Sunday, February 8, 2009

A novel quality-control system in protein synthesis

Protein synthesis must proceed with great accuracy, as errors may cause severe problems in the cell. Despite this need for perfection, errors are thought to occur with a rate of about 1 in 20,000 amino acids.
In the cell, the accuracy of protein synthesis is controlled by specific mechanisms at each stage.
Aminoacyl-tRNA synthetases provide the first level of control in this process, matching amino acids with specific tRNAs with an error rate of less than one per 104–105 (1).
Accuracy is further enhanced during the selection of the correct aminoacyl-tRNA by the ribosome, through its base pairing with the mRNA. This process is facilitated by a GTPase called EF1a (in bacteria, formerly known as EF-TU), or eEF1A in eukaryotes (note the extra "e", which denotes 'eukaryotes').
Kinetic proofreading (2) have been proved for both processes.

In this article published on Nature, the authors suggest the existance of a 'retrospective control mechanism' which acts after peptide bond formation (please note how the aforementioned control mechanisms act before the formation of this bond), using an in vitro bacterial translation system. A misincorporation appears to alter the translation mechanism in the ribosome somehow, increasing miscoding and also accelerating the release of the polypeptides. This is mediated by release factors, despite the absence of a stop codon.
In general, the idea seems to be that errors in translation may induce premature termination of the faulty polypeptides, in a way to avoid their synthesis. I imagine that if this mechanism indeed does take place in vivo, the early-released peptides should be rapidly targeted for degradation to avoid any chance of dominant negative effects.

As commented by Frederick and Ibba on the corresponding 'News & Views"(3)

the author's work reveals a facet of quality control in protein synthesis that depends on an unanticipated level of complexity in the workings of the ribosome

Here's the citation and abstract:

Quality control by the ribosome following peptide bond formation.

Zaher HS, Green R.

Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

The overall fidelity of protein synthesis has been thought to rely on the combined accuracy of two basic processes: the aminoacylation of transfer RNAs with their cognate amino acid by the aminoacyl-tRNA synthetases, and the selection of cognate aminoacyl-tRNAs by the ribosome in cooperation with the GTPase elongation factor EF-Tu. These two processes, which together ensure the specific acceptance of a correctly charged cognate tRNA into the aminoacyl (A) site, operate before peptide bond formation. Here we report the identification of an additional mechanism that contributes to high fidelity protein synthesis after peptidyl transfer, using a well-defined in vitro bacterial translation system. In this retrospective quality control step, the incorporation of an amino acid from a non-cognate tRNA into the growing polypeptide chain leads to a general loss of specificity in the A site of the ribosome, and thus to a propagation of errors that results in abortive termination of protein synthesis.

Nature. 2009 Jan 8;457(7226):161-6

1Loftfield RB, Vanderjagt D. The frequency of errors in protein biosynthesis. Biochem J. 1972;128:1353–6.
2Hopfield JJ. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci U S A. 1974;71(10):4135-9
3 Nature. 2009 Jan 8;457(7226):157-8.