what is a promoter region? how RNA polymerase recognize it?

1. Promoter region and how it is recognize by RNA polymerase
What is the promoter region?
A promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near
the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5' region
of the sense strand). Promoters can be about 100–1000 base pairs long.( "Analysis of Biological
Networks: Transcriptional Networks – Promoter Sequence Analysis" (PDF). Tel Aviv University.
Retrieved 30 December 2012)
The promoter region controls when and where the RNA polymerase will attach to DNA so transcription
can commence. DNA sequences called response elements are located within promoter regions, and they
provide a stable binding site for RNA polymerase and transcription fact. In bacteria, RNA polymerase
only requires the associated protein sigma factor to bind the promoter. On the other hand, the process in
eukaryotes is much more complex. Eukaryotes require a minimum of seven transcription factors in order
for the binding of RNA polymerase II (eukaryote-specific RNA polymerase) to the promoter.
There are three main portions that make up a promoter: core promoter, proximal promoter, and distal
promoter.
The core promoter region is located most proximally and contains the RNA polymerase binding site,
TATA box, and transcription start site (TSS). RNA polymerase will bind to this core promoter region
stably and transcription of the template strand can initiate. The TATA box is a DNA sequence (5'-
TATAAA-3) within the core promoter region where general transcription factor proteins and histones can
bind. Histone binding will prevent the initiation of transcription whereas transcription factors will drive
the onset of transcription. The most 3' portion of the core promoter is the TSS which is where
transcription literally is initiated. However, only eukaryotes and archaea contain this TATA box.
Prokaryotes contain something called the Pribnow box which usually consists of the six nucleotides
TATAAT.
Further upstream from the core promoter you will find the proximal promoter which contains many
primary regulatory elements. The proximal promoter is found approximately 250 base pairs upstream
from the TSS and it is the site where general transcription factors bind.
The final portion of the promoter region is called the distal promoter which is anything further upstream
from the gene. The distal promoter also contains transcription factor binding sites, but mostly contains
regulatory elements.
Prokaryotic Promoters: Promoters in prokaryotic organisms are two short DNA sequences located at the
-10 (10bp 5' or upstream) and -35 positions from the transcription start site (TSS). Their equivalent to the
eukaryotic TATA box, the Pribnow box (TATAAT) is located at the -10 position and is essential for
transcription initiation. The -35 position typically consists of the sequence TTGACA and this element
controls the rate of transcription. Prokaryotic cells contain sigma factors which assist the RNA
polymerase in binding to the promoter region. Each sigma factor recognizes different core promoter
sequences.

2. Eukaryotic Promoters: Eukaryotic promoters span a wide range of DNA sequences. Eukaryotic Promoters
are so complex in structure that the DNA tends to fold back on itself which explains how a lot of
regulatory sequences can effect transcription while being physically located far from the initiation
transcription site. The TATA-binding protein binds the TATA box and helps in the subsequent binding of
the RNA polymerase. A transcription complex is constructed from the RNA polymerase and several
transcription factor proteins.
(Reference: www.addgene.org)
How RNA polymerase recognize the promoter region?
The RNA polymerase is a holoenzyme having α2ββ′ σ subunits. The α2ββ′ core of RNA polymerase is
unable to start transcription at promoter sites. Rather, the complete α2ββ′σ holoenzyme is essential for
initiation at the correct start site. The σ subunit contributes to specific initiation in two ways. First, it
decreases the affinity of RNA polymerase for general regions of DNA by a factor of 104
. In its absence,
the core enzyme binds DNA indiscriminately and tightly. Second, the σ subunit enables RNA polymerase
to recognize promoter sites. A large fragment of a σ subunit was found to have an α helix on its surface;
this helix has been implicated in recognizing the 5′-TATAAT sequence of the -10 region. The
holoenzyme binds to duplex DNA and moves along the double helix in search of a promoter, forming
transient hydrogen bonds with exposed hydrogen-donor and -acceptor groups on the base pairs. The
search is rapid because RNA polymerase slides along DNA instead of repeatedly binding and dissociating
from it. In other words, the promoter site is encountered by a random walk in one dimension rather than
in three dimensions. The σ subunit is released when the nascent RNA chain reaches nine or ten
nucleotides in length. After its release, it can assist initiation by another core enzyme.
E. coli contains multiple σ factors to recognize several types of promoter sequences contained in E.
coli DNA. The type that recognizes the consensus sequences described earlier is called σ70
because it has
a mass of 70 kd. A different σ factor comes into play when the temperature is raised abruptly. E.
coli responds by synthesizing σ32
, which recognizes the promoters of heat-shock genes. These promoters
exhibit -10 sequences that are somewhat different from the -10 sequence for standard promoters. The
increased transcription of heat-shock genes leads to the coordinated synthesis of a series of protective
proteins. Other σ factors respond to environmental conditions, such as nitrogen starvation. These findings
demonstrate that σ plays a key role in determining where RNA polymerase initiates transcription.
Eukaryotic Polymerase use a complex set of general transcription factors (GTFs) that function in
promoter recognition. In eukaryotic cells, there are also 3 different kinds of RNA polymerase, each that
transcribes a different type of RNA. Once a RNA polymerase binds to its respective promoter region
(equipped with transcription factors), it creates a transcription initiation complex (core promoter), which
traverses the DNA. Eukaryotes also have two promoter sites, one is called the TATA or Hogness box
which is at location -25 and has the sequence TATAAA, and the CAAT box, which is located at -75 and
has the sequence GGNCAATCT. Transcription is initiated by stimulation by the enhancer sequence.
(Reference: NCBI U.S. National library of medicine)
Regulation of gene transcription:

3. In the regulation of gene expression in prokaryotes, anti-sigma factors bind to sigma factors and
inhibit transcriptional activity. Anti-sigma factors are antagonists to the sigma factors, which regulate
numerous cell processes including flagellar production, stress response, transport and cellular growth. For
example, anti-sigma factor 70 Rsd in E. coli is present in the stationary phase and blocks the activity of
sigma factor 70 which in essence initiate gene transcription. This allows the sigma S factor to associate
with RNA polymerase and direct the expression of the stationary genes. Let us first consider an example
from prokaryotes called the lac operon.
What is the lac operon? An operon is a group of bacterial genes located adjacent to each other, and
controlled as a single unit by the same promoter. The lac operon is one such group of genes that encode
proteins needed for the uptake and breakdown of the sugar lactose.
The lac operand is controlled by both an activator and a repressor system. Transcription of the lac cluster
of genes is primarily controlled by a repressor protein that binds to a region of the DNA just downstream
of the -10 sequence of the lac promoter. The place where the repressor is bound is called the operator.
When the repressor is bound at this position, it physically blocks the RNA polymerase from transcribing
the genes. In order for transcription to occur, the repressor must be removed from the operator. When the
sugar lactose is present, it binds to the repressor and changes its shape so that it no longer binds to the
operator. When the repressor falls off, the RNA polymerase can start transcribing the genes of the cluster.
Turning on these genes requires lactose to be present. When the lactose is broken down, the repressor
binds to the operator once more and the lac genes are no longer expressed. This allows the genes to be
expressed only when they are needed
(Oregon state university lecture© 2008 Indira Raja gopal)
(Internet data. Collected and combined by Musaddaq Hafeez GCUF)