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Determinants of translation efficiency and accuracy.

Gingold H, Pilpel Y - Mol. Syst. Biol. (2011)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

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.

Show MeSH
Advanced challenges in assessing translation efficiency. New evidences challenge the common simplified assumptions in assessing translation efficiency. Shown in all sub-figures are two codon types, which may differ in their translation elongation efficiency, a ‘blue' and a ‘orange', served respectively by a ‘blue' and a ‘orange' types of tRNA. Some of the amino acids on the polypeptides are also colored blue or orange, reflecting the different efficiency of the codons that code for them. The following lines of further research into the mechanisms of translation are suggested: (A) The order of high- and low-efficiency codons (the later are colored in orange) is meaningful and can be utilized by evolution to design an optimal schedule for ribosomal flow on transcripts. In particular, the slow ‘ramp' observed in the 5′ end, especially of highly expressed genes, may avoid jamming of ribosomes once they passed it. (B) A local concentration of a tRNA molecule that was just released from the ribosome is high in the vicinity of the subsequent codons. Thus, although some tRNAs might be at low concentration over the entire cell volume, they might be present at relatively higher level in proximity of the codons they just finished translating. According to this possibility, the efficiency of translation of a codon depends also on whether that codon was used a few codons upstream on the same mRNA molecule. An indication for the mechanism might be that similar codons tend to cluster together on mRNA sequences. (C) Regulation of expression of the tRNAs could lead to dynamic changes in their availability in time or space dimensions, e.g., under various conditions, differential developmental stages, or at different tissues. (D) The efficiency of translation is a function of the ratio between the supply and the demand for each tRNA. The demand for different tRNAs, namely—the actual representation of the 61 codons at the transcriptome, might vary between different cell types, different environmental conditions and different time points along organism's life. Here, during the transition from condition I to II, the transcriptome changes from mainly consisting of genes that are rich in the blue codon to genes that more heavily biased towards the orange one; as a result the demand for the corresponding orange tRNA increases in the second condition.
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f2: Advanced challenges in assessing translation efficiency. New evidences challenge the common simplified assumptions in assessing translation efficiency. Shown in all sub-figures are two codon types, which may differ in their translation elongation efficiency, a ‘blue' and a ‘orange', served respectively by a ‘blue' and a ‘orange' types of tRNA. Some of the amino acids on the polypeptides are also colored blue or orange, reflecting the different efficiency of the codons that code for them. The following lines of further research into the mechanisms of translation are suggested: (A) The order of high- and low-efficiency codons (the later are colored in orange) is meaningful and can be utilized by evolution to design an optimal schedule for ribosomal flow on transcripts. In particular, the slow ‘ramp' observed in the 5′ end, especially of highly expressed genes, may avoid jamming of ribosomes once they passed it. (B) A local concentration of a tRNA molecule that was just released from the ribosome is high in the vicinity of the subsequent codons. Thus, although some tRNAs might be at low concentration over the entire cell volume, they might be present at relatively higher level in proximity of the codons they just finished translating. According to this possibility, the efficiency of translation of a codon depends also on whether that codon was used a few codons upstream on the same mRNA molecule. An indication for the mechanism might be that similar codons tend to cluster together on mRNA sequences. (C) Regulation of expression of the tRNAs could lead to dynamic changes in their availability in time or space dimensions, e.g., under various conditions, differential developmental stages, or at different tissues. (D) The efficiency of translation is a function of the ratio between the supply and the demand for each tRNA. The demand for different tRNAs, namely—the actual representation of the 61 codons at the transcriptome, might vary between different cell types, different environmental conditions and different time points along organism's life. Here, during the transition from condition I to II, the transcriptome changes from mainly consisting of genes that are rich in the blue codon to genes that more heavily biased towards the orange one; as a result the demand for the corresponding orange tRNA increases in the second condition.

Mentions: The tAI and the CAI measures predict gene expression with reasonable accuracy, yet alleviating some of the assumptions on which they are based might lead to more accurate models of translation efficiency (see Figure 2).


Determinants of translation efficiency and accuracy.

Gingold H, Pilpel Y - Mol. Syst. Biol. (2011)

Advanced challenges in assessing translation efficiency. New evidences challenge the common simplified assumptions in assessing translation efficiency. Shown in all sub-figures are two codon types, which may differ in their translation elongation efficiency, a ‘blue' and a ‘orange', served respectively by a ‘blue' and a ‘orange' types of tRNA. Some of the amino acids on the polypeptides are also colored blue or orange, reflecting the different efficiency of the codons that code for them. The following lines of further research into the mechanisms of translation are suggested: (A) The order of high- and low-efficiency codons (the later are colored in orange) is meaningful and can be utilized by evolution to design an optimal schedule for ribosomal flow on transcripts. In particular, the slow ‘ramp' observed in the 5′ end, especially of highly expressed genes, may avoid jamming of ribosomes once they passed it. (B) A local concentration of a tRNA molecule that was just released from the ribosome is high in the vicinity of the subsequent codons. Thus, although some tRNAs might be at low concentration over the entire cell volume, they might be present at relatively higher level in proximity of the codons they just finished translating. According to this possibility, the efficiency of translation of a codon depends also on whether that codon was used a few codons upstream on the same mRNA molecule. An indication for the mechanism might be that similar codons tend to cluster together on mRNA sequences. (C) Regulation of expression of the tRNAs could lead to dynamic changes in their availability in time or space dimensions, e.g., under various conditions, differential developmental stages, or at different tissues. (D) The efficiency of translation is a function of the ratio between the supply and the demand for each tRNA. The demand for different tRNAs, namely—the actual representation of the 61 codons at the transcriptome, might vary between different cell types, different environmental conditions and different time points along organism's life. Here, during the transition from condition I to II, the transcriptome changes from mainly consisting of genes that are rich in the blue codon to genes that more heavily biased towards the orange one; as a result the demand for the corresponding orange tRNA increases in the second condition.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3101949&req=5

f2: Advanced challenges in assessing translation efficiency. New evidences challenge the common simplified assumptions in assessing translation efficiency. Shown in all sub-figures are two codon types, which may differ in their translation elongation efficiency, a ‘blue' and a ‘orange', served respectively by a ‘blue' and a ‘orange' types of tRNA. Some of the amino acids on the polypeptides are also colored blue or orange, reflecting the different efficiency of the codons that code for them. The following lines of further research into the mechanisms of translation are suggested: (A) The order of high- and low-efficiency codons (the later are colored in orange) is meaningful and can be utilized by evolution to design an optimal schedule for ribosomal flow on transcripts. In particular, the slow ‘ramp' observed in the 5′ end, especially of highly expressed genes, may avoid jamming of ribosomes once they passed it. (B) A local concentration of a tRNA molecule that was just released from the ribosome is high in the vicinity of the subsequent codons. Thus, although some tRNAs might be at low concentration over the entire cell volume, they might be present at relatively higher level in proximity of the codons they just finished translating. According to this possibility, the efficiency of translation of a codon depends also on whether that codon was used a few codons upstream on the same mRNA molecule. An indication for the mechanism might be that similar codons tend to cluster together on mRNA sequences. (C) Regulation of expression of the tRNAs could lead to dynamic changes in their availability in time or space dimensions, e.g., under various conditions, differential developmental stages, or at different tissues. (D) The efficiency of translation is a function of the ratio between the supply and the demand for each tRNA. The demand for different tRNAs, namely—the actual representation of the 61 codons at the transcriptome, might vary between different cell types, different environmental conditions and different time points along organism's life. Here, during the transition from condition I to II, the transcriptome changes from mainly consisting of genes that are rich in the blue codon to genes that more heavily biased towards the orange one; as a result the demand for the corresponding orange tRNA increases in the second condition.
Mentions: The tAI and the CAI measures predict gene expression with reasonable accuracy, yet alleviating some of the assumptions on which they are based might lead to more accurate models of translation efficiency (see Figure 2).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

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.

Show MeSH