Excessive Clustering of Third Codon Position Pyrimidines in Prokaryotes

Abstract

The third codon positions are generally thought to be largely neutral, allowing for synonymous mutations. To see how much the third positions are loaded in general we analyzed the sequences of the nucleotides in the third positions. Simple word count analysis revealed excessive clustering of pyrimidines in the third position sequences of prokaryotic mRNA. The clusters have a clear tendency to follow one after another at characteristic distance of 25–30 triplets. Thus, the third codon positions do carry a rather strong message. Possible connection with loop-fold structure of proteins and (cotranslational) protein folding is discussed.

Key words:

• Closed loops
• Clustering of pyrimidines
• Code degeneracy
• Neutral evolution
• Protein folding
• Third codon positions
• Transcription pausing