The search for the optimal ribosome 3' tail end in E. coli

Abstract

The 16s ribosomal tail end has been conjectured to play an important role in the regulation of protein production and of translation efficiency. Using E. coli K-12 as our model organism, we generate sequences of 13 base pairs as hypothetical ribosome tail ends. We analyzed the distributions of these random hypothetical ribosome tail ends and found the actual E. coli ribosome tail end to be significantly different from a randomly generated ribosome tail in the magnitude of the lock and synchronization signals, and the signal to noise ratio. We then designed and ran a genetic algorithm to optimize hypothetical ribosome tail ends simultaneously for these three signal criteria. We found that the actual E. coli ribosome tail end was among the best by these measures.