MBE Advance Access originally published online on March 16, 2005
Molecular Biology and Evolution 2005 22(6):1403-1411; doi:10.1093/molbev/msi135
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Context-Dependent Codon Bias and Messenger RNA Longevity in the Yeast Transcriptome
Department of Biology, American University
E-mail: carlini{at}american.edu.
Context-dependent codon bias and its relationship with messenger RNA (mRNA) longevity was examined in 4,648 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 1,000 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 nonrare 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 open reading frame 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'–5' degradation by endonucleolytic cleavage.
Key Words: context-dependent codon bias • mRNA half-life • mRNA stability • gene expression • yeast
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Y. Huang, E. V. Koonin, D. J. Lipman, and T. M. Przytycka Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage Nucleic Acids Res., September 10, 2009; (2009) gkp712v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Suzuki, C. J. Brown, L. J. Forney, and E. M. Top Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria DNA Res, December 1, 2008; 15(6): 357 - 365. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Siwach, S. D. Pophaly, and S. Ganesh Genomic and Evolutionary Insights into Genes Encoding Proteins with Single Amino Acid Repeats Mol. Biol. Evol., July 1, 2006; 23(7): 1357 - 1369. [Abstract] [Full Text] [PDF]
|
|