DNA sequence from E. coli in the promoter region for the Fis gene. Below the sequence are sequence walkers for Fis sites in front of rectangles (called petals) with various shades of pink to indicate different information contents. There are also a number of sigma 70 promoters shown by walkers in front of blue boxes (for the -35) and green boxes (for the -10). It is clear that Fis regulates itself from this genetic map. The graphic was created by the lister program, part of the Delila system.
The image above will vary in width to fit the size of your browser window. The figure is also available as: Fis Promoter Map (PDF), Fis Promoter Map (jpg)
At the top, under the page number, you see the line that begins with 'piece 1 ...' which describes the graph. Below that is a bunch of numbers which are the positions of DNA bases on the chromosome of the Escherichia coli (E. coli) bacterial genome. So this is a place at 3.4 million bases from the (arbitrary!) start of the coordinate system, out of 4.6 million bases.
I picked this place because it is in front of the fis gene. The fis gene is turned on when a bacterial cell goes from being starved, when there are no Fis protein molecules, to having lots of nutrients, the number is then 50,000 Fis molecules in each cell!
The letters over pink and red rectangles are representing Fis sites. A cluster of adjacent letters is a 'sequence walker' - we have an expired patent on the method. The colored rectangles, show how strong the site should be (using the mathematics of information theory). The cool thing about this new 'instrument' is that you can see which sites are strong and which are weak in a instant. Before now you had to read the labels, like 4.8 bits or 1.0 bits.
But I also like it because one can see so much in an instant.
See those purple and blue rectangles? They come in pairs, and there are dashed lines directly below the green bar of each that connect them. These represent the places RNA polymerase binds to the DNA to start making RNA. The RNA runs into the fis gene (and from that the Fis protein itself is made) and so this is the genetic control region for Fis. (The purple rectangles are behind the "-35" part of the promoter while the blue rectangles are behind the "-10" part.)
The reason I love this region is that how it works is obvious. If
the cell makes too much Fis protein (from the fis gene)
then Fis protein will
bind all over this region and turn off the promoters! So it is a
nifty feed-back loop, and you can see that in an instant from this ...
Here's the same image with 'artmode' turned on and other parameters switched to remove the black lettering:
Art: Fis Promoter Map (PDF), Art: Fis Promoter Map (jpg)
2016 Oct 09: NEW: vertical bars connect the parts making it easy to see multi-part binding sites as a single object! The previous images without vertical bars: Fis Promoter Map (PDF), Fis Promoter Map (jpg). I also added a ribosome binding site model. The Shine/Dalgarno is in light green and the initiation codon; ATG in this case is in chartreuse. The resulting short reading frame is shown under the DNA sequence ending in a stop sign. The startpoint for Fis is about 1000 bp downstream from this region, past another gene, so it is not shown.
For the colored rectangles behind the walkers, called "petals", the HSB (hue saturation brightness) colors are set automatically by the script mkpetals. The brightness is set to 1 (full). For the hue (such as red, green and purple), the color spectrum is divided up evenly and assigned to the various sequence walker models. The saturation (e.g. white-pink-red) of each rectangle behind the walker is determined by the ratio between the walker total individual information and and the maximum information for the walker weight matrix (i.e., the information of the "consensus"). This turns out to work well visually. One can override the color choices but not the brightness and saturation.
|Paul N. Hengen, Stacy L. Bartram, Lisa E. Stewart and Thomas D. Schneider, Information analysis of Fis binding sites, Nucleic Acids Research, Volume 25 (24): 4994-5002, 1997|
|P. N. Hengen, I. G. Lyakhov, L. E. Stewart and T. D. Schneider, Molecular Flip-Flops Formed by Overlapping Fis Sites, Nucleic Acids Res., 31 (22): 6663-6673, 2003|
origin: 2004 Jul 27
updated: 2019 Jun 22