RNA polymerase
RNA polymerase is a key enzyme responsible for
synthesizing RNA from a DNA template through a process called transcription.
Its main function is to build an RNA molecule by reading the sequence of a gene
and using it as a template to form a complementary RNA strand. Here’s a
detailed explanation of RNA polymerase and its role:
Types of RNA Polymerase in Eukaryotes
In eukaryotes (organisms like humans, plants, fungi),
there are three main types of RNA polymerases, each responsible for
transcribing different classes of RNA:
1. RNA Polymerase I (Pol I):
Synthesizes ribosomal RNA (rRNA), except for the 5S
rRNA.
rRNA is essential for ribosome formation, which is
critical for protein synthesis.
Found in the nucleolus, a specialized region in the
nucleus.
2. RNA Polymerase II (Pol II):
Transcribes messenger RNA (mRNA), which carries the
genetic code from DNA to the ribosome for protein synthesis.
Also synthesizes some small nuclear RNAs (snRNAs) and
microRNAs (miRNAs) involved in RNA processing and gene regulation.
Most of the genes in eukaryotes are transcribed by RNA
Pol II, making it essential for gene expression.
3. RNA Polymerase III (Pol III):
Synthesizes transfer RNA (tRNA), 5S rRNA, and some
other small RNAs.
tRNA is crucial for translating mRNA into protein
during translation.
Prokaryotic RNA Polymerase
Prokaryotes (like bacteria) typically have one type of
RNA polymerase that synthesizes all types of RNA (mRNA, rRNA, and tRNA). This
RNA polymerase has a simpler structure compared to eukaryotic RNA polymerases.
Structure of RNA Polymerase
RNA polymerase is a multi-subunit enzyme. The core
enzyme structure is similar across prokaryotes and eukaryotes, but it becomes
more complex in eukaryotes. The key subunits include:
α subunits (alpha):
Involved in the assembly of the enzyme.
β subunit (beta):
Contains the catalytic site where RNA synthesis occurs.
β' subunit (beta prime):
Binds to the DNA template.
ω subunit (omega):
Stabilizes the enzyme.
In prokaryotes, an additional subunit called the σ
factor (sigma factor) is required for transcription initiation. It allows RNA
polymerase to recognize the promoter sequence in DNA and initiate
transcription.
Mechanism of RNA Polymerase Action
The transcription process involves several steps:
1. Initiation:
Promoter recognition:
RNA polymerase binds to specific sequences on the DNA called promoters,
typically located just upstream of the gene to be transcribed. In prokaryotes,
the σ factor plays a critical role in recognizing these sequences.
Transcription bubble formation:
RNA polymerase unwinds a short region of the DNA helix to expose the template
strand.
First nucleotide addition:
The enzyme catalyzes the addition of the first ribonucleotide triphosphate
(rNTP) to the template DNA strand.
2. Elongation:
After the initial binding, RNA polymerase moves along
the DNA template, adding complementary RNA nucleotides (A, U, C, G) in the 5'
to 3' direction.
During this process, RNA polymerase synthesizes a
single-stranded RNA molecule complementary to the DNA template strand.
The enzyme maintains a transcription bubble (unwound
region of DNA) as it progresses, where only a small portion of the DNA is
unwound at any time.
3. Termination:
In prokaryotes, there are specific termination
sequences that signal the end of transcription, either through Rho-dependent or
Rho-independent mechanisms.
In eukaryotes, termination occurs at specific
sequences after RNA Pol II passes through the polyadenylation signal (for mRNA
transcription), and the RNA transcript is cleaved and processed further.
RNA Processing in Eukaryotes
After transcription in eukaryotes, the RNA (especially
mRNA) undergoes several processing steps before becoming mature and functional:
Capping: Addition of a 5'
cap (modified guanine nucleotide) to the 5' end of the mRNA.
Splicing: Removal of
introns (non-coding regions) and joining of exons (coding regions).
Polyadenylation:
Addition of a poly-A tail to the 3' end of the mRNA, enhancing stability and
export from the nucleus.
Regulation of Transcription
The activity of RNA polymerase is tightly regulated to
ensure that the correct genes are transcribed at the appropriate times and in
response to specific signals. Key regulatory mechanisms include:
Transcription factors:
Proteins that bind to DNA sequences near the promoter to either enhance or
repress transcription.
Enhancers and silencers:
DNA regions that influence the rate of transcription by interacting with
transcription factors and RNA polymerase.
Chromatin structure:
In eukaryotes, the packaging of DNA into chromatin can affect the accessibility
of RNA polymerase to specific genes, with modifications like histone
acetylation facilitating transcription.
Inhibitors of RNA Polymerase
Certain antibiotics and toxins target RNA polymerase
to inhibit transcription:
Rifampicin:
Inhibits bacterial RNA polymerase by binding to the β subunit, commonly used as
an antibiotic.
α-Amanitin:
A potent toxin from the Amanita phalloides mushroom, it inhibits eukaryotic RNA
Pol II, causing severe liver damage if ingested.
Conclusion
RNA polymerase is a critical enzyme for gene
expression, orchestrating the transcription of DNA into RNA. In both
prokaryotes and eukaryotes, it plays a fundamental role in cellular processes,
and its function is finely regulated to ensure proper gene expression. Its
actions, while conserved across species, show complexity and specialization,
especially in higher organisms.