REGULATION OF GENE EXPRESSION.

E. coli contains ~ 4,000 genes and ~ 107protein molecules per cell. If each gene is expressed at the same level, then each protein would be present in 107/4,000 = 2,500 copies. However, this is not observed. Instead, some genes are expressed more than others. For instance, there are more than 10,000 copies of ribosomal proteins but only 10 copies of lac repressor per cell. Clearly, cells are capable of differentially regulating gene expression. In addition, cells can respond to environmental cues by altering their pattern of gene expression.

A. Constitutive expression

B. Overview of positive and negative regulation

Cells constantly make decisions about which proteins to make, and they are very economical.
 
Positive Regulation: Negative Regulation: 
1. Purpose Primarily for decisions about utilizing the best sources of carbon, nitrogen, electron donor, electron acceptor, etc. Primarily for decisions about whether to synthesize something that might be available from the environment. 
2. Protein required  An activator  A repressor 
3. Effectors: small molecules that act as signals. Inducer - In positive regulation, an inducer will bind and activate the activator protein.  a. Co-repressors - repressors may not function unless they are first bound to a small co-repressor molecule. 

b. Inducer - repression may be relieved when a small inducer binds and inactivates the repressor. 
4. Relevant DNA sequences -  Specific activator binding sites are recognized by activator proteins.  Specific operator sites are recognized by repressors. 
5. Examples:  The activator protein CAP (Catabolite Activator Protein) of E. coli interacts with the inducer cAMP. The protein subsequently binds CAP binding sites in DNA and stimulates transcription of downstream genes. This system is involved in the use of alternate carbon sources when the primary source, glucose, is in short supply.  The lac repressor binds the inducer (allo)lactose. This relieves repression of transcription of the lac operon and allows the expression of genes encoding proteins involved in the metabolism of lactose when other carbon sources (e.g. glucose) are not available. 

C. Specific examples of regulation: the lac operon.
Operon - a group of genes jointly transcribed and whose expression is jointly regulated. This is a
    prokaryotic feature.
The lac operon contains genes encoding proteins required to metabolize the sugar lactose.

1. Glucose is the favorite carbon source of  E. coli. However, other sugars such as lactose can
    be utilized if glucose is in short supply.
2. Relevant molecules:
     a. Lactose - a disaccharide containing one glucose and one galactose residue. In order for
                          it to serve as a carbon/energy source, the enzyme beta-galactosidase must
                          cleave lactose into its component monosaccharides: galactose and glucose.
     b. cAMP - a "starvation signal"; elevated levels of this molecule indicate that the supply
                          of  glucose is low.
3. Some observations: E. coli growth curves in the presence of various carbon sources.
    In cultures containing glucose and lactose, the glucose is completely exhausted before the
    cells begin utilizing the lactose. There is a pause in growth during the transition from
    metabolizing the two carbon sources, during which time the cells are synthesizing the
    proteins required for using lactose (i.e. the lac operon is being expressed).

4. Catabolite repression and cAMP/CAP activation
    a. CAP (Catabolite Activator Protein) - an activator protein; functions as an activator only
        when cAMP is bound
    b. Levels of cAMP are inversely proportional to glucose levels. i.e. when [glucose] is high,
        [cAMP] is low and when [glucose] is low, [cAMP] is high (this is the reason that cAMP
        is a "starvation signal"- it indicates that there is not much glucose around).
        When bound with cAMP, CAP binds the CAP binding site located just ahead of the
        promoter. This facilitates the binding of RNA polymerase at the promoter. It is important
        to note that this positive regulatory system is necessary but not sufficient to express the
        lac operon. Utilizing carbon sources other than glucose requires two signals:

The commonly used term "glucose repression" is slightly misleading because glucose does not directly repress the expression of operons involved in utilizing other sugars (such as the lac operon). High glucose levels are reported to the cell by a low cAMP level. Without cAMP, CAP cannot function as an activator protein and so "repression" appears to occur when glucose is present.

5. Induction of the lac operon: relief of repression
    a. When glucose is in short supply and lactose is absent, cAMP-CAP will be bound to the
        CAP binding site but the lac repressor will still be bound to the lac operator. The lac
        repressor physically blocks the access of RNA polymerase to the lac promoter. Thus
        repression will not be relieved under these conditions. This makes sense - since lactose
        is absent, there is no need to transcribe the genes encoding proteins required to degrade
        lactose!
   b. When glucose is in short supply and lactose is present, the inducer (allo)lactose binds
        the lac repressor and causes it to be removed from the lac operator. This allows RNA
        polymerase to transcribe the genes encoding proteins needed for lactose metabolism.