Promoters of prokaryotic organisms, e.g., such as bacteria, have similar elements as the eukaryotic promoters although there are a few basic differences. Prokaryotic promoters contain at least three conserved features defining the region where the RNA polymerase binds:
- the start point, defined as +1;
- the TATA box is located at -10 position to the start point; in contrast to the -35 bp in eukaryotic promoters; and
- the TTGACA sequence, also called the -35 sequence, located around 35 bp upstream of the start point.
An additional feature, much more common in prokaryotic organisms, is that a promoter serves to initiate the transcription of multiple structural genes that are immediately adjacent to it. This arrangement is called an operon. A single transcribed mRNA is translated into several proteins whose functions are interrelated. In operons, promoters have adjacent, juxtaposed or interspersed regulatory sites to which regulatory proteins bind. In eukaryotic promoters, the regulatory sites are spread out over a longer distance.
There are two modes of regulation of the initiation of transcription in operons:
- Positive control mode, where the interaction between the regulatory protein and regulatory region on the DNA turn the transcription on. The genes are off by default and are turned on by the activators. Transcription factors interact with the RNA polymerase and assist the enzyme in initiating transcription at the promoter. This positive fashion of controlling gene expression is more common in eukaryotes than in prokaryotes.
- Negative control mode, where the interaction turns the genes off. In this case, a repressor protein binds the operator, a DNA sequence of approximately 20 to 25 nucleotides, which is next to the promoter or juxtaposed, and prevents the RNA polymerase from initiating transcription. To switch on the system, small molecules called inducers trigger the production of proteins by binding to the repressor protein and changing its conformation. This change alters the operator-repressor interaction, so that the repressor can no longer remain attached to the operator. Negative control is widely used among prokaryotes, which need to respond swiftly to changes in the environment.
One of the best-studied operon systems is the lac operon from Escherichia coli (E. coli). Since its discovery in the 1960s, other operon systems have been extensively studied in other organisms and are currently being adapted to plant systems with the aim of tightly regulating the expression of genes in transgenic plants.
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