Control of Genetic Systems in Prokaryotes and Eukaryotes


Genetic Control in Prokaryotes

Prokaryotes have two levels of metabolic control Prokaryotes are "simple," single celled organisms, so they have "simple" systems

lac operon in E. coli

lac operon

Operation - If lactose is not present:

repressed lac operon

Operation - if lactose is present:

active lac operon

The lac operon is an example of an inducible operon - it is normally off, but when a molecule called an inducer is present, the operon turns on.
The trp operon is an example of a repressible operon - it is normally on but when a molecule called a repressor is present the operon turns off.

 


trp Operon - and example of a repressible operon



It Gets More Complicated - the lac Operon Revisited

It is not enough for lactose to be present to induce the lac operon

Gene Control in Eukaryotes

Much more complex - take humans for example

Gene Regulation in Eukaryotes

The latest estimates are that a human cell, a eukaryotic cell, contains approximately 35,000 genes.

How is gene expression regulated?

There are several methods used by eukaryotes.


Transcriptional Control 

 

Transcription start site

This is where a molecule of RNA polymerase II (pol II) binds. Pol II is a complex of some 10 different proteins (shown in the figure in yellow with small colored circles superimposed on it). The start site is where transcription of the gene into mRNA begins.

The basal promoter

The basal promoter contains a sequence of 7 bases (TATAAAA) called the TATA box. It is bound by Transcription Factor IID (TFIID) which is a complex of some 10 different proteins including

The basal or core promoter is found in all protein-encoding genes. This is in sharp contrast to the upstream promoter whose structure and associated binding factors differ from gene to gene (i.e. they are unique to each specific gene).

Although the figure is drawn as a straight line, the binding of transcription factors to each other probably draws the DNA of the promoter into a loop.

Many different genes and many different types of cells share the same transcription factors - not only those that bind at the basal promoter but even some of those that bind upstream. What turns on a particular gene in a particular cell is probably the unique combination of promoter sites and the transcription factors that are chosen.  To see how this all comes together, click here.

An Analogy

The rows of lock boxes in a bank provide a useful analogy.

To open any particular box in the room requires two keys:

Hormones exert many of their effects by forming transcription factors.

The complexes of hormones with their receptor represent one class of transcription factor. Hormone "response elements", to which the complex binds, are promoter sites. Link to a discussion of these.

Just how do proteins bind to DNA?

DNA:Protein and Protein:Protein interactions are important for transcription factor function. Note modular structure of transcription factors: one part of the protein is responsible for DNA binding, another for dimer formation, another for transcriptional activation (i.e. interaction with basal transcription machinery). 

Dimer formation adds an extra element of complexity and versatility. Mixing and matching of proteins into different heterodimers and homodimers means that three distinct complexes can be formed from two proteins. 

Diverse in nature, but several common structures are found:

 

Enhancers

Some transcription factors ("Enhancer-binding protein") bind to regions of DNA that are thousands of base pairs away from the gene they control. Binding increases the rate of transcription of the gene.

Enhancers can be located upstream, downstream, or even within the gene they control.

How does the binding of a protein to an enhancer regulate the transcription of a gene thousands of base pairs away?

One possibility is that enhancer-binding proteins - in addition to their DNA-binding site, have sites that bind to transcription factors ("TF") assembled at the promoter of the gene.

This would draw the DNA into a loop (as shown in the figure).

Silencers

Silencers are control regions of DNA that, like enhancers, may be located thousands of base pairs away from the gene they control. However, when transcription factors bind to them, expression of the gene they control is repressed.

Insulators

A problem:

As you can see above, enhancers can turn on promoters of genes located thousands of base pairs away. What is to prevent an enhancer from inappropriately binding to and activating the promoter of some other gene in the same region of the chromosome?

One answer: an insulator.

Insulators are

Their function is to prevent a gene from being influenced by the activation (or repression) of its neighbors.

Example:

The enhancer for the promoter of the gene for the delta chain of the gamma/delta T-cell receptor for antigen (TCR) is located close to the promoter for the alpha chain of the alpha/beta TCR (on chromosome 14 in humans). A T cell must choose between one or the other. There is an insulator between the alpha gene promoter and the delta gene promoter that ensures that activation of one does not spread over to the other.

All insulators discovered so far in vertebrates work only when bound by a protein designated CTCF ("CCCTC binding factor"; named for a nucleotide sequence found in all insulators). CTCF has 11 zinc fingers. 

Another example: In mice (and humans), only the allele for insulin-like growth factor 2 (Igf2) inherited from one's father is active; that inherited from the mother is not - a phenomenon called imprinting.

The mechanism: the mother's allele has an insulator between the Igf2 promoter and enhancer. So does the father's allele, but in his case, the insulator has been methylated. CTCF can no longer bind to the insulator, and so the enhancer is now free to turn on the father's Igf2 promoter.


Post-Transcriptional Control

RNA Processing: pre-mRNA e mRNA

All the primary transcripts produced in the nucleus must undergo processing steps to produce functional RNA molecules for export to the cytosol. We shall confine ourselves to a view of the steps as they occur in the processing of pre-mRNA to mRNA.

The steps:

Split Genes

Most eukaryotic genes are split into segments. In decoding the open reading frame of a gene for a known protein, one usually encounters periodic stretches of DNA calling for amino acids that do not occur in the actual protein product of that gene. Such stretches of DNA, which get transcribed into RNA but not translated into protein, are called introns. Those stretches of DNA that do code for amino acids in the protein are called exons. Examples: In general, introns tend to be much longer than exons. An average eukaryotic exon is only 140 nts long, but one human intron stretches for 480,000 nucleotides!

The cutting and splicing of mRNA must be done with great precision. If even one nucleotide is left over from an intron or one is removed from an exon, the reading frame from that point on will be shifted, producing new codons specifying a totally different sequence of amino acids from that point to the end of the molecule (which often ends prematurely anyway when the shifted reading frame generates a STOP codon).

The removal of introns and splicing of exons is done with the spliceosome. This is a complex of several snRNA molecules and some 145 different proteins.

The introns in most pre-mRNAs begin with a GU and end with an AG. Presumably these short sequences assist in guiding the spliceosome.


Translational Control

translational regulation

Post-Translational