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Our work highlights the essential role of elongation factor Tu for accurate genetic code translation in both initial codon selection and proofreading.Our results have implications for the evolution of efficient and accurate genetic code reading through multistep proofreading, which attenuates the otherwise harmful effects of the obligatory tradeoff between efficiency and accuracy in substrate selection by enzymes.

A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.Reprint requests to: Rachel Green, Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; e-mail: [email protected]; fax: (410) 502-6718.Here we use an in vitro selection approach to isolate t RNA miscoding variants that exhibit a globally perturbed t RNA tertiary structure.Docked atomic coordinates are shown by using the Ribbons and Insight II (Accelrys) programs.Fitting coordinates for EF-Tu•GDPNP (mustard color) were used from Protein Data Bank ID code 1B23; the x-ray crystal structure of TLD-Smp Bs (Protein Data Bank ID code 1P6V) was used in two ways, once for the structure of a tm RNA-Smp B moiety, and once using a single Smp B structure (see text); pink for Smp B-2 on the 30S, and gray for Smp B-1 on the 50S subunit.In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (Arf A).

We used electron cryomicroscopy to determine structures of Arf A bound to the ribosome with 3'-truncated m RNA, at resolutions ranging from 3.0 to 3.4 angstroms.Our findings identify the molecular basis of proofreading in bacteria, highlight the pivotal role of EF-Tu for fast and accurate protein synthesis, and illustrate the importance of multistep substrate selection in intracellular processing of genetic information.We have found that the bacterial ribosome uses two proofreading steps following initial selection of transfer RNAs (t RNAs) to maintain high accuracy of translation of the genetic code.First, aa-t RNAs in ternary complex with EF-Tu·GDP are selected in a step where the accuracy increases linearly with increasing aa-t RNA affinity to EF-Tu.Then, following dissociation of EF-Tu·GDP from the ribosome, the accuracy is further increased in a second and apparently EF-Tu−independent step.Quantification was processed by using Image Quant software (Amersham Pharmacia, Piscataway, NJ).

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