Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins

Hudson, Nicholas J., Gu, Quan, Nagaraj, Shivashankar H., Ding, Yong-Sheng, Dalrymple, Brian P. and Reverter, Antonio (2011) Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins. PLoS ONE, 6 9: . doi:10.1371/journal.pone.0025457

Author Hudson, Nicholas J.
Gu, Quan
Nagaraj, Shivashankar H.
Ding, Yong-Sheng
Dalrymple, Brian P.
Reverter, Antonio
Title Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins
Journal name PLoS ONE   Check publisher's open access policy
ISSN 1932-6203
Publication date 2011-09-23
Sub-type Article (original research)
DOI 10.1371/journal.pone.0025457
Open Access Status DOI
Volume 6
Issue 9
Total pages 11
Place of publication San Francisco, United States
Publisher Public Library of Science
Language eng
Abstract Codon bias in the genome of an organism influences its phenome by changing the speed and efficiency of mRNA translation and hence protein abundance. We hypothesized that differences in codon bias, either between-species differences in orthologous genes, or within-species differences between genes, may play an evolutionary role. To explore this hypothesis, we compared the genome-wide codon bias in six species that occupy vital positions in the Eukaryotic Tree of Life. We acquired the entire protein coding sequences for these organisms, computed the codon bias for all genes in each organism and explored the output for relationships between codon bias and protein function, both within- and between-lineages. We discovered five notable coordinated patterns, with extreme codon bias most pronounced in traits considered highly characteristic of a given lineage. Firstly, the Homo sapiens genome had stronger codon bias for DNA-binding transcription factors than the Saccharomyces cerevisiae genome, whereas the opposite was true for ribosomal proteins - perhaps underscoring transcriptional regulation in the origin of complexity. Secondly, both mammalian species examined possessed extreme codon bias in genes relating to hair - a tissue unique to mammals. Thirdly, Arabidopsis thaliana showed extreme codon bias in genes implicated in cell wall formation and chloroplast function - which are unique to plants. Fourthly, Gallus gallus possessed strong codon bias in a subset of genes encoding mitochondrial proteins - perhaps reflecting the enhanced bioenergetic efficiency in birds that co-evolved with flight. And lastly, the G. gallus genome had extreme codon bias for the Ciliary Neurotrophic Factor - which may help to explain their spontaneous recovery from deafness. We propose that extreme codon bias in groups of genes that encode functionally related proteins has a pathway-level energetic explanation.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Agriculture and Food Sciences
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