1. Chapter 18
Regulation of Gene Expression

2. Regulation of a Metabolic Pathway
Bacterial often regulate their metabolism based on what is present in their environment.
Regulation can be controlled in two ways:
One, cell can adjust the activity of enzymes already present through a process called feedback inhibition.

3. Regulation of a Metabolic Pathway
Bacterial often regulate their metabolism based on what is present in their environment.
Regulation can be controlled in two ways:
The second way bacteria control their metabolism is by regulating transcription of the gene producing the enzyme.

4. The Operon
An operon is a unit of genetic function common to bacteria and phages that consist of coordinately controlled clusters of genes with similar functions.
An operon consists of an operator, a promoter, and the genes that code for the enzymes they control in a particular pathway.

5. The Basics of the Operon
The operator is the segment of the DNA that acts as a switch.
A repressor is a protein that can bind to the operon and switch it off.
The repressor is usually a product of a regulatory gene often acting allosterically.
Corepressors are small molecules that cooperate with repressor proteins to switch operons off.

6. The Basics of the Operon
Inducers are small molecules that inactivate repressors.
Activators are proteins that bind to DNA and stimulate transcription of specific genes.

7. The Basics of the Operon
Operons move back and forth between 2 states:
One with a repressor bound, and one without.
Also, most regulatory proteins are allosterically controlled.
That is, there is an active state and an inactive state.
Controlled by the amount of gene product available.

8. Inducible and Repressible Operons
There are two main types of operons: inducible and repressible.
Inducible operons are always off, but can be “induced” to turn on when the products they make are needed.
The lac operon.
Repressible operons are always on, but can be “repressed” when there is an abundance of product they make.
The trp operon.

9. Tryptophan: A Basic Example
When the cell lacks tryptophan in its medium, a series of steps can be activated so that the cell can synthesize it.
When tryptophan is synthesized from a precursor molecule, a series of steps are activated and each is catalyzed by a specific enzyme.
The 5 genes that code for the enzymes are clustered together in a single stretch on the bacterial chromosome.

10. Tryptophan: A Basic Example
A single promoter serves all 5 genes.
This constitutes a transcriptional unit, and when the mRNA is synthesized, it codes for all five enzymes in the pathway.
The mRNA is punctuated with start and stop codons that signal where the coding sequences begin and end.
Thus, the 5 separate polypeptides can be translated as needed.

11. Tryptophan: A Basic Example
The advantage to this is that there is one on-off switch for the series of genes related to tryptophan synthesis.
When the cell needs tryptophan, all enzymes are switched on.
The “switch” is the segment of DNA called the operator.
The operator is positioned within or between the promoter and the enzyme-coding genes.
The operator controls the access of RNA polymerase to the genes.

12. The trp Operon, a Repressible Operon
The operon is switched off and on by a protein called a repressor.
The operon, in this case, is always on and binding of the repressor blocks the attachment of RNA polymerase to the promoter and thus transcription of the genes.
This blocking action is very specific and has no effect on other genes within the cell.

13. The trp Operon, a Repressible Operon
In our example using tryptophan, the trp repressor is the product of a regulatory gene (trpR) which is located some distance from the trp operon it is controlling.
It has its own promoter.
Regulatory genes are always on and always expressed within a cell. However, they bind reversibly.

14. The trp Operon, a Repressible Operon
If the active genes ultimately produce tryptophan, and it’s available, it will bind to and alter the function of the trp repressor protein.
That is, it binds to the protein, activating it and enabling it to bind to the operon shutting it off.
Tryptophan is a corepressor.

15. The lac Operon, An Inducible Operon
The lac operon is an example of an inducible operon.
β-galactosidase is an enzyme that breaks down lactose into glucose and galactose.
Most E. coli cells only have a few molecules of β- galactosidase available at any one time.
When you add lactose to the medium in which they are growing, the amount of β-galactosidase increases sharply.

16. The lac Operon, An Inducible Operon
The gene encoding for β-galactosidase is part of the lac operon.
It includes 2 other genes that code for enzymes that function in lactose metabolism.
The whole thing is considered one transcriptional unit and is under the control of 1 operator and 1 promoter.

17. The lac Operon, An Inducible Operon
The lacI gene is a regulatory gene located outside of the operon. It encodes for an allosteric repressor protein that can switch off the lac operon by binding to the operator.
The reason it is called an inducible operon is because the lac repressor is active by itself, and binds to the operator and shuts the lac operon off.

18. The lac Operon, An Inducible Operon
To inactivate the repressor, an inducer is needed. An inducer is a small molecule which binds to and inactivates a repressor.
In the case of the lac operon, allolactose is the inducer.
Allolactose is an isomer of lactose found in small amounts when lactose enters a cell.

19. The lac Operon, An Inducible Operon
When lactose is present, allolactose binds to the repressor altering its conformation, preventing the ability of the repressor from binding to the operator. When the repressor is unable to bind to the operator, the genes in the lac operon can be transcribed into mRNA which can be translated into lactose- metabolizing enzymes.

20. Summary
The regulation of the trp and lac operons involves negative control of genes--their operons are switched off by the active form of the repressor gene.
Gene regulation is said to be under positive control only when a regulatory protein interacts directly with the genome to switch transcription on.

21. Positive Control of the lac Operon
Not only are the lactose utilizing enzymes working and on when lactose is present, but they are also working when glucose is in short supply.
E. coli cells can sense low concentrations of glucose and relay the information to the genome.
It does so with the interaction of an allosteric regulatory protein and a small organic molecule.

22. Positive Control of the lac Operon
When glucose is scarce, cAMP accumulates in the cell. When accumulation occurs, it interacts with the regulatory protein called catabolite activator protein (CAP).
CAP acts as an activator of transcription.

23. Positive Control of the lac Operon
When cAMP binds to CAP, CAP assumes an active shape, binds to a specific site on the lac promoter stimulating gene expression.
This is called positive regulation.

24. Positive Control of the lac Operon
When glucose levels within the cell increase, cAMP falls and CAP detaches from the operon.
When CAP is inactive, transcription of the lac operon proceeds at a low level.

25. Summary
The state of the lac repressor determines whether or not transcription of the lac operon’s genes occurs at all. The state of CAP controls the rate of transcription if the operon is repressor free.
In both cases, when glucose is available, it will be used preferentially by the cell. Lactose enzymes will only be made when lactose is available and glucose is not.

26. Summary
In our example involving tryptophan, the trp operon, is a repressible operon because its transcription is usually on but can be turned off.
In contrast, the example involving lactose, the lac operon, is an inducible operon. Transcription is normally off, but can be turned on.

27. Summary
When looking at the figure at the right, keep in mind the following 2 things:
Negative control, binding has a negative effect, it shuts down transcription.
Positive control, binding has a positive effect, it stimulates transcription.