Dataset Information

Stops making sense: translational trade-offs and stop codon reassignment.

ABSTRACT:

Background

Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature.

Results

In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences.

Conclusions

We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants.

SUBMITTER: Johnson LJ

PROVIDER: S-EPMC3161013 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Stops making sense: translational trade-offs and stop codon reassignment.

Johnson Louise J LJ Cotton James A JA Lichtenstein Conrad P CP Elgar Greg S GS Nichols Richard A RA Polly P David PD Le Comber Steven C SC

BMC evolutionary biology 20110729

<h4>Background</h4>Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codo ...[more]

PMID: 21801361

Similar Datasets

Project description:Value-based decision-making involves trading off the cost associated with an action against its expected reward. Research has shown that both physical and mental effort constitute such subjective costs, biasing choices away from effortful actions, and discounting the value of obtained rewards. Facing conflicts between competing action alternatives is considered aversive, as recruiting cognitive control to overcome conflict is effortful. Moreover, engaging control to proactively suppress irrelevant information that could conflict with task-relevant information would presumably also be cognitively costly. Yet, it remains unclear whether the cognitive control demands involved in preventing and resolving conflict also constitute costs in value-based decisions. The present study investigated this question by embedding irrelevant distractors (flanker arrows) within a reversal-learning task, with intermixed free and instructed trials. Results showed that participants learned to adapt their free choices to maximize rewards, but were nevertheless biased to follow the suggestions of irrelevant distractors. Thus, the perceived cost of investing cognitive control to suppress an external suggestion could sometimes trump internal value representations. By adapting computational models of reinforcement learning, we assessed the influence of conflict at both the decision and learning stages. Modelling the decision showed that free choices were more biased when participants were less sure about which action was more rewarding. This supports the hypothesis that the costs linked to conflict management were traded off against expected rewards. During the learning phase, we found that learning rates were reduced in instructed, relative to free, choices. Learning rates were further reduced by conflict between an instruction and subjective action values, whereas learning was not robustly influenced by conflict between one's actions and external distractors. Our results show that the subjective cognitive control costs linked to conflict factor into value-based decision-making, and highlight that different types of conflict may have different effects on learning about action outcomes.

Dataset Information

Stops making sense: translational trade-offs and stop codon reassignment.

Background

Results

Conclusions

Publications

Stops making sense: translational trade-offs and stop codon reassignment.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets