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Energy efficiency trade-offs drive nucleotide usage in transcribed regions

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Item Type:Article
Title:Energy efficiency trade-offs drive nucleotide usage in transcribed regions
Creators Name:Chen, W.H. and Lu, G. and Bork, P. and Hu, S. and Lercher, M.J.
Abstract:Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of 'A' versus 'T' and 'G' versus 'C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides 'U' and 'C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides 'A' and 'G' at non-synonymous coding sites.
Keywords:Amino Acids, Bacteria, Base Composition, Base Pairing, Biological Evolution, Codon, Genetic Models, Genetic Selection, Genetic Transcription, Mutation, Nucleotides, Operon, Protein Biosynthesis, Thermodynamics
Source:Nature Communications
Publisher:Nature Publishing Group (U.K.)
Page Range:11334
Date:21 April 2016
Official Publication:https://doi.org/10.1038/ncomms11334
PubMed:View item in PubMed

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