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MBE Advance Access published online on March 16, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi135
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted February 28, 2005

Research Article

Context-Dependent Codon Bias and mRNA Longevity in the Yeast Transcriptome

David B. Carlini 1*

1 Department of Biology, American University, 4400 Massachusetts Avenue, NW, Washington, DC 20016-8007, (202) 885-2184, (202) 885-2182

* To whom correspondence should be addressed.
David B. Carlini, E-mail: carlini{at}american.edu


  Abstract

Context-dependent codon bias and its relationship to mRNA longevity was examined in 4648 mRNA transcripts of the Saccharomyces cerevisiae transcriptome for which mRNA half-lives have been empirically determined. Surprisingly, rare codon usage (codons used <13 times per 1000 codons in the genome) increased with mRNA half-life. However, it is shown that this pattern was not due to preference for rare codon use within codon families containing both rare and non-rare codons. Rather, the pattern was due to an increase in the frequency of amino acids encoded solely by rare codons, and a decrease in the frequency of amino acids never encoded by rare codons, with mRNA half-life. When standardized by ORF length, the use of consecutive rare codons was also positively correlated with mRNA half-life. There was negative correlation between the usage of synonymous A|T dinucleotides spanning codon boundaries and mRNA half-life, despite the fact that the frequency of AT dinucleotide usage overall, and AT dinucleotide usage at other codon position contexts (e.g., 1-2, 2-3, or 3|1 total) was not correlated with mRNA half-life. The use of A|T dinucleotides at synonymous dicodon boundaries could potentially allow for more efficient 3' to 5' degradation by endonucleolytic cleavage.

Keywords: context-dependent codon bias; mRNA half-life; mRNA stability; gene expression; yeast.
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