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The catabolite activator protein (CAP) activates the expression of more than 100 genes involved in secondary sugar metabolism in E.coli. Apparently, it always binds in sites that are away from -10 and -35 elements of the promoter by multiples of 10 base pairs (-70 or -60, for example). How could this be related to its mechanism of action?

I've searched about this particular activator and I found that it acts mainly by recruiting RNAP to weak promoters, although it does alter the architecture of the DNA, introducing an abrupt bend (for some CAP-dependent genes, this favours conformational changes in RNAP involved in the initialization of transcription): here's the crystallographic data.

However, I did not find anything conclusive about the pattern of binding to distances which are usually multiple of 10 base pairs (which is close to the number of base pair in a complete turn of the double helix).

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  • $\begingroup$ The spacing between TF binding sites is often important as it directly relates to their relative orientation. If two binding sites were, say, 15 bp apart, the TFs would actually be on opposite sides of the DNA helix. This is why the spacing between -10 and -35 is so critical for efficient initiation. I don't know if this effect applies to the spacing you mentioned (60 to 70 bp); at first thought, it seems like it would be less relevant as there is greater flexibility over such a distance. $\endgroup$ – canadianer Mar 12 '15 at 5:57
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I found a great article that might help. To summarize the contents of the article, there are two classes of CAP dependent promoters/genes, and the distance of the CAP bindings site in these classes are different. Also the actions in which CAP is involved are different in the two classes of promoters. In the first class it does not overlap with the promoter region and is only involved in RNAP recruitment. In the second class it overlaps with -35 element of the core promoter and is involved in multiple interactions. So the binding distance of the CAP is determines what interactions is it involved.

You can see the difference between the two classes on the picture below (taken from the article i linked). And I think this answers your question on why the patterns are multiples of ten - because this is the space needed for alpha-CTD to make a bridge between the protein complexes, or the CAP to interact with the RANP complex.

enter image description here

I only took a glance at the paper I linked and quickly extracted the info, but I hope it still helps

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