Insights into the molecular determinants of EF-G catalyzed translocation

Translocation, the directional movement of transfer RNA (tRNA) and messenger RNA (mRNA) substrates on the ribosome during protein synthesis, is regulated by dynamic processes intrinsic to the translating particle. Using single-molecule fluorescence resonance energy transfer (smFRET) imaging, in combination with site-directed mutagenesis of the ribosome and tRNA substrates, we show that peptidyl-tRNA within the aminoacyl site of the bacterial pretranslocation complex can adopt distinct hybrid tRNA configurations resulting from uncoupled motions of the 3'-CCA terminus and the tRNA body. As expected for an on-path translocation intermediate, the hybrid configuration where both the 3'-CCA end and body of peptidyl-tRNA have moved in the direction of translocation exhibits dramatically enhanced puromycin reactivity, an increase in the rate at which EF-G engages the ribosome, and accelerated rates of translocation. These findings provide compelling evidence that the substrate for EF-G catalyzed translocation is an intermediate wherein the bodies of both tRNA substrates adopt hybrid positions within the translating ribosome.

RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria

We are now aware that RNA-based regulatory mechanisms are commonly used to control gene expression in many organisms. These mechanisms offer the opportunity to exploit relatively short, unique RNA sequences, in altering transcription, translation, and/or mRNA stability, in response to the presence of a small or large signal molecule. The ability of an RNA segment to fold and form alternative hairpin secondary structures -- each dedicated to a different regulatory function -- permits selection of specific sequences that can affect transcription and/or translation. In the present paper I will focus on our current understanding of the RNA-based regulatory mechanisms used by Escherichia coli and Bacillus subtilis in controlling expression of the tryptophan biosynthetic operon. The regulatory mechanisms they use for this purpose differ, suggesting that these organisms, or their ancestors, adopted different strategies during their evolution. I will also describe the RNA-based mechanism used by E. coli in regulating expression of its operon responsible for tryptophan degradation, the tryptophanase operon.

Mechanism of protein chain termination: further characterization of a mutant defective in a new protein synthesis factor

Mutant N4316 is conditionally lethal at 43 degrees . At 36 degrees it suppresses the termination codons UGA and UAA, but not the UAG codon or a missense mutant of T4 bacteriophage. In vitro, a factor rescues protein synthesis from a temperature-dependent arrest when N4316 extracts are used with RNA from bacteriophage f2. Analyses of the substrate in the arrested synthesis and of the product of the rescue reaction indicate that the factor works at the level of coat protein termination, and that it also affects the synthesis of noncoat protein products. The rescue factor is different from the release factors RF-1, RF-2, and RF-3. Model systems previously used to study release fail to score for at least one vital function in protein chain termination.

Peptidyl-puromycin synthesis on polyribosomes from Escherichia coli

Peptide bond synthesis was studied with native polyribosomes of E. coli. With the use of this system for transpeptidation, it was possible to show that a single K(+) activates the ribosome monomers of polyribosomes; that protonation of a single group (probably imidazole or an N-terminal amino group) with a pK(a) equal to about 7.2 inactivates the transpeptidase complex; that Mn(++) can substitute for Mg(++), but that Ca(++), spermidine, and putrescine do so only very poorly; and that the K(m) for puromycin in this system is about 2.4 x 10(-6) M.

Activity of ribosomes containing 5S RNA with a chemically modified 3'-terminus

Ribosomes containing 5S RNA in which the 3'-terminus has been modified chemically, either by periodate oxidation or by conversion of the terminal ribose to a morpholine derivative, are fully as active in peptidebond formation and polypeptide synthesis as those ribosomes with unmodified 5S RNA. These results exclude models for protein synthesis in which peptidyl-5S RNA is formed as an intermediate.