair recognition, we demonstrate that new arrest-inducing peptides can be created through remodeling of the SecM C terminus. We found that R163 is indispensable but that flanking residues that vary in number and position play an important secondary role in translation arrest. The observation that individual SecM variants showed a distinct pattern of crosslinking to ribosomal proteins suggests that each peptide adopts a unique conformation inside the tunnel. Based on the results, we propose that translation arrest occurs when the peptide conformation specified by flanking residues moves R163 into a precise intratunnel location. Our data indicate that translation arrest results from extensive communication between SecM and the tunnel and help to explain the striking diversity of arrest-inducing peptides found throughout nature.

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Available from: Mee-Ngan F Yap, Feb 19, 2015
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    • "Cloning and Purification of ADR1a-SecM (Ms-Sup1; L = 25) RNCs The E. coli SecM stalling sequence in the ADR1a-SecM (L = 25) construct was modified by mutating five residues to obtain the Sup1 version of the Mannheimia succiniciproducens SecM AP (HPPIRGSP) (Yap and Bernstein, 2009), yielding ADR1a-SecM (Ms-Sup1; L = 25). The construct was subsequently cloned into the p7XNH vector. "
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    • "Stall sequences within nascent chains dramatically alter elongation, leading to a prolonged arrest of translation and controlling expression of cotranscribed genes (Ito and Chiba, 2013; Oliver et al., 1998). The SecM stall sequence from Escherichia coli relies solely on peptide-ribosome interactions to stall elongation (Nakatogawa and Ito, 2001; Yap and Bernstein, 2009). In secretion-deficient conditions, SecM-induced stalling upregulates SecA expression , an ATPase secretion protein (McNicholas et al., 1997; Schmidt et al., 1988; Yap and Bernstein, 2011). "
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    Full-text · Article · May 2014 · Cell Reports
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    • ", 2009 ; Vazquez - Laslop et al . , 2008 ; Yap and Bernstein , 2009 ) . Interaction of a stalling polypeptide with the ribosome near or at the PTC could be a straightforward way to inhibit the catalytic activity . "
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