Difference # Prokaryotic Promoters:
In prokaryotes, the promoter consists of two short sequences at -10 and -35 positions upstream from the transcription start site.
i. The sequence at -10 is called the Pribnow box, or the -10 element, and usually consists of the six nucleotides TATAAT. The Pribnow box is absolutely essential to start transcription in prokaryotes (Fig. 8.6).
ii. The other sequence at -35 (the -35 element) usually consists of the six nucleotides TTGACA. Its presence allows a very high transcription rate.
Difference # Eukaryotic Promoters:
Eukaryotic promoters are extremely diverse and are difficult to characterize. They typically lie upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site. In eukaryotes, the transcriptional complex can cause the DNA to bend hack on itself, which allows for placement of regulatory sequences far from the actual site of transcription. Many eukaryotic promoters, contain a TATA box (sequence TA- TAAA), which in turn binds a TATA binding protein which assists in the formation of the RNA polymerase transcriptional complex. The TATA box typically lies very close (Fig. 8.7) to the transcriptional start site (often within 50 bases).
Promoters in eukaryotic organisms- e.g. plants, animals- comprise multiple elements, some of which are found in nearly all promoters (Table 8.3).
i. CAAT box:
A consensus sequence close to -80 bp from the start point (+1). It plays an important role in promoter efficiency, by increasing its strength, and it seems to function in either orientation. This box is replaced in plants by a consensus sequence called the AGGA box.
ii. TATA box:
A sequence usually located around 25 bp upstream of the start point. The TATA box tends to be surrounded by GC rich sequences. The TATA box binds RNA polymerase II and a series of transcription factors [TFIIX, X being a letter that identifies an individual transcription factor (TF)] to form an initiation complex.
iii. GC box:
A sequence rich in guanidine (G) and cytidine (C) nucleotides, is usually found in multiple copies in the promoter region, normally surrounding the TATA box.
iv. CAP site:
A transcription initiation sequence or start point defined as +1, at which the transcription process actually starts.
RNA polymerase II is the enzyme that transcribes a gene into RNA. It works in conjunction with other transcription factors that recognize signals embodied in the promoter region. RNA polymerase II starts its “journey” at the TATA region where it binds and travels along the DNA until it reaches the CAP site where the actual synthesis of RNA starts. The transcription process only takes place in the downstream direction, from 5′ (left) to 3′ (right).