Energy efficiency trade-offs drive nucleotide usage in transcribed regions

Wei-Hua Chen (), Guanting Lu, Peer Bork, Songnian Hu and Martin J. Lercher ()
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Wei-Hua Chen: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences
Guanting Lu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences
Peer Bork: Structural and Computational Unit, European Molecular Biology Laboratory
Songnian Hu: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences
Martin J. Lercher: Institute for Computer Science and Cluster of Excellence on Plant Sciences, Heinrich Heine University

Nature Communications, 2016, vol. 7, issue 1, 1-10

Abstract: 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.

Date: 2016
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DOI: 10.1038/ncomms11334

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