Operon promoter site

The galactose (gal) operon of E. coli is negatively controlled and inducible by D-galactose or D-fucose, which bind to the gal repressor. There are two overlapping promoter sites, one of which is stimulated... 

Translation Initiation Site. In eukaryotes, if the transcription start site is known, and there is no intron interrupting the 5 UTR, Kozak s rule (Kozak, 1996) probably will locate the correct initiation codon in most cases. Splicing is normally absent in prokaryotes, yet because of the existence of multicitronic operons, promoter location is not the key information. Rather, the key is reliable localization of the ribosome binding site. The TATA sequence about 30 bp from the transcription start site may be used as a possible resource. 

Figure 13.1 Operon model for control of protein synthesis. The example chosen is the lactose (lac) operon. I, regulatory gene p, promoter site o, operator gene z, y, and a represent the structural genes for j8-galactosidase, permease, and transacetylase, respectively.

In an inducible system, the repressor protein normally binds to a modulator site called the operator, O, and consequently blocks transcription of the adjacent structural genes. However, when the specific inducer for the system is present in an appropriate environment, inducer binds to the repressor and alters its conformation so that the repressor is released from the operator site. The promoter site is thereby freed, and the transcription machinery can initiate synthesis of mRNA. The mRNA, in turn, is translated to yield the protein products of the operon. In a repressive system, the operon is normally expressed because the repressor protein normally has a conformation that prevents its binding to the operator site. However, when the specific corepressor for the system is present, corepressor binds to the (apojreoressor protein and alters its conformation so that repressor now binds the operator and blocks the initiation of transcription at the promoter site. 

In an inducible system, the activator protein normally has a conformation that prevents it from interacting with a modulator site called the initiator, I. Without this specific interaction, transcription is not initiated and there is no expression of the operon. However, when inducer is present in an appropriate environment, activator is converted to a conformation that can bind the initiator site and facilitate the initiation of transcription at the promoter. In a repressible system, the activator protein normally interacts with the initiator site to facilitate initiation of transcription. However, when the specific corepressor (antagonist) is present, activator is no longer able to facilitate the initiation of transcription at the promoter site and expression of the operon is turned off. See also Figure I. 

In Fig. 5 is shown an alignment between the DNA sequence flanking the bchCA transcript 5 end and proposed oxygen-regulated puf operon promoter sequences (7,8). Identical sequences are enclosed in boxes and consist of (i) a conserved 5 -CGGGC-3 that is located 23 nt upstream of the puf +1 site and 19 nt upstream of the major bchCA 5 end (ii) a 5-TTCA-3 located 6 nt (p /promoter) or 7 nt (putative bdhCA promoter) downstream of the 5 -CGGGC-... 

The possibility has been considered that the I mutation may have introduced a new initiator or promoter site [70] or a translation-restart signal [71,72]. As I" produces a constitutive phenotype and function in deletion 766, the latter seems unlikely, since translation-restart is dependent on both normal transcription (for example, induction of the operon) and the immediate proximity of a nonsense codon. 

For the sake of simplicity we shall assume that the era/site is a highly specialized promoter site, that is, the site for RNA polymerase attachment, and initiation of mRNA synthesis, the activator functional site, and that it includes the binding site for the cyclic AMP-activated CAP. AraO is the site on the DNA for repressor attachment. The efficiency of transcription of the operon is therefore dependent upon the concentration of (1) cyclic AMP (which is controlled by accumulated intermediates in L-arabinose metabolism through their effect on cyclic AMP synthesis... 

---