To economize, many genes are only transcribed when the gene product is needed but are turned off when the product is not needed (energy is not wasted on the synthesis of many unnecessary mRNAs and proteins). Of course vital genes are always transcribed.
Usually the synthesis of an mRNA is not turned off completely just turned down. When it is called "off" it usually means low.
Two general categories of regulation
EXAMPLE FOR NEGATIVE CONTROL
The very first model of gene regulation ever proposed was by François Jacob and Jacques Monod in the 1950s: an important advance in molecular biology.
Jacob and Monod analyzed the expression of enzymes involved in lactose metabolism in E. coli. Lactose is the sugar found in milk. E. coli can grow on lactose because it can cleave this disaccharide into its two components glucose and galactose.
Enzymes necessary for lactose metabolism:
DNA: .......
Jacob and Monod proposed their model of regulation solely on the basis of genetic data derived from mutants. We will only talk about the model and not about the genetic data that led them to this model.
Mutants showed that there are two distinctive DNA sequences that are
necessary for lac operon regulation (Fig. 6.8):
The lac operon model of Jacob and Monod already shows a central principle of gene regulation which is true in both prokaryotes and eukaryotes: control of transcription is mediated by the interaction of regulatory proteins with specific DNA sequences.
Specific regulatory DNA sequences are called cis-acting control elements because they only affect the regulation of genes they are linked to on the same DNA molecule (cis is latin for something like "this side").
Regulatory proteins are called trans-acting factors because as proteins they can diffuse and affect the regulation of genes on other chromosomes as well (trans is latin for something like "the other side").
EXAMPLE FOR POSITIVE CONTROL
The lac operon is also subject to positive regulation.
But first some negative regulatory appearances:
If E. coli has a choice, it will always prefer glucose over any other sugar.
For example, when E. coli is grown in a medium with both glucose and lactose present, it cannot metabolize lactose, because glucose somehow prevents the transcription from the lac operon even in the presence of the inducer (lactose).
However, glucose does not act via a repressor on the lac operon but acts via the inability of an activator to perform its function.
Glucose levels are correlated to the concentration of cAMP via the enzyme that synthesizes cAMP, adenylyl cyclase.
High glucose levels ------ low activity of adenylyl cyclase ------
low cAMP levels
Low glucose levels ----- high activity of adenylyl cyclase ------ high
cAMP levels
only at high cAMP levels and therefore at low glucose concentrations can cAMP bind to a trans-acting factor called catabolite activator protein (CAP). This binding makes it possible for CAP to bind to its specific regulatory sequences on the DNA (Fig. 6.10).
Many operons that are important for the metabolism of other carbon sources than glucose contain such a specific regulatory DNA sequence for CAP-binding. In the lac operon this sequence lies just upstream of the promoter.
If CAP binds, the lac operon is weakly activated but can now fully be activated if lactose is present.
EXAMPLE FOR CONTROL AT THE LEVEL OF ELONGATION
Regulation of elongation: additional mechanism of control for gene expression.
therefore called transcriptional attenuation.
Used only for limited number of genes, best described for E. coli
trp operon.
Trp stands for tryptophan: operon contains 5 structural genes
important in the synthesis of the amino acid tryptophan.
Tryptophan is only synthesized in E. coli, if it is not available
in the food source.
Regulation of the trp operon at the level of initiation of
transcription
Initiation of transcription blocked when abundant tryptophan is available:
High level of tryptophan ---- tryptophan can bind to repressor ----
repressor is now able to bind to trp operon and inhibit initiation
of transcription (Fig. 6.11).
But transcriptional initiation never totally blocked. Transcriptional attenuation increases stringency of inhibition.
Mechanism of transcriptional attenuation: (Fig. 6.12) animation later
Requires a specific regulatory sequence called attenuator. It lies somewhere downstream of the transcription start site in the transcribed and translated region of the operon.
The attenuator contains a premature termination signal (a GC-rich inverted repeat followed by adenines, sequences 3 and 4 in Figure). If transcription and translation proceed normally (under high tryptophan levels) the mRNA is terminated prematurely and no complete protein can be synthesized.
However, under low levels of tryptophan premature termination
is inhibited because the stem loop cannot form from this inverted
repeat
----- there is another GC-rich sequence complementary to the first
repeat in front of the termination signal (sequence 2 in Figure). This
sequence takes part in forming an alternative stem loop, which does
not lead to premature termination because it is not followed by a strech
of adenines.
Why does this alternative stem loop not form normally? Because if translation occurs with normal speed, the ribosome will already cover the alternative complementary GC-rich sequence and prevent alternative stem loop formation.
Under low tryptophan levels translation is slowed at an earlier sequence of the mRNA (sequence 1 in Figure) simply because it contains codons for tryptophan, and tryptophan is scarce for translation.
So the level of tryptophan directly determines the speed of translation, which in turn determines the kind of stem loop that is formed, either the one that can prematurely terminate transcription (high tryptophan levels) or the one that cannot (low tryptophan levels).