Atomic structure
of 14-subunit RNA
polymerase I: insight into
ribosomal RNA synthesis
We have determined the first
crystallographic structure of RNA
polymerase I, a large and complex
enzyme responsible of one of the
fundamental mechanisms of all eukaryotic
cells. This work was conducted in a
collaboration between Christoph Müller’s
team at the European Molecular Biology
Laboratory (EMBL) in Heidelberg, Carlos
Fernández-Tornero’s lab at the Centro
de Investigaciones Biológicas in Madrid,
and researchers from the University
of Göttingen and SOLEIL synchrotron,
where some of the structural data
was obtained. Structural data was also
obtained at the Petra III ring at EMBL
Hamburg.
Although first life forms are thought
to have been initiated exclusively
by RNA molecules, all known living
organisms on earth are now relying
on three specialized molecule types
to build up their core machinery: DNA,
RNA and proteins. RNA molecules are
synthesized from DNA templates by RNA
polymerases. There are three different
RNA polymerases in eukaryotes (such as
animals, plants, fungi) nucleus that are
each specifically regulated and devoted
to synthesize dedicated RNA molecules.
All are multisubunit complexes. RNA
polymerase II (Pol II) makes a precursor
of messenger RNA that carries genome
information to ribosomes to make proteins.
RNA polymerases I (Pol I) and III make
parts of the machinery which reads that
messenger RNA: Pol I builds the RNA that
will eventually built into the ribosome
(rRNA), while Pol III makes the transfer
RNA (tRNA) that carries the protein
building blocks to the ribosome. While the
crystallographic structure of Pol II – the
most studied type – is known since 2001
[1], obtaining detailed information on the
structures of Pol I has proven extremely
difficult. Part of the difficulty is that Pol I is
bigger (590 versus 550 kDa) and contains
more subunits (14 versus 12) than Pol II.
While the overall architecture and
horseshoe shape of Pol I is similar to that
of Pol II, this new structure reveals some
important insight that helps to understand
some of its specific features, like its high
productivity: its product, rRNA, being the
most abundant RNA in eukaryotic cells.
To achieve this high synthesis rates, we
have found that the Pol I A12.2 subunit
contains a domain that is remarkably
similar to TFIIS, a separate protein that
Pol II transiently recruits in case of
transcription pauses or to cleave wrongly
synthesized RNA. Achieving the same
function through a permanently integrated
factor allows Pol I to avoid long arrests and
thus to achieve higher transcription rates.
In another part of the molecule, a simple
pivoting of the A43-A14 subcomplex could
be sufficient to switch between active or
inactive conformation of Pol I, whereas in
the Pol II case the functional equivalent
subcomplex (Rpb4-Rpb7) forms a more
detachable element. Two other specific
subunits (A49-A34.5, equivalent to TFIIF)
form a tight complex anchored onto Pol
I by what looks like two extended arms,
one contributed by each supplementary
subunit (see figure1). The interaction
of this subcomplex with part of A12.2
explains its positive effect on A12.2
dependent RNA cleavage.
All these differences suggest that
eukaryotic cells have fewer ways of
controlling Pol I’s activity, since they
cannot influence it by regulating the
availability of helper proteins as it is the
case for RNA polymerase II. This is where
another finding becomes interesting:
One specific feature of Pol I discovered
in this structure is what we have called
the “DNA-mimicking loop”, an extended
conserved loop that occupies the position
of transcribed DNA in the enzyme’s
cleft, close to the active site. This could
be a built-in regulatory mechanism: its
positioning could promote or inhibit the
enzymatic activity.
Together, these findings can help to
explain why this enzyme works faster
than its Pol II counterpart: rather than
relying on certain external components
or rearrangements, Pol I has them already
integrated, which also explains why it is
bigger, and less regulated, but at the same
time more efficient.
BIOLOGY AND HEALTH SCIENCES
62
SYNCHROTRON
HIGHLIGHTS
2013
