Between-strain variation in nucleotide sequence is greatly reduced at positions that are part of the USS motif. This is clearly seen in the figure to the left, where the blue bars representing the amount of variation for each position are small at the positions where the motif bases are tall (strong consensus). The error bars are the standard deviations of the six datasets (forward and reverse strands of the three readily available genomes) This was about 5000 alignments.
For the flanking AT-rich segments the magnitude of the reduction is proportional to the strength of the motif consensus, but variation in the USS core is most strongly reduced in the initial As.
This result was predicted last year by one of the post-docs, but at that time I didn't see an easy way to test it. How should we interpret it? Perhaps it means that most of the USSs in the genome have evolved to the optimum compromise between the preference of the uptake machinery and the needs of within-cell functions. Why don't the differences in % variation map precisely onto the logo?
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