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      Determinants of translation efficiency and accuracy

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          Abstract

          A given protein sequence can be encoded by an astronomical number of alternative nucleotide sequences. Recent research has revealed that this flexibility provides evolution with multiple ways to tune the efficiency and fidelity of protein translation and folding.

          Abstract

          Proper functioning of biological cells requires that the process of protein expression be carried out with high efficiency and fidelity. Given an amino-acid sequence of a protein, multiple degrees of freedom still remain that may allow evolution to tune efficiency and fidelity for each gene under various conditions and cell types. Particularly, the redundancy of the genetic code allows the choice between alternative codons for the same amino acid, which, although ‘synonymous,' may exert dramatic effects on the process of translation. Here we review modern developments in genomics and systems biology that have revolutionized our understanding of the multiple means by which translation is regulated. We suggest new means to model the process of translation in a richer framework that will incorporate information about gene sequences, the tRNA pool of the organism and the thermodynamic stability of the mRNA transcripts. A practical demonstration of a better understanding of the process would be a more accurate prediction of the proteome, given the transcriptome at a diversity of biological conditions.

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          Most cited references101

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          The transcriptional landscape of the yeast genome defined by RNA sequencing.

          The identification of untranslated regions, introns, and coding regions within an organism remains challenging. We developed a quantitative sequencing-based method called RNA-Seq for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome. We applied RNA-Seq to generate a high-resolution transcriptome map of the yeast genome and demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed. We confirmed many known and predicted introns and demonstrated that others are not actively used. Alternative initiation codons and upstream open reading frames also were identified for many yeast genes. We also found unexpected 3'-end heterogeneity and the presence of many overlapping genes. These results indicate that the yeast transcriptome is more complex than previously appreciated.
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            The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.

            P. Sharp, W Li (1987)
            A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.
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              Inherent toxicity of aggregates implies a common mechanism for protein misfolding diseases.

              A range of human degenerative conditions, including Alzheimer's disease, light-chain amyloidosis and the spongiform encephalopathies, is associated with the deposition in tissue of proteinaceous aggregates known as amyloid fibrils or plaques. It has been shown previously that fibrillar aggregates that are closely similar to those associated with clinical amyloidoses can be formed in vitro from proteins not connected with these diseases, including the SH3 domain from bovine phosphatidyl-inositol-3'-kinase and the amino-terminal domain of the Escherichia coli HypF protein. Here we show that species formed early in the aggregation of these non-disease-associated proteins can be inherently highly cytotoxic. This finding provides added evidence that avoidance of protein aggregation is crucial for the preservation of biological function and suggests common features in the origins of this family of protein deposition diseases.
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                Author and article information

                Journal
                Mol Syst Biol
                Molecular Systems Biology
                Nature Publishing Group
                1744-4292
                2011
                12 April 2011
                12 April 2011
                : 7
                : 481
                Affiliations
                [1 ]simpleDepartment of Molecular Genetics Weizmann Institute of science , Rehovot, Israel
                Author notes
                [a ]Department of Molecular Genetics, Weizmann Institute of science, Herzel, Rehovot 76100, Israel. Tel.: +97 28 934 6058; Fax: +97 28 934 4108; pilpel@ 123456weizmann.ac.il
                Article
                msb201114
                10.1038/msb.2011.14
                3101949
                21487400
                4cf13e9c-db82-4528-9f00-8d5ddb3110b5
                Copyright © 2011, EMBO and Macmillan Publishers Limited

                This is an open-access article distributed under the terms of the Creative Commons Attribution Noncommercial No Derivative Works 3.0 Unported License, which permits distribution and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation or the creation of derivative works without specific permission.

                History
                : 29 October 2010
                : 15 February 2011
                Categories
                Review Article

                Quantitative & Systems biology
                codon usage,trna,translation accuracy,translation efficiency
                Quantitative & Systems biology
                codon usage, trna, translation accuracy, translation efficiency

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