trans

72 POST-TRANSCRIPTIONAL REGULATION
a decapping enzyme complex. In yeast, decapping
involves at least two proteins, Dcp1p and
Dcp2p. The removal of the cap leaves the naked
5-end of the RNA exposed for degradation by
5→ 3 exonucleases. Usually, the enzyme
Xrn1p is the main enzyme involved. There is
evidence that capping and 5→ 3 degradation
enzymes are linked in a larger complex including
seven other proteins, which presumably
has some regulatory role. Although yeast lacking
XRN1 and DCP1 genes are viable, they grow
poorly and accumulate partially degraded
RNAs. Yeast have another 5→ 3 exonuclease,
Rat1p, which is normally found in the nucleus.
If the nuclear targeting signal of Rat1p is
removed the protein stays in the cytoplasm;
then it can complement the defect in XRN1.
The cells that were just mentioned, which
have a defective 5→ 3 degradation pathway,
can only live because another system is there
to eliminate unwanted mRNA. This system
degrades the mRNAs from the other end. The
enzymes involved in this 3→ 5 degradation
are found in a complex called the exosome
(Figure 4.2D). The exosome is involved in maturation
of several stable RNAs, such as rRNA
and U RNAs, as well as in 3→ 5 degradation of
mRNAs, so mutations and deletions that eliminate
exosome function are lethal. The yeast
exosome has a molecular weight of 350 kDa
and contains at least eleven subunits, all of
which are probably 3→ 5 exonucleases in their
own right. Many stable RNAs have to be very
precisely trimmed to give the correct product.
The association of the different enzymes may
be important in regulation or coordination
of these processes; mutations in the different
enzymes have subtly different phenotypes.
Additional proteins may be associated with the
exosome in different cellular compartments,
to give a further level of regulation.
In general, the basal components of the RNA
degradation machinery, including the 5→ 3
exonucleases and the exosome, are conserved
from yeast to mammals. However, mammals
have some mechanisms that have not yet been
found in yeast. Probably the best understood
example is the regulation of transferrin receptor
mRNA, shown in the lower part of Figure
4.2. Transferrin receptor is needed for the cell
to take up iron. The transferrin mRNA has an
IRE structure, just like the ferritin mRNA, but
this time the IRE is in the 3-untranslated
region. Degradation of this mRNA is initiated
by cleavage within this IRE. When there is little
iron, the IRP binds the IRE and stops the
degradation (Figure 4.1E, F, G). Thus transferrin
receptor is only produced when there is little
iron available – a mode of regulation complementary
to that of ferritin, which is only needed
when iron is in excess (see above). There are
several other examples of endonuclease cleavage
within 3-untranslated regions, but despite
intensive efforts the endonucleases responsible
have not been definitively identified.
Many mammalian mRNAs involved in cell
growth and differentiation contain destabilizing
elements in the 3-untranslated region which
are rich in A and U residues. These ‘AU rich
elements’ (AREs) often contain copies of the
sequence AUUUA (or similar). Several proteins
that bind to AREs have been identified
(Figure 4.2G). It is suspected that some of these
proteins serve to protect the ARE-containing
mRNAs from degradation, whereas others may
stimulate degradation, but in no case is the
precise function clear. One possibility is that
the ARE stimulates deadenylation of the transcript;
alternatively, the ARE may be targeted
by an endonuclease, like the IRE.
Protein degradation and modification
Modification and degradation of proteins are
the final stages in post-transcriptional regulation.
The activities of many enzymes are
MOLECULAR BIOLOGY