RNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the
transcription of DNA to synthesize precursors of mRNA and most snRNA and
microRNA. A 550 kDa complex of 12 subunits, RNAP II is the most studied
type of RNA polymerase. A wide range of transcription factors are required for
it to bind to upstream gene promoters and begin transcription.
Subunits The eukaryotic core RNA polymerase II
was first purified using transcription assays. The purified enzyme has
typically 10-12 subunits and is incapable of specific promoter
recognition. Many subunit-subunit interactions are known.
DNA-directed RNA polymerase II subunit RPB1 - an enzyme that in humans is
encoded by the POLR2A gene and in yeast is encoded by RPO21. RPB1 is the largest
subunit of RNA polymerase II. It contains a carboxy terminal domain
composed of up to 52 heptapeptide repeats that are essential for
polymerase activity.The CTD was first discovered in the laboratory of C.J.
Ingles at the University of Toronto and by JL Corden at John's Hopkins
University. In combination with several other polymerase subunits, the RPB1
subunit forms the DNA binding domain of the polymerase, a groove in which the
DNA template is transcribed into RNA. It strongly interacts with RPB8.
RPB2 - the second-largest subunit that in combination with at least two other
polymerase subunits forms a structure within the polymerase that maintains
contact in the active site of the enzyme between the DNA template and the newly
synthesized RNA. RPB3 - the third-largest subunit. Exists
as a heterodimer with another polymerase subunit, POLR2J forming a core
subassembly. RPB3 strongly interacts with RPB1-5, 7, 10-12.
RNA polymerase II subunit B4 - encoded by the POLR2D gene is the fourth-largest
subunit and may have a stress protective role.
RPB5 - In humans is encoded by the POLR2E gene. Two molecules of this
subunit are present in each RNA polymerase II. RPB5 strongly interacts
with RPB1, RPB3, and RPB6. RPB6 - forms a structure with at least
two other subunits that stabilizes the transcribing polymerase on the DNA
template. RPB7 - encoded by POLR2G and may play a
role in regulating polymerase function. RPB7 interacts strongly with RPB1 and
RPB5. RPB8 - interacts with subunits RPB1-3,
5, and 7. RPB9 - The groove in which the DNA
template is transcribed into RNA is composed of RPB9 and RPB1.
RPB10 - the product of gene POLR2L. It interacts with RPB1-3 and 5, and
strongly with RPB3. RPB11 - the RPB11 subunit is itself
composed of three subunits in humans: POLR2J, POLR2J2, and POLR2J3.
RPB12 - Also interacting with RPB3 is RPB12.
Assembly RPB3 is involved in RNA polymerase II
assembly. A subcomplex of RPB2 and RPB3 appears soon after subunit synthesis.
This complex subsequently interacts with RPB1. RPB3, RPB5, and RPB7 interact with
themselves to form homodimers, and RPB3 and RPB5 together are able to contact
all of the other RPB subunits, except RPB9. Only RPB1 strongly binds to RPB5.
The RPB1 subunit also contacts RPB7, RPB10, and more weakly but most
efficiently with RPB8. Once RPB1 enters the complex, other subunits such as RPB5
and RPB7 can enter, where RPB5 binds to RPB6 and RPB8 and RPB3 brings in RPB10,
RPB 11, and RPB12. RPB4 and RPB9 may enter once most of the complex is
assembled. RPB4 forms a complex with RPB7.
Kinetics Enzymes can catalyze up to several
million reactions per second. Enzyme rates depend on solution conditions and
substrate concentration. Like other enzymes POLR2 has a saturation curve and
a maximum velocity. It has a Km and a kcat. The specificity constant is given
by kcat/Km. The theoretical maximum for the specificity constant is the
diffusion limit of about 108 to 109, where every collision of the enzyme with
its substrate results in catalysis. In yeast, mutation in the Trigger-Loop
domain of the largest subunit can change the kinetics of the enzyme.
The turnover number for RNA polymerase II is 0.16 s−1 subject to concentration.
Bacterial RNA polymerase, a relative of RNA Polymerase II, switches between
inactivated and activated states by translocating back and forth along the
DNA. Concentrations of [NTP]eq = 10 μM GTP, 10 μM UTP, 5 μM ATP and 2.5 μM CTP,
produce a mean elongation rate, turnover number, of ~1 bp−1 for bacterial RNAP, a
relative of RNA polymerase II. RNA Polymerase II is inhibited by
α-amanitin and other amatoxins. Holoenzyme
RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is
recruited to the promoters of protein-coding genes in living cells. It
consists of RNA polymerase II, a subset of general transcription factors, and
regulatory proteins known as SRB proteins.
Part of the assembly of the holoenzyme is referred to as the preinitiation
complex, because its assembly takes place on the gene promoter before the
initiation of transcription. The mediator complex acts as a bridge
between RNA polymerase II and the transcription factors.
Control by chromatin structure This is an outline of an example
mechanism of yeast cells by which chromatin structure and histone
posttranslational modification help regulate and record the transcription of
genes by RNA polymerase II. This pathway gives examples of
regulation at these points of transcription:
Pre-initiation Initiation
Elongation Please note that this refers to various
stages of the process as regulatory steps. It has not been proven that they
are used for regulation, but is very likely they are.
RNA Pol II elongation promoters can be summarised in 3 classes.
Drug/sequence-dependent arrest-affected factors
Chromatin structure-oriented factors RNA Pol II catalysis-improving factors.
Protein Complexes Involved Chromatin structure oriented
factors:(HMTs): COMPASS§† - - Methylates lysine 4 of
histone H3. Set2 - Methylates lysine 36 of histone
H3. (interesting irrelevant example: Dot1*‡
- Methylates lysine 79 of histone H3.) (Other): Bre1 - Ubiquinates lysine 123
of histone H2B. Associated with pre-initiation and allowing RNA Pol II
binding. = CTD of RNA polymerase =
The C-terminus of RPB1 is appended to form the C-terminal domain. The
carboxy-terminal domain of RNA polymerase II typically consists of up
to 52 repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. The RNA
Polymerase CTD was discovered first in the laboratory of C.J.Ingles at the
University of Toronto and also in the laboratory of J Corden at Johns Hopkins
University during the processes of sequencing the DNA encoding the RPB1
subunit of RNA polymerase from Yeast and Mice respectively. Other proteins often
bind the C-terminal domain of RNA polymerase in order to activate
polymerase activity. It is the protein domain that is involved in the
initiation of transcription, the capping of the RNA transcript, and attachment to
the spliceosome for RNA splicing. See also
RNA polymerase I RNA polymerase III
RNA polymerase II holoenzyme Post-transcriptional modification
Transcription Eukaryotic transcription
References External links
More information at Berkeley National Lab
RNA Polymerase II at the US National Library of Medicine Medical Subject
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