(38)
8. Beskrive de grundlæggende træk for typiske prokaryote og eukaryote promotorer
Stryer, s. 784-785
Stryer, s. 794-795
Devlin, s.216-217

Promoter – specific sequence on the DNA template that direct the RNA polymerase to the proper initiation site for transcription.
 

Prokaryotic promoter

A striking pattern is evident when the sequences of many prokaryotic promoters are compared. Two common motifs, each 6 nucleotides long, are present on the upstream side of the start site.

• The first one is the -10 sequence, called also the “Pribnow box”, which is located 10 nucleotides upstream from the start site and has the consensus (average) sequence of TATAAT. This sequence is recognised by the s factor in prokaryotes.
   

• The second one is the -35 sequence, TTGACA, located 35 nucleotides upstream from the start site. It is also recognised by the σ-factor, which is a part of the RNA polymerase.

Therefore, it is the RNA polymerase itself that recognizes the promoter sequences in the prokaryotes, in comparison to eukaryotes, where a special protein, called the transcription factor recognizes a specific sequence and binds the RNA polymerase afterwards.
 

Promoters can be strong and weak.

Strong promoters have sequences that correspond closely to the consensus sequence. Genes with strong promoters are transcribed very often because the s-factor recognizes the promoter sequence more often (fx. Every 2 sec. in E.Coli)
Weak promoters have multiple substitutions in comparison to the consensus sequence. Genes with weak promoters are transcribed not that frequently. (fx. Every 10 min. in E.Coli)

Thus, the strength of a promoter sequence serves to regulate transcription. Regulatory proteins that bind to specific sequences near promoter sites and interact with the RNA polymerase also markedly influence the transcription of many genes.    

Eukaryotic promoter:

In eukaryotes, each of the three types of the RNA polymerases has its distinct promoter.

RNA polymerase I – transcribes from a single type of promoter, present only in rRNA genes, that encompasses the initiation site.

RNA polymerase III - responds to promoters that lie upstream or downstream the initiation site.

RNA polymerase II has a more complex mechanism. As already mentioned, RNA polymerase transcribes mRNA.  

Promoters for RNA polymerase II are also located upstream from the start site. The three most important promoter consensus sequences are:

• The TATA-box, called the proximal promoter, usually located between -30 and -100 (devlin, -25) nucleotides from the start site. The mutation of a single base of the TATA-box markedly impairs promoter activity.
   

• The CAAT and the GC box, the distal promoters, which are located further upstream, between -40 and -150 nucleotides away from the start site.

The positions of these upstream sequences can vary in comparison to prokaryotic promoters that have quite constant locations at -10 and -35.

The promoter sequences do not contact the RNA polymerase II directly. Rather, they require the binding of a transcription factor, a protein, in order to function. These protein factors do not bind only to their promoter, but also to another transcription factors and to RNA polymerase creating a large enzyme complex.

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