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Silent mutations are not silent after all

We briefly mentioned the idea of silent mutation in the lab meeting the other day when we discussed how DNA mutations can cause diseases. In general, a polymorphism in the wobble (3rd) position of the DNA codon often would not change the amino acid sequence. However, that doesn’t mean everything would be the same or the polymorphism would have no effect on the resulting system. It has long been known that there is codon bias, the preference of using particular codons, among different organisms. This may have implications on the fitness of the animals and evolution.

Josh Plotkin’s group at the University of Pennsylvania has recently done a very interesting study on this topic in Science magazine. They synthesized a synthetic library of 154 green fluorescent protein (GFP) with an average of 114 silent mutations between each pair. They found the expressing of these GFPs in E. Coli, as measured by fluorescence of the GFP, can vary as much as 250 fold! Further analyses revealed that this expression difference did not correlate with the codon bias but more to the secondary structures of the RNA.

As it turned out, RNA with more stable secondary structure was harder to be translated into protein and hence a lower expression level. Also, the stability near 5′ start codon explained most of the expression variation, which indicates the rate limiting step of gene expression was primarily translation initiation. They further predicted and experimentally validated GFP variants with rare codon usage, which presumably were more difficult to produce, would be highly expressed if attached with a 5′ sequence with weaker RNA secondary structure. Therefore silent mutations are not that silent after all, it depends on whether you have the right ear to hear.


Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009 Apr 10;324(5924):255-8.Click here to read [PubMed][Science]