Regulation of gene expression

Prokaryotes: In prokaryotes, genes are clustered into operon. Operon is a gene cluster that encodes
the protein necessary to perform coordinated function, such as a biosynthesis of given amino acids or
synthesis of enzymes for energy cycle. Hence it is also known as the coordinated unit of genetic
expression in bacteria.
In general operon consists of followings:
a. Regulatory gene
b. Promoter site
c. Operator gene
d. Structural gene
In prokaryotes gene expression is regulated predominately by manipulating the rate of transcription
initiation. Manipulation of initiation involves control of promoter, as RNA polymerase bind to
promoter, hence commencing the mRNA synthesis. It is imperative for the regulation of gene
expression
Whether RNA polymerase will recognize the promoter or not depends on the interaction between
accessory protein and operator gene adjacent to promoter region. Accessory proteins are product of
constitutive gene and are of two types:-
a. Activator: Positively regulate promoter. i.e. Enables RNA polymerase to recognize promoter
b. Repressor: Negatively regulate promoter
As the accessory protein binds with operator gene it may cause positive or negative regulation of
gene expression.
Regulatory gene: Regulatory genes are coded for accessory proteins. They produces at constant
rate, irrespective of cell types, the accessary protein for regulation of mRNA synthesis
What to regulate in prokaryotics:
1. Products requires for energy utilization (catabolite-regulated operons) such as lac operon
2. Products require for biosynthesis of biomolecules such as amino acid synthesis. e.g. trp operon
Lac operon: Products of lac operon-
a. β- galactosidase Hydrolyses lactose
b. Galactoside permease Controls the entry of lactose in cell
c. Galacoside acetylase Produces transacetylase
Negative regulation of lac operon:
a. By lac repressor
b. By glucose
Structure of lac operon: The lac operon consists of a regulatory gene (I; I for inhibition), operator gene (O) and three
structural genes (Z, Y, A). Besides these genes, there is a promoter site (P), next to the operator gene, where the
enzyme RNA polymerase binds. The structural genes Z, Y and A respectively, code for the enzymes β-galactosidase,
galactoside permease and galactoside acetylase. β-Galactosidase hydrolyses lactose (β-galactoside) to galactose and
glucose while permease is responsible for the transport of lactose into the cell. The function of acetylase (coded by A
gene) remains a mystery. The structural genes Z, Y and A transcribe into a single large mRNA with 3 independent
translation units for the synthesis of 3 distinct enzymes. An mRNA coding for more than one protein is known as
polycistronic mRNA. Prokaryotic organisms contain a large number of polycistronic mRNAs.
Repression of lac operon: The regulatory gene (I) is constitutive. It is expressed at a constant rate leading to the
synthesis of lac repressor. Lac repressor is a tetrameric (4 subunits) regulatory protein (total mol. wt. 150,000)
which specifically binds to the operator gene (O). This prevents the binding of the enzyme RNA polymerase to
the promoter site (P), thereby blocking the transcription of structural genes (Z, Y and A). This is what happens in
the absence of lactose in E. coli. The repressor molecule acts as a negative regulator of gene expression.
Derepression of lac operon: In the presence of lactose (inducer) in the medium, a small amount of it can enter the
E. coli cells. The repressor molecules have a high affinity for lactose. The lactose molecules bind and induce a
conformational change in the repressor. The result is that the repressor gets inactivated and, therefore, cannot bind
to the operator gene (O). The RNA polymerase attaches to the DNA at the promoter site and transcription proceeds,
leading to the formation of polycistronic mRNA (for genes Z, Y and A) and, finally, the 3 enzymes. Thus, lactose
induces the synthesis of the three enzymes β-galactosidase, galactoside permease and galactoside acetylase. Lactose
acts by inactivating the repressor molecules, hence this process is known as derepression of lac operon.
The catabolite gene activator protein : The cells of E. coli utilize glucose in preference to lactose; when both of
them are present in the medium. After the depletion of glucose in the medium, utilization of lactose starts. This
indicates that glucose somehow interferes with the induction of lac operon. This is explained as follows. The
attachment of RNA polymerase to the promoter site requires the presence of a catabolite gene activator protein
(CAP) bound to cyclic AMP. The presence of glucose lowers the intracellular concentration of cAMP by
inactivating the enzyme adenylyl cyclase responsible for the synthesis of cAMP. Due to the diminished levels of
cAMP, the formation of CAP-cAMP is low. Therefore, the binding of RNA polymerase to DNA (due to the absence
of CAP-cAMP) and the transcription are almost negligible in the presence of glucose. Thus, glucose interferes with
the expression of lac operon by depleting cAMP levels. Addition of exogenous cAMP is found to initiate the
transcription of many inducible operons, including lac operon. It is now clear that the presence of CAP-cAMP is
essential for the transcription of structural genes of lac operon. Thus, CAP-cAMP acts as a positive regulator for
the gene expression. It is, therefore, evident that lac operon is subjected to both positive (by repressor, described
above) and negative regulation.
Eukaryotes: Each cell of the higher organism contains the entire genome. As in prokaryotes, gene expression in
eukaryotes is regulated to provide the appropriate response to biological needs. This may occur in the following
ways
-Expression of certain genes (housekeeping genes) in most of the cells.
-Activation of selected genes upon demand.
-Permanent inactivation of several genes in all but a few types.
In case of prokaryotic cells, most of the DNA is organized into genes which can be transcribed. In contrast, in
mammals, very little of the total DNA is organized into genes and their associated regulatory sequences. The
function of the bulk of the extra DNA is not known. Eukaryotic gene expression and its regulation are highly
complex
Epigenetic control: Epigenetic refers to the study of heritable changes in phenotype or expression of genes that are not due to
changes in the sequences of DNA.
Epigenetic gene expression is important for-
-Normal development and function of cell
- Tissue specific gene expression
- development of different diseases
Epigenetic regulation involves following process to regulate the expression of gene:
a. DNA methylation
b. Chromatin structure and modification
c. Modification of untranslated RNA etc
Methylation of DNA and inactivation of genes: Cytosine in the sequence CG of DNA gets methylated to form 5c-
methylcytosine. A major portion of CG sequences (about 20%) in human DNA exists in methylated form. In general,
methylation leads to loss of transcriptional activity, and thus inactivation of genes. This occurs due to binding of
methylcytosine binding proteins to methylated DNA. As a result, methylated DNA is not exposed and bound to transcription
factors. It is interesting to note that methylation of DNA correlates with deacetylation of histones. This provides a double
means for repression of genes.
CHROMATIN SRUCTURE AND GENE EXPRESSION: The DNA in higher organisms is
extensively folded and packed to form protein-DNA complex called chromatin. The structural
organization of DNA in the form of chromatin plays an important role in eukaryotic gene
expression. In fact, chromatin structure provides an additional level of control of gene
expression.. In general, the genes that are transcribed within a particular cell are less condensed
and more open in structure. This is in contrast to genes that are not transcribed which form highly
condensed chromatin.