Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

326 Chapter 6: How Cells Read the Genome: From DNA to Protein
and other RNA debris (excised intron sequences, for example) are retained in the
nucleus, where they are eventually degraded by the nuclear exosome, a large protein
complex whose interior is rich in 3ʹ-to-5ʹ RNA exonucleases (Figure 6–36).
Eukaryotic cells thus export only useful RNA molecules to the cytoplasm, while
debris is disposed of in the nucleus.
Of all the proteins that assemble on pre-mRNA molecules as they emerge from
transcribing RNA polymerases, the most abundant are the hnRNPs (heterogeneous
nuclear ribonuclear proteins). Some of these proteins (there are approximately
30 different ones in humans) unwind the hairpin helices in the RNA so
that splicing and other signals on the RNA can be read more easily. Others preferentially
package the RNA contained in the very long intron sequences typical
in complex organisms (see Figure 6–31) and these may play an important role in
distinguishing mature mRNA from the debris left over from RNA processing.
Successfully processed mRNAs are guided through the nuclear pore
complexes (NPCs)—aqueous channels in the nuclear membrane that directly
connect the nucleoplasm and cytosol (Figure 6–37). Small molecules (less than
60,000 daltons) can diffuse freely through these channels. However, most of the
macromolecules in cells, including mRNAs complexed with proteins, are far too
large to pass through the channels without a special process. The cell uses energy
to actively transport such macromolecules in both directions through the nuclear
pore complexes.
As explained in detail in Chapter 12, macromolecules are moved through
nuclear pore complexes by nuclear transport receptors, which, depending on the
identity of the macromolecule, escort it from the nucleus to the cytoplasm or vice
versa. For mRNA export to occur, a specific nuclear transport receptor must be
loaded onto the mRNA, a step that, in many organisms, takes place in concert
with 3ʹ cleavage and polyadenylation. Once it helps to move an RNA molecule
through the nuclear pore complex, the transport receptor dissociates from the
mRNA, re-enters the nucleus, and is then used to export a new mRNA molecule.
The export of mRNA–protein complexes from the nucleus can be readily
observed with the electron microscope for the unusually abundant mRNA of the
insect Balbiani Ring genes. As these genes are transcribed, the newly formed RNA
is seen to be packaged by proteins, including hnRNPs, SR proteins, and components
of the spliceosome. This protein–RNA complex undergoes a series of structural
transitions, probably reflecting RNA processing events, culminating in a
curved fiber (see Figure 6–37). This curved fiber moves through the nucleoplasm
and enters the nuclear pore complex (with its 5ʹ cap proceeding first), and it then
undergoes another series of structural transitions as it moves through the pore.
These and other observations reveal that the pre-mRNA–protein and mRNA–protein
complexes are dynamic structures that gain and lose numerous specific proteins
during RNA synthesis, processing, and export (Figure 6–38).
The analysis just described has been complemented by new methods that
allow researchers to track the fate of more typical mRNA molecules, which can
Figure 6–36 Structure of the core of
human RNA exosome. RNA is fed
into one end of the central pore and is
degraded by RNAses that associate
with the other end. Nine different protein
subunits (each represented by a different
color) make up this large ring structure.
MBoC6 n6.600/6.36
Eukaryotic cells have both a nuclear
exosome and a cytoplasmic exosome; both
forms include the core exosome shown
here and additional subunits (including
specialized RNAses) that differentiate the
two forms. The nuclear exosome degrades
aberrant RNAs before they are exported to
the cytosol. It also processes certain types
of RNA (for example, the ribosomal RNAs)
to produce their final form. The cytoplasmic
form of the exosome is responsible for
degrading mRNAs in the cytosol, and is
thus crucial in determining the lifetime of
each mRNA molecule. (PDB code: 2NN6.)
NUCLEUS
CYTOSOL
RNA as it emerges
from RNA
polymerase
“export-ready”
RNA
nuclear pore
complex
chromatin
TRANSCRIPTION
NUCLEUS
CYTOPLASM
(A)
(B)
200 nm
Figure 6–37 Transport of a large mRNA molecule through the nuclear pore complex. (A) The maturation of an mRNA molecule as it is
synthesized by RNA polymerase and packaged by a variety of nuclear proteins. This drawing of an unusually large and abundant insect RNA, called
the Balbiani Ring mRNA, is based on electron microscope micrographs such as that shown in (B). (A, adapted from B. Daneholt, Cell 88:585–588,
1997. With permission from Elsevier; B, from B.J. Stevens and H. Swift, J. Cell Biol. 31:55–77, 1966. With permission from The Rockefeller
University Press.)