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DNA Research Advance Access published online on November 1, 2007
DNA Research, doi:10.1093/dnares/dsm019
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© The Author 2007. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

DNA Asymmetric Strand Bias Affects the Amino Acid Composition of Mitochondrial Proteins

Xiang Jia Min and Donal A. Hickey*

Department of Biology, Concordia University, 7141 Sherbrooke West, Montreal, Quebec, Canada H4B 1R6

Received 20 July 2007 ; accepted 4 October 2007.

Variations in GC content between genomes have been extensively documented. Genomes with comparable GC contents can, however, still differ in the apportionment of the G and C nucleotides between the two DNA strands. This asymmetric strand bias is known as GC skew. Here, we have investigated the impact of differences in nucleotide skew on the amino acid composition of the encoded proteins. We compared orthologous genes between animal mitochondrial genomes that show large differences in GC and AT skews. Specifically, we compared the mitochondrial genomes of mammals, which are characterized by a negative GC skew and a positive AT skew, to those of flatworms, which show the opposite skews for both GC and AT base pairs. We found that the mammalian proteins are highly enriched in amino acids encoded by CA-rich codons (as predicted by their negative GC and positive AT skews), whereas their flatworm orthologs were enriched in amino acids encoded by GT-rich codons (also as predicted from their skews). We found that these differences in mitochondrial strand asymmetry (measured as GC and AT skews) can have very large, predictable effects on the composition of the encoded proteins.

Key words: mitochondrion; strand asymmetry; amino acids; codon usage

* To whom correspondence should be addressed. Tel. +1 514-848-2424 ext 5184. Fax. +1 514-848-2881. E-mail: dhickey{at}alcor.concordia.ca

Edited by Dr. Katsumi Isono


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