Different Types of Promoter Sequences in Eukaryotes

A promoter is a specific region of DNA where the RNA polymerase binds to and initiates transcription. Such a binding mechanism is similar to that of an enzyme-substrate complex. Here, the promoter sequence is a specific sequence that the component in RNA polymerase identifies and binds to. Promoters are critical for initiating transcription. This exact mechanism is different for prokaryotes and eukaryotes.

In eukaryotes, multiple sequences serve as promoter such as the TATA Box, CAAT box, GC Box, etc. The location of these will be different, extending from -45 to +20 base pairs from the initiation site. They may be located upstream or downstream.

Promoter sequences are located in the upstream and downstream regions are used by RNA pol III. Thus, there are three types of promoters that this enzyme identifies. Two of these are internal promoter sequences, each having a bipartite structure.

A bipartite structure refers to two short sequences separated by a variable sequence. For eg, type I internal promoter has box A separated from box B. The promoter of RNA polymerase II has two regions with short sequences.

RNA Synthesis

The start point for RNA synthesis is identified by the TATA box close to it. 3 short sequence promoters are located at -30, -75, and -100 base pairs.

The TATA box is located at -30, which shows lukewarm response to transcription. However, the TATA box is a crucial position and component of the core promoter.
The short sequence promoter at -75 is the CAA box, which is often located at -80. It is significant for determining the efficiency of the promoter and also accelerates promoter strength.
The third promoter GC box is centered at -90, which contains the consensus sequence – GGGCGG. There are also multiple copies of these.

Pic Credit: Blanco, A., & Blanco, G

The promoter TATA facilitates transcription only in the downstream direction, while CAAT and GC boxes can function in both directions.

Apart from the promoter sequences, there is also a fourth element to help the RNA polymerase bind. This is called an octamer, which is an 8-base pair element.

Different transcription factors bind to different promoters.

C/EBP binds to the CAAT box
TFIID binds to the TATA box
Oct-1 binds to the octamer
Sp₁ binds to the GC box

Transcription initiates when these promoter genes bind to their transcription factors.

Plant Gene Promoter

In plants, the promoter gene TATA box is located at -20 to -25 base pairs from the transcription site.

Light Responsive Promoter

Plants have certain photoreceptors that receive light of a certain wavelength. They signal regulatory pathways that trigger photomorphogenic sequences in some light-regulated genes. The elements in these promoters include GT-I site, GATA or I-box, elements rich in G box and AT, as well as 5’GGTTAA3’. These are seen in the promoter rbc-3A.

The GATA-box is common in many light-regulated promoters. Another common element is the 5’-CACGTG-3’ found in the G box. The G box is also called G-box binding factors (GBFs) because many transcription factors prefer the G-box.

The AT-rich element in the pea plant and in the glutamine synthetase gene promoter are activators, while the AT-rich elements in the chlorophyll a and b binding cab-E gene function as a negative regulatory element.

Heat Responsive Promoter

Some plants have heat shock responsive genes which contain 3 base pairs (5’-GAA-3’). This heat shock promoter element is located at 15-118 base pairs upstream of the TATA box. Some are also at 50-100 bp upstream of the CCAAT box.

Seed Specific Promoter

The genes that are activated during seed development mainly code for storage proteins, such as lectin. The promoters for these genes include E-box and G-box. Vicilin. 5’-GCCACCTCAG-3’, 5’-ACACACGTCAA-3’, and CATGCATG for the legumin promoter.