Promoter

Promoter is the DNA region where the transcription initiation takes place.  In prokaryotes, the sequence of a promoter is recognized by the Sigma (s) factor of the RNA polymerase.  In eukaryotes, it is recognized by specific transcription factors.

E. coli

E. coli has five sigma factors:

• Sigma 70: Regulate expression of most genes.
• Sigma 32: Regulate expression of heat shock proteins.
• Sigma 28: Regulate expression of flagellar operon (involved in cell motion).
• Sigma 38: Regulate gene expression against external stresses.
• Sigma 54: Regulate gene expression for nitrogen metabolism.

Table 4-C-1.  E. coli s  factors and the consensus sequences of their recognition sites (promoters).

Table 4-C-1 shows the consensus sequences of the promoters recognized by E. coli s factors (except for Sigma 38 which is not clear).  The consensus sequence is an ideal sequence for the interaction with its regulatory protein.  A promoter should contain an element which is identical to or very close to the consensus sequence.  

Example: The lac operon promoter

Eukaryotes

In eukaryotes, there is a significant difference between the transcription of protein genes and RNA genes.  Most sections in Chapter 4 are devoted to the transcription of protein genes.   RNA genes are discussed in Section I.

The most common promoter element in eukaryotic protein genes is the TATA box, located at -35 to -20.  Its consensus sequence, TATAAA, is quite similar to the -10 region of the Sigma 70 recognition site.  Another promoter element is called the initiator (Inr).  It has the consensus sequence PyPyAN(T/A)PyPy, where Py denotes pyrimidine (C or T), N = any, and (T/A) means T or A.  The base A at the third position is located at +1 (the transcriptional start site).

TATA box and initiator are the core promoter elements.  There are other elements often located within 200 bp of the transcriptional start site, such as CAAT box and GC box which may be referred to as promoter-proximal elements.

Table 4-C-2.  Eukaryotic promoter elements.

The protein which interacts with the initiator and TATA box is known as the TATA-box binding protein (TBP), because the TATA box was discovered earlier than the initiator.  TBP recognizes not only the core promoter of protein genes, but also RNA promoters (Section I).  It is a subunit of the general transcription factor TFIID.  In eukaryotes, transcription requires several different general transcription factors and, in most cases, the regulatory transcription factors. 

Example:

The promoter region of the IL-2 gene - contains TATA box and the binding sites of transcription factors: NFAT, Oct-1, NF-kB and AP-1.

Review Articles:

Biological Role of the CCAAT/Enhancer-binding Protein Family of Transcription Factors - J. Biol. Chem., 1998.

C/EBP and the Control of Phosphoenolpyruvate Carboxykinase Gene Transcription in the Liver - J. Biol. Chem., 1998.

Core promoters: active contributors to combinatorial gene regulation - Genes and Development, 2001.

A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription - Genes and Development, 2002.