Regulation of a gene usually occurs through transcriptional control. Operon theory states that genes that function together are often regulated together and are known as an operon. The most famous operon is the lac operon which was first discovered in E. Coli. The genes in the lac operon are responsible for lactose metabolism. The three genes that are regulated together in the lac operon are the beta-galactosidase which breaks down lactose, galactoside permease which gets lactose into the cell, and galactoside transacetylase whose function is uncertain. The operator site is a site downstream of the promoter which serves as a binding site for a control molecule which regulates the lac operon. Nearby on the DNA is the lac repressor gene which makes a lac repressor protein. The lac repressor protein can bind to the operator and interfere with the binding of RNA polymerase to the lac operon. When repressor is bound to the operator, even if the RNA polymerase with sigma factor binds to the promoter, it cannot begin gene transcription because it is physically blocked by the lac repressor protein bound to the operator.
If we add lactose to the system and remove glucose the cell is in dire need of metabolizing this lactose as an energy source. The lactose will bind to the repressor thereby changing the shape of the repressor. The lactose-repressor complex can no longer recognize the operator sequence and bind to the DNA. Now the RNA polymerase can move down the DNA and carry out transcription. The restoration of gene expression from the lac operon in this case is an example of de-repression.
A mutation in the DNA of the operator sequence which prevented the repressor from binding would result in the lac operon genes being turned on.
A mutation in the lac repressor gene which would cause it to lose its ability to recognize the operator would also cause the operon to turn on even in the absence of lactose because the repressor would be incapable of recognizing and binding to the operator.
If there was a mutation in both the lac repressor gene and the operator region they might compensate for each other and a control could be restored.
A mutation in a repressor that prohibits the lactose from binding to it turns the synthesis off even if there is lactose in the medium.
Glucose is the preferred sugar as an energy source for cells; therefore, if glucose is present the lactose metabolism needs to be turned off to maintain efficiency. To deal with this contingency there is an activator site in front of the promoter and operator. An "activator" protein with cAMP bound to it must be present to bind to this activator for transcription to start. Without the activator protein-cAMP, there will be no synthesis from the lactose operon. The level of cAMP is affected by levels of glucose in the cell. If the cell has high glucose levels it leads to low cAMP levels. This means a lot of the activator proteins will not have cAMP and thus cannot bind to the activator.
The control system utilizing the cAMP and its binding protein influences the expression from many operons. For efficiency, the cell prefers to utilize glucose over any other energy source. Thus high levels of glucose will prevent expression from any operon that metabolizes an alternative energy source. If glucose levels drop (and cAMP levels rise as a consequence), alternative energy sources can be utilized.
The trp operon is responsible for synthesizing the amino acid tryptophan. Here when tryptophan is present the cell turns the tryptophan synthesis off because there is no need to make more. This is, therefore, opposite from the lac operon.
A trp repressor is made which cannot bind to the trp operator. When there is an abundance of tryptophan in the medium, the tryptophan binds to the trp repressor which allows the repressor to bind to the operator. Thus increasing levels of trp turn off the expression from the trp operon.
A bacteriophage attaches to the surface of a bacterial cell, and the base plate of the phage anchors into the cell wall. The sheath of the phage tail then contracts causing the phage DNA to be injected into the cell. The phage DNA begins to take over its host cell. The cell eventually breaks open and the new baby phages are released into the medium. See figure 4.4 in text.
The phage must be able to regulate the expression of all its genes so that, for example, the lysis gene which causes the cell to burst is expressed towards the end of the infective cycle when all of the DNA has replicated and new phages have been assembled.
The E. coli RNA polymerase binds to the early promoter on the phage DNA. This results in the synthesis of the early genes and includes a new RNA polymerase - the T7 RNA polymerase. T7 RNA polymerase binds to the late promoter of phage DNA and causes the synthesis of the late genes. Among the late genes is a lysis gene that causes the host cell to lyse and release the progeny phage.
The E coli RNA polymerase binds to early promoter when the phage DNA first enters the cell. Among the early gene products is one that binds to the host sigma factor and prevents it from binding to the core RNA polymerase. This eliminates transcription from the early operon. At the same time, one of the other early gene products is a new middle specific sigma factor which allows the core to start transcription at the middle promoter. A similar process allows the switch to occur between the middle and late promoters.
Control of gene expression in lambda phage utilizes antitermination as well as the mechanisms discussed previously. The first genes to be turned on in the lambda phage infection are the integration genes which cause the DNA of lambda to integrate into the host cell's DNA. The integrated lambda DNA is called a prophage. The host cell lives happily until the lambda gets prompted to grow and take over the cell. This infection is called a lysogenic infection. It does not result in the immediate production and release of progeny phage. However, the lambda prophage now behaves like a time bomb that can be triggered to enter into a lytic infection, just like for the T7 and T4 infections.
During the immediate early infection, a product is made which interferes with the host rho factor. Interfering with rho causes the RNA polymerase to ignore rho termination signals and results in the RNA polymerase reading DNA past the normal transcription termination site. These delayed early genes can lead directly to a lytic infection rather that a lysogenic infection.
Deciding whether to be in the lysogenic or lytic infection is based a variety of factors resulting from the current state of the host cell and the growth conditions present in the medium. If the integration process dominates upon infection, then the infection will be lysogenic. If the antitermination process dominates and the late genes end up being expressed, then the infection will be lytic. A prophage can be activated if the cell's growth conditions change - this results in a lysogenic infection becoming a lytic infection.