Chapter 22

mRNA Stability and Localization

22.2 Messenger RNAs Are Unstable Molecules
mRNA instability is due to the action of ribonucleases.
Ribonucleases differ in their substrate preference and
mode of attack.
endoribonuclease (endonuclease) A ribonuclease that
cleaves an RNA at internal site(s).
exoribonuclease (exonuclease) A ribonuclease that removes
terminal ribonucleotides from RNA.
llgure 22.02
22.2 Messenger RNAs Are Unstable Molecules
processive (nuclease) An enzyme that remains associated with the
substrate while catalyzing the sequential removal of nucleotides.
distributive (nuclease) An enzyme that catalyzes the removal of only
one or a few nucleotides before dissociating from the substrate.
mRNAs exhibit a wide range of half-lives.
llgure 22.03: MeLhod for deLermlnlng
m8nA half-llves.
22.2 Messenger RNAs Are Unstable Molecules
mRNA decay mRNA degradation, assuming that the
degradation process is stochastic.
Differential mRNA stability is an important contributor to
mRNA abundance and therefore the spectrum of
proteins made in a cell.
steady state (molecular concentration) The
concentration of population of molecules when the rates
of synthesis and degradation are constant.
22.3 Eukaryotic mRNAs Exist in the Form of
mRNPs from Their Synthesis to Their Degradation
mRNA associates with a changing population of proteins
during its nuclear maturation and cytoplasmic life:
ribonucleoprotein particles (RNPs).
Some nuclear-acquired mRNP proteins have roles in
the cytoplasm.
A very large number of RNA-binding proteins (RBPs)
exist, most of which remain uncharacterized.
Different mRNAs are associated with distinct, but
overlapping, sets of regulatory proteins, creating RNA
regulons.
22.4 Prokaryotic mRNA Degradation Involves
Multiple Enzymes
Prokaryotic mRNA degradation occurs during translation.
polyribosome (or polysome) An mRNA that is
simultaneously being translated by multiple ribosomes.
monocistronic mRNA mRNA that codes for one
polypeptide.
The main degradation enzymes work as a complex
called the degradosome.
22.4 Prokaryotic mRNA
Degradation Involves
Multiple Enzymes
Degradation of bacterial mRNAs
is initiated by removal of a
pyrophosphate from the 5!
terminus.
Monophosphorylated mRNAs
are degraded during translation
in a two-step cycle involving
endonucleolytic cleavages
(endonuclease such as RNase
E), followed by 3! to 5! digestion
(3-5 exonuclease such as
PNPase) of the resulting
fragments.
llgure 22.03: uegradauon of
bacLerlal m8nAs.
22.5 Most Eukaryotic mRNA is Degraded via Two
Deadenylation-Dependent Pathways
The modifications at both ends of mRNA protect it
against degradation by exonucleases: 5 cap & 3 poly(A)
tail
poly(A) binding protein (PABP) The protein that
binds to the 3! stretch of poly(A) on a eukaryotic mRNA.
22.5 Most Eukaryotic mRNA is Degraded via Two
Deadenylation-Dependent Pathways
The two major mRNA decay pathways are initiated by deadenylation
catalyzed by poly(A) nucleases (deadenylases).
Deadenylation may be followed either by decapping and 5! to 3!
exonuclease digestion or by 3! to 5! exonuclease digestion.
llgure 22.06: 1he ma[or deadenylauon-dependenL decay paLhways ln eukaryoLes.
22.5 Most Eukaryotic mRNA is Degraded via Two
Deadenylation-Dependent Pathways
The exosome, which catalyzes 3! to 5! mRNA digestion,
is a large, evolutionarily conserved complex.
Degradation may occur within discrete cytoplasmic
particles called processing bodies (PBs).
A variety of particles containing translationally repressed
mRNAs exist in different cell types.
maternal mRNA granules Oocyte particles containing
translationally repressed mRNAs awaiting activation later in
development.
neuronal granules Particles containing translationally
repressed mRNAs in transit to final cell destinations.
stress granules Cytoplasmic particles, containing
translationally inactive mRNAs, that form in response to a
general inhibition of translation initiation.
22.6 Other Degradation Pathways Target Specific
mRNAs
Deadenylation-independent decapping proceeds in the
presence of a long poly(A) tail ! processes after decapping
are similar to those in deadenylation-dependnet pathway.
llgure 22.08
22.6 Other Degradation Pathways Target Specific
mRNAs
The degradation of the nonpolyadenylated histone
mRNAs is initiated by 3! addition of a poly(U) tail.
llgure 22.08
22.6 Other Degradation Pathways Target Specific
mRNAs
Degradation of some mRNAs may be initiated by
sequence-specific or structure-specific endonucleolytic
cleavage.
llgure 22.08
22.6 Other Degradation Pathways Target Specific
mRNAs
An unknown number of mRNAs are target for
degradation or translational repression by microRNAs.
llgure 22.08
22.6 Other Degradation Pathways Target Specific
mRNAs
llgure 22.09: 1able summarlzlng key elemenLs of m8nA decay paLhways ln eukaryouc cells.
22.7 mRNA-Specific Half-Lives Are Controlled by
Sequences or Structures within the mRNA
Specific cis-elements in an mRNA affect its rate of
degradation: most common in 3UTR.
Destabilizing elements (DEs) can accelerate mRNA decay,
while stabilizing elements (SEs) can reduce it.
AU-rich elements (AREs) are common destabilizing
elements in mammals, and are bound by a variety of proteins.
Some DE-binding proteins interact with components of the
decay machinery and probably recruit them for degradation.
Stabilizing elements occur on some highly stable mRNAs.
mRNA degradation rates can be altered in response to a
variety of signals.
22.7 mRNA-Specific Half-Lives Are Controlled by
Sequences or Structures within the mRNA
llgure 22.10: Mechanlsms by whlch desLablllzlng elemenLs (uLs) and sLablllzlng elemenLs
(SLs) funcuon.
22.7 mRNA-Specific Half-Lives Are Controlled by
Sequences or Structures within the mRNA
iron-response element (IRE) A cis sequence found in
certain mRNAs whose stability or translation is regulated
by cellular iron concentration.
llgure 22.11: 8egulauon of Lransferrlng m8nA sLablllLy by lron levels.
22.8 Newly Synthesized RNAs Are Checked for
Defects via a Nuclear Surveillance System
Aberrant RNAs are identified and destroyed by an RNA
surveillance system In the nucleus and the cytoplasm.
The nuclear exosome functions both in the processing of
normal substrate RNAs and in the destruction of aberrant
RNAs.
The yeast TRAMP complex recruits the exosome to
aberrant RNAs and facilitates its 3! to 5! exonuclease
activity.
22.8 Newly Synthesized RNAs Are Checked for
Defects via a Nuclear Surveillance System
oligo(A) tail a short poly(A) tail, generally referring to a stretch of
less than 15 adenylates.
Substrates for TRAMP-exosome degradation include unspliced or
aberrantly spliced pre-mRNAs and improperly terminated RNA Pol II
transcripts lacking a poly(A) tail.
llgure 22.12: 1he role of 18AM and Lhe exosome ln degradlng aberranL nuclear 8nAs.
22.9 Quality Control of mRNA Translation Is
Performed by Cytoplasmic Surveillance Systems
Three types of mRNA defects are detected; all three
systems involve abnormal translation termnation.
release factor (RF) A protein required to terminate
polypeptide translation to cause release of the
completed polypeptide chain and the ribosome from
mRNA.
22.9 Quality Control of mRNA Translation Is
Performed by Cytoplasmic Surveillance Systems
Nonsense-mediated decay (NMD) targets mRNAs with
premature stop codons.
Recognition of a termination codon as premature involves
unusual 3! UTR structure or length in many organisms and
the presence of downstream exon junction complexes
(EJC) in mammals.
NMD requires Upf and Smg proteins.
pioneer round of translation The first translation event
for a newly synthesized and exported mRNA.
22.9 Quality Control of mRNA Translation Is
Performed by Cytoplasmic Surveillance Systems
llgure 22.14: 1wo mechanlsms by whlch a Lermlnauon codon ls recognlzed as premaLure.
llgure 22.13: SubsLraLes for cyLoplasmlc survelllance sysLems.
22.9 Quality Control of mRNA Translation Is
Performed by Cytoplasmic Surveillance Systems
Nonstop decay (NSD) targets mRNAs lacking an in frame
termination codon due to premature transcription
termination and requires a conserved set of SKI proteins.
No-go decay (NGD) targets mRNAs with stalled ribosomes
in their coding regions.
llgure 22.13: SubsLraLes for cyLoplasmlc survelllance sysLems.
22.10 Some Eukaryotic mRNAs Are Localized to
Specific Regions of a Cell
Localization of
mRNAs serves
diverse functions in
single cells and
developing
embryos.
llgure 22.16: 1hree maln funcuons of m8nA locallzauon.
22.10 Some Eukaryotic mRNAs Are Localized to
Specific Regions of a Cell
Localization requires (1) cis-
elements on the target mRNA,
(2) trans-factors to that attach
mRNA to motor protein, (3)
trans-factors repressing
translation, and (4) an
anchoring system at the
destination.
zipcode (in RNA) Any of the
number of RNA cis elements
involved in directing cellular
localization.
llgure 22.17: Locallzauon of Ash1
m8nA.