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RNA
Processing -
Once
transcription
has
begun,
it
is
likely
that
the
RNA
polymerase
works
like
that
in
bacteria,
though
details
are
not
well
known.
Details
of
termination
are
likewise
less
well
defined.
Termination
signals
of
eukaryotic
genes
read
by
RNA
polymerases
I
and
III
seem
to
be
poly(U)
sequences
embedded
in
GC-rich
regions.
The
same
goes
for
prokaryotic
termination
signals.
The
termination
signals
for
eukaryotic
genes
read
by
RNA
polymerase
II
have
not
yet
been
determined.
The
RNA
that
is
the
product
of
transcription
is
not
immediately
useful
as
mRNA.
It
is
more
properly
called
nRNA
or
hnRNA
(nuclear
RNA
or
heterogeneous
nuclear
RNA).
This
reflects
the
fact
that
this
RNA
must
pass
through
another
set
of
steps,
called "RNA
processing",
before
it
can
be
translated.
Most
of
the
hnRNA
is
unstable
and
quickly
breaks
down
in
the
nucleus.
Only
a
small
fraction
is
selected
for
processing.
Despite
the
importance
of
selection
in
the
eventual
expression
of
the
genetic
information
contained
in
the
RNA
base
sequence,
it
is
not
known
how
that
fraction
is
selected.
We
do
know
that
selection
is
not
random.
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Processing
and
maturation
of
mRNA
precursors
in
eukaryotic
cells
involves
a
number
of
steps.
The
first
step
in
RNA
processing
is
capping,
Le.,
the
addition
of
a
cap
structure
to
the
5'-end
of
the
RNA
by
the
enzyme
guanyl
transferase.
This
cap
consists
of
a
7-methyl
guanosine
residue
attached
in
inverted
(Le.,
5'-5')
orientation.
Caps
have
been
demonstrated
in
a
number
of
plant
messenger
RNAs,
for
example
from
Avena
sativa,
and
appear
to
increase
the
efficiency
of
translation,
although
uncapped
messages
can
also
be
translated.
The
structure
of
the
cap
is
given
in
Figure
1.8.
This
cap
is
connected
so
that
its
5'-end
is
attached
to
the
triphosphate
at
the
5'-end
of
the
RNA,
thus:
G(5')ppp(5')NpNp
(N
stands
for
any
ribonucleoside).
As
part
of
capping,
methyl
groups
are
added
to
the
7
-carbon
of
the
terminal
G
and
some times
,to
adjacent
bases.
A
second
processing
step
involves
cleavage
of
the
nRNA
to
form
a
new
3'-end.
The
3'-end
is
then
elongated
with
a
chain
of
adenosines.
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A
sequence
AAUAAA
is
located
6
to
26
bases
from
the
cleavage
sites
of
almost
all
animal
cell
nRNAs
and
is
required
for
efficient
cleavage.
Polyadenylation,
catalyzed
by
the
enzyme
poly(A)
polymerase,generally
follows
cleavage
but
does
not
specifically
require
the
AAUAAA
sequence.
Seventy
percent
of
the
RNAs
destined
to
become
messengers
get
a
poly(A)
tail,
which
is
called
poly(A)
+
RNA.
Poly
(A)
tails
have
been
found
on
many
plant
messenger
RNAs
including
those
for
hordein,
a
small
subunit
of
ribulose
bisphosphate
carboxylase
(RuBPCase)
and
leg
hemoglobin.
The
length
of
the
tail
is
variable,
reaching
up
to
200
residues.
Apart
from
a
possible
role
in
increasing
the
stability
of
mRNA,
the
function
of
the
poly
(A)
tail
is
not
understood.
A
third
processing
step
is
related
to
the
genetic
structure
of
eukaryotic
DNA.
When
coding
sequences
(exons)
are
separated
by
introns,
the
whole
assembly
(exons
plus
introns)
is
transcribed
onto
one
nRNA.
Then
the
introns
are
removed
and
the
coding
sequences
spliced
together.
The
mechanism
of
this
reaction
and
the
way
in
which
the
intron-exon
junctions
are
so
carefully
delimited,
was
a
mystery
when
the
process
was
first
discovered.Then
it
was
found
that
ribosomal
RNA
from
Tetrahymena
catalyzes
the
removal
of
its
own
intron
without
the
aid
of
an
enzyme.
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It
thus
seems
possible
that
a
similar
process
occurs
with
nRNA
in
the
process
of
becoming
mRNA.
Other
steps
in
the
processing
of
nRNA
include
a
complexing
with
several
proteins
and
small
RNA
molecules
found
in
the
nucleus
to
form
a
body
called
a "splicesome".
The
proteins
and
small
RNAs
probably
hold
the
ends
of
the
RNA
together
during
the
splicing
process
and
may
contribute
to
the
accuracy
and
specificity
of
the
process.
Eventually,
the
RNA
is
transported
out
of
the
nucleus
and
into
the
cytoplasm,
where
it
can
be
translated.There
is
considerable
evidence
that
cells
regulate
the
RNA
processing
steps
so
that
only
subsets
of
nRNAs
become
mRNAs.
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The
subset
differs
in
differentiated
cells
of
various
types.
Liver
and
kidney
tissues
in
mice
have
the
same
base
sequences
in
their
nRNAs
but
different
subsets
of
base
sequences
in
their
mRNAs.
The
same
holds
true
for
tobacco
plants.
In
tobacco
plants
both
stem
and
leaf
tissues
have
nRNA
base
sequences,
which
total
about
108
bases;
about
three-quarters
of
these
base
sequences
are
present
in
both
tissues.
The
base
sequences
in
the
mRNAs
of
stems
and
leaves
total
only
about
3
x
107
bases
and
very
few
of
these
sequences
are
present
in
both
tissues.
Therefore,
most
of
the
nRNA
that
is
translated
from
active
DNA
templates
is
broken
down
and
only
a
selected
fraction
is
processed
into
mRNA
and
transported
to
the
cytoplasm.Of
course,
if
there
are
control
signals
that
influence
translation,
the
mRNA
may
not
be
translated
even
if
it
reaches
the
cytoplasm.
One
possible
alternative
fate
for
the
messenger,
albeit
temporary,
is
to
be
complexed
with
protein
to
make
a "ribonucleoprotein" (RNP)
stored
in
an
inactive
state.
This "masked
messenger
RNA" was
originally
discovered
in
sea
urchin
eggs.
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Pre
transcribed
and
preprocessed
mRNA
is
stored
in
sea
urchin
eggs,
ready
to
be
translated
following
fertilization.
A
similar
protein
complexed
mRNA
has
been
found
in
wheat-seed
embryos.
Conceivably,
it
serves
a
similar
function
in
the
early
stages
of
germination.Another
alternative
fate
of
mRNA
is
decay.
An
mRNA
will
eventually
be
broken
down
by
nucleases
in
the
cytoplasm.
In
general,
mRNA
lasts
much
longer
in
eukaryotes
than
in
prokaryotes
(hours
instead
of
minutes)
but
the
rate
of
breakdown
varies
widely,
and
sometimes
specifically,
for
certain
mRNAs.
For
instance,
the
stability
of
the
mRNA
for
nitrate
reductase
in
cultured
plant
cells
may
vary
as
much
as
two
fold,
depending
on
the
presence
or
absence
of
a
source
of
reduced
nitrogen
for
the
cells nutrition.
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