Are all prokaryotic promotor regions the same or do they differ depending on the protein encoded by the mRNA being transcribed?
What I am thinking is that if activator proteins are a method of transcription regulation, then shouldn't promoter regions differ so that activator proteins have an effect on the expression of a specific gene?
Please tell me if this is correct, or if I misunderstand something.
Definitely not. There is a ton of variation from gene to gene, otherwise, as you say, regulation wouldn't work.
That said, the word "promoter" sometimes gets used in different ways. Especially in eukaryotic systems, people will sometimes say "promoter" to mean the entire region upstream of the gene where transcription factors can bind (for yeast, typically within a few hundred base pairs, for mammals, could be many kb away). These regions are extremely variable from gene to gene in all organisms. But for bacteria, the word is more commonly used in a much stricter sense, to mean the region where the polymerase and the associated sigma factor binds -- this is typically one or two very short stretches of DNA (maybe 5-10 base pairs) very precisely located at a specific position from the start of the gene. These regions are much more conserved, but there will still be some variation. Check out http://nar.oxfordjournals.org/content/40/7/2907.full for a very detailed characterization of some of these sequences in E. coli.
This is not my area, but as nobody has answered yet I'll start the ball rolling to try to encourage a more authoratative response.
Long, long ago, before the internet, when I was a post-doc and the emphasis was on bacterial rather than eukaryotic gene expression, I remember hearing something about specific sigma factors differentially controlling initiation of different bacterial genes. A quick internet search brought up something in Wikipedia (section on Specialized sigma factors), a recent review on sigma factors by Chandrangsu et al. (2014), and a more general review of the regulation of bacterial transcription initiation by Browning and Busby(2004).
In general it would appear that you are correct in thinking that promotor regions will differ to some extent, depending on how they are regulated.
