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M605137200v1
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Papers In Press, published online ahead of print July 24, 2006
J. Biol. Chem, 10.1074/jbc.M605137200
Submitted on May 30, 2006
Revised on July 5, 2006
Accepted on July 24, 2006

Role of conserved surface amino acids in binding of smpB protein to SsrA RNA

Daniel P. Dulebohn, Hye Jin Cho, and A. Wali Karzai

Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794

Corresponding Author: akarzai{at}ms.cc.sunysb.edu

Bacteria possess a unique salvage mechanism for rescuing ribosomes stalled on aberrant mRNAs. A complex of SmpB protein and SsrA RNA orchestrates this salvage process. The specific and direct binding of SmpB facilitates recognition and delivery of SsrA RNA to stalled ribosomes. The SmpB protein is conserved throughout the bacterial kingdom and contains several conserved amino acid sequence motifs. We present evidence to demonstrate that amino acid residues E31, L91, and K124, which are highly conserved and clustered along an exposed surface of the protein, play a crucial role in the SsrA-mediated peptide tagging process. Our analysis suggests that the peptide-tagging defect exhibited by these SmpB variants is due to their inability to facilitate the delivery of SsrA RNA to stalled ribosomes. Moreover, we present evidence to demonstrate that the ribosome association defect of these variants is due to their reduced SsrA binding affinity. Consistent with these findings, we present biochemical evidence to demonstrate that residues E31, L91, and K124 are essential for the SsrA binding activity of SmpB protein. Furthermore, we have investigated the interactions of SmpB-SsrA orthologues from the thermophilic bacterium T. tengcongensis. Our investigations demonstrate an analogous role for the equivalent T. tengcongensis residues in SmpB-SsrA interactions, hence further validating our findings for the E. coli SmpB-SsrA system. These results demonstrate the functional significance of this cluster of conserved residues in SmpB binding to SsrA RNA, suggesting they might represent a core contact surface for recognition of SsrA RNA.


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