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

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, m...

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Autores principales:	Nicholas J Hudson, Quan Gu, Shivashankar H Nagaraj, Yong-Sheng Ding, Brian P Dalrymple, Antonio Reverter
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/18a227090fe3406283de048b5af4eb87
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spelling	oai:doaj.org-article:18a227090fe3406283de048b5af4eb872021-11-04T06:07:51ZEukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.1932-620310.1371/journal.pone.0025457https://doaj.org/article/18a227090fe3406283de048b5af4eb872011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21966531/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Codon 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.Nicholas J HudsonQuan GuShivashankar H NagarajYong-Sheng DingBrian P DalrympleAntonio ReverterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 9, p e25457 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Nicholas J Hudson Quan Gu Shivashankar H Nagaraj Yong-Sheng Ding Brian P Dalrymple Antonio Reverter Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.
description	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.
format	article
author	Nicholas J Hudson Quan Gu Shivashankar H Nagaraj Yong-Sheng Ding Brian P Dalrymple Antonio Reverter
author_facet	Nicholas J Hudson Quan Gu Shivashankar H Nagaraj Yong-Sheng Ding Brian P Dalrymple Antonio Reverter
author_sort	Nicholas J Hudson
title	Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.
title_short	Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.
title_full	Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.
title_fullStr	Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.
title_full_unstemmed	Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.
title_sort	eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/18a227090fe3406283de048b5af4eb87
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Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.

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