ArticleEvolutionary bioinformatics online2007
Identification of conflicting selective effects on highly expressed genes.
Article in Evolutionary bioinformatics online, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
4 citing papers in PubMed, 20 citations in OpenAlex.
- Detecting positive and purifying selection at synonymous sites in yeast and worm.Molecular biology and evolution · 2010Article
- The evolutionary consequences of erroneous protein synthesis.Nature reviews. Genetics · 2009Review
- A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code.Biology direct · 2009Article
- The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behavior of taxa.BMC evolutionary biology · 2008Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many different selective effects on DNA and proteins influence the frequency of codons and amino acids in coding sequences. Selection is often stronger on highly expressed genes. Hence, by comparing high- and low-expression genes it is possible to distinguish the factors that are selected by evolution. It has been proposed that highly expressed genes should (i) preferentially use codons matching abundant tRNAs (translational efficiency), (ii) preferentially use amino acids with low cost of synthesis, (iii) be under stronger selection to maintain the required amino acid content, and (iv) be selected for translational robustness. These effects act simultaneously and can be contradictory. We develop a model that combines these factors, and use Akaike's Information Criterion for model selection. We consider pairs of paralogues that arose by whole-genome duplication in Saccharmyces cerevisiae. A codon-based model is used that includes asymmetric effects due to selection on highly expressed genes. The largest effect is translational efficiency, which is found to strongly influence synonymous, but not non-synonymous rates. Minimization of the cost of amino acid synthesis is implicated. However, when a more general measure of selection for amino acid usage is used, the cost minimization effect becomes redundant. Small effects that we attribute to selection for translational robustness can be identified as an improvement in the model fit on top of the effects of translational efficiency and amino acid usage.
Indexed as
Identifiers
19430600PMC2674637W219915190What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.