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Science 13 June 2003:
Vol. 300. no. 5626, pp. 1718 - 1722
DOI: 10.1126/science.1083811
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Research Articles

Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage

Johan Elf,1 Daniel Nilsson,2 Tanel Tenson,3 Måns Ehrenberg1*

We modeled how the charged levels of different transfer RNAs (tRNAs) that carry the same amino acid (isoacceptors) respond when this amino acid becomes growth-limiting. The charged levels will approach zero for some isoacceptors (such as Formula) and remain high for others (such as Formula), as determined by the concentrations of isoacceptors and how often their codons occur in protein synthesis. The theory accounts for (synonymous) codons for the same amino acid that are used in ribosome-mediated transcriptional attenuation, the choices of synonymous codons in trans-translating transfermessenger RNA, and the overrepresentation of rare codons in messenger RNAs for amino acid biosynthetic enzymes.

1 Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 751 24 Uppsala, Sweden.
2 Center for Genomicsand Bioinformatics, Karolinska Institutet, 17177 Stockholm, Sweden.
3 Institute of Molecular and Cell Biology, Tartu University, Riia 23, Tartu, Estonia.

* To whom correspondence should be addressed. E-mail: ehrenberg{at}xray.bmc.uu.se

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