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GENE REGULATION IN PROKARYOTES AND EUKARYOTES
There are two topics to discuss before we move out of the nucleus: gene regulation in prokaryotes
and eukaryotes and alternative mRNA splicing in eukaryotes. We are only going to consider the regulation of
genes that code for proteins i.e. only those genes involved in the making of mRNA. The diagram below is from
the first year book
The overall idea of transcription is the same in prokaryotes (Bacteria and Archaea) and
eukaryotes but there are also some very important differences, some of which are shown in the diagram
below.
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Here is list some differences;
(1) Transcription in prokaryotes is simultaneous with translation. But in eukaryotes the
mRNA must be exported from the nucleus before it can be translated. This means that
other factors being equal, protein synthesis in a prokaryote can be faster than in a
eukaryote. It also means that the primary mRNA transcript can be processed before it is
exported from the nucleus, with translation only being possible for the final mRNA
send into the cytoplasm.
(2) The regulation of transcription in prokaryotes depends mainly upon the ability of RNA
polymerase to bind to the promoter region and to form an effective initiation complex.
This is also necessary for transcription in eukaryotes but, as we have said, there is a
higher order control that “silences” gene by re-modelling of the chromatin to form
localized regions of heterochromatin along a chromosome. This re-modelling is
greatly influenced by the nature of the histone tail modifications. Overall, acetylation of
histone tails results in opening access to nucleosomes whereas methylation condenses
chromatin to from heterochromatin of various degrees of condensation.
(3) Eukaryotic mRNA has a methyl-guanosine “cap” (methyl-G) and a long tail (100s) of
adenine ribonucleotides (the so-called polyA-tail). The poly-A tail does not result from
transcription, as there is no complementary template strand consisting of a poly –
thymine deoxyribonucleotides. Instead the A’s are added to the mRNA primary
transcript one it has been transcribed. The enzyme that does this is poly-A polymerase
and, as noted, it does not use a DNA, or any other, template.
(4) Apart from some cases in the Archaea, the primary rRNA transcript in prokaryotes is
what is actually translated. That is, there is no processing of the primary mRNA
transcript to produce the mRNA that is translated. This is not true for eukaryotes, and
the more recent the evolution of the eukaryote being considered, the more processing of
the primary mRNA transcript there tends to be. The processing of the mRNA primary
transcript allows for alternative splicing, allowing more than one type of mRNA to be
produced. In eukaryotes, the old idea of “one gene, one protein” is most definitely not
true. Alternative splicing is the reason that, with only about 20,000 different genes,
humans can make more than 100,000 different proteins.
(5) Related to alternative splicing is that eukaryotes have intervening sequences (introns) in
many of their genes. It seems that the presence of introns is essential for alternative
splicing and when we look at the mechanism of this splicing you will see why it is
essential. It is not at all obvious, however, why introns have to be so long!
(6) Unlike the prokaryotic RNA polymerase, the eukaryotic RNA polymerase II cannot
recognize promoter regions directly! What it recognizes are other proteins (called
transcription factors) that have bound to the “open” promoter,
RNA polymerases
To understand transcription and gene regulation one has to know something about the RNA
polymerases. In eukaryotes there are four types of template-dependent RNA polymerase:
(1) RNA polymerase I
(2) RNA polymerase II
transcription of 45S rRNA genes
transcription of mRNA genes
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(3) RNA polymerase III
transcription of tRNA genes; genes for various other
small rRNAs (e.g. the SRP RNA)
Let us just consider RNA polymerase II, the most complex of the three types and how it binds,
indirectly, to a promoter. (As mentioned earlier, RNA polymerase II cannot recognize promoters by
itself. Whereas bacterial RNA polymerases can recognize promoters.):
departments.oxy.edu/.../rna_polymerases.htm
Let us note the following in this diagram:
CTD “tail” of RNA
polymerase II
(1) The promoter region of eukaryotes often has the
sequence TATAAAA in one strand (ATATTTT
in the complementary strand). This segment of
the promoter is called the “TATA box”.
(2) The transcription factor TFIID (a protein) binds
to this region. (If the nucleosomes have been
acetylated enough to allow the close approach of
TFIID to the promoter!)
(3) And the TFIIB binds to TFIID abd DNA in the
promoter region.
(4) RNA polymerase can recognize TFIID and
TFIIB when they are bound to a promoter.
(5) RNA polymerase binds to the TFIID and the
TFIIB.
(6) At the same time other transcription factors (all
proteins) pile onto the RNA polymerase.
(7) The RNA polymerase has a tail. This tail is the
elongated region of the C-terminal end of one of
the polypeptides that make up the RNA
polymerase II. The tail is called the CTD (CTerminal Domain), and is it important! (Yes!!).
(8) Many of the serines in the RNA polymerase II
are now phosphorylated by a specific CTDkinase.
(9) The tail is now said to be hyperphosphorylated.
This phosphorylation undoes the binding of the
tail to TFIID and TFIIB. The RNA polymerase
can now start its journey down the DNA,
transcribing it. Well at least it could if there were
not nucleosomes in the way!
We will see that the CTD “tail” of RNA polymerase II serves as a “workbench” for a wide
variety of mRNA processing enzymes. None of the other RNA polymerases have this tail.
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Nucleosomes and transcription
Exposing the promoter
Many proteins are involved in remodelling the chromatin to convert heterochromatin to
euchromatin so the promoters are exposed and so that the genes can be transcribed. In fact even experts
describe what they call a “bewildering array” of proteins that are involved in this remodelling! And to
make things more difficult the exact function of a lot of these proteins remains unknown and the
proteins are mostly named only with acronyms and numbers! But there are some useful things to
consider as long as we don’t get bogged down in fine details.
(1) Acetylation of histone tails causes nucleosomes tom pack less tightly with each other. The
enzymes involved are called histone acetyltransferases (HATs).
(2) Methlyation of histone tails causes the nucleosomes to pack together more tightly. The enzymes
involved are called histone methyltansferases (HMTs).
(3) So-called chromatin remodelling complexes contain a variety of theses enzymes, as well as
other proteins.
(4) Some of the transcription factors have HAT activity.
How is the promoter exposed?
(1) Histone tails will be acetylated
to convert 30nm compact
chromatin fibers to the 10 nm fibres
(not shown here. This will involve
the so-called chromatin
remodelling complexes, which
contain HATs and other proteins.
(2) Certain transcription factors
(TFs) will bind to the nucleosomes
containing the promoter region.
These TFs have HAT abibilty and
can loosen up the nucleosomes so
much that the histones “fall out”
(3) These histones bind to histone
chaperones (called carrier proteins
in this diagram).
(4) With the promoter exposed
TFIID and TFIIB can now bind to
the promoter.
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