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Science 10 April 2009:
Vol. 324. no. 5924, pp. 255 - 258
DOI: 10.1126/science.1170160
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Reports

Coding-Sequence Determinants of Gene Expression in Escherichia coli

Grzegorz Kudla,1* Andrew W. Murray,2 David Tollervey,3 Joshua B. Plotkin1{dagger}

Synonymous mutations do not alter the encoded protein, but they can influence gene expression. To investigate how, we engineered a synthetic library of 154 genes that varied randomly at synonymous sites, but all encoded the same green fluorescent protein (GFP). When expressed in Escherichia coli, GFP protein levels varied 250-fold across the library. GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression. Rather, the stability of mRNA folding near the ribosomal binding site explained more than half the variation in protein levels. In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.

1 Department of Biology and Program in Applied Mathematics and Computational Science, The University of Pennsylvania, Philadelphia, PA 19104, USA.
2 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
3 Wellcome Trust Centre for Cell Biology and Centre for Systems Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.

* Present address: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK.

{dagger} To whom correspondence should be addressed. E-mail: jplotkin{at}sas.upenn.edu

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