The genetic code is nearly optimal for allowing additional information within protein-coding sequences
Shalev Itzkovitz1,2 and Uri Alon1,2,3
Author Affiliations
1 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel;
2 Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
Abstract
DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.
Footnotes
3 Corresponding author.
3 E-mail uri.alon@weizmann.ac.il; fax 972-8-934125.
Article published online before print. Article and publication date are at
Received September 22, 2006.
Accepted November 29, 2006.
Freely available online through the Genome Research Open Access option.
Copyright © 2007, Cold Spring Harbor Laboratory Press
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