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Nucleic Acids Res. 2014 Mar;42(5):3261-71. doi: 10.1093/nar/gkt1296. Epub 2013 Dec 13.

Molecular evolution of protein-RNA mimicry as a mechanism for translational control.

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Department of Microbiology, Ohio State University, Columbus, OH 43210, USA, Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada and Ohio State Biochemistry Program, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA.


Elongation factor P (EF-P) is a conserved ribosome-binding protein that structurally mimics tRNA to enable the synthesis of peptides containing motifs that otherwise would induce translational stalling, including polyproline. In many bacteria, EF-P function requires post-translational modification with (R)-β-lysine by the lysyl-tRNA synthetase paralog PoxA. To investigate how recognition of EF-P by PoxA evolved from tRNA recognition by aminoacyl-tRNA synthetases, we compared the roles of EF-P/PoxA polar contacts with analogous interactions in a closely related tRNA/synthetase complex. PoxA was found to recognize EF-P solely via identity elements in the acceptor loop, the domain of the protein that interacts with the ribosome peptidyl transferase center and mimics the 3'-acceptor stem of tRNA. Although the EF-P acceptor loop residues required for PoxA recognition are highly conserved, their conservation was found to be independent of the phylogenetic distribution of PoxA. This suggests EF-P first evolved tRNA mimicry to optimize interactions with the ribosome, with PoxA-catalyzed aminoacylation evolving later as a secondary mechanism to further improve ribosome binding and translation control.

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