From the
Transposable elements in the yeast Saccharomyces cerevisiae consist of a family of retrotransposons, Ty 1(1) ,
Ty 2(2) , Ty 3(3) , Ty 4(4, 5) , and Ty 5(6) .
Ty elements are composites of an approximately 5-kilobase
central region flanked by long terminal repeats, LTRs
Ty elements encode a protein of the size predicted for the
TYA product and a second product of the size predicted for a
TYA- TYB fusion protein
(20, 21, 26, 27) . Expression of the
putative fusion protein as expected required continued translation
through TYA(20) . RNA mapping studies eliminated the
hypothesis that expression of TYB occurred by RNA splicing
(20, 21) . Another hypothesis, that the editing of the
transcript by eliminating one nucleotide might fuse the TYA and TYB reading frames, was definitively eliminated by
cDNA sequencing of the mRNA, which showed that the mRNA was colinear
with the DNA template
(28) .
What function does translational frameshifting serve for Ty
elements? Clearly, the near ubiquity among retroviruses and
retrotransposons of alternative translational events in generating
Gag-Pol fusion proteins (reviewed in Refs. 31 and 32) speaks to the
importance of this event in the life cycle of the elements. One purpose
of this mechanism is that it allows for regulation of the stoichiometry
of the structural ( i.e. Gag) and enzymatic (Pol) products,
which appears crucial for efficient reverse transcription
(33) .
Since reverse transcription occurs within gag-encoded viral
core particles, the gag portion of a Gag-Pol fusion protein
targets it to assemble as part of that core, placing the enzymatic
activities within the forming particle (reviewed in Ref. 34). The
second purpose of frameshifting relates to the fact that a packaging
signal, termed
The
fact that frameshifting is crucial to the life cycle of the element is
demonstrated by the fact that altering the efficiency of frameshifting
can interfere with transposition. Xu and Boeke
(37) demonstrated that overproducing the AGG-decoding
tRNA
Ty elements encode two primary translation products (except
Ty 5), both of which are proteolytically processed during
formation of mature virus-like particles (VLPs). A protease (PR),
encoded as part of the TYB gene, is responsible for this
proteolysis. Processing has been studied in both Ty 1 and
Ty 3 elements, with similar results (see Fig. 3
).
Early work on Ty 1 identified three predominant protein
products, termed p1 (58 kDa), p2 (54 kDa), and p3 (190 kDa)
(13, 26, 28, 43) . Two of the proteins
are primary products, p1 from the TYA gene and p3 as a fusion
product jointly encoded by TYA and TYB. The third,
p2, is a processed TYA product generated when PR removes an
extreme C-terminal oligopeptide
(13, 15) . The p2
protein is the major protein constituent of the VLPs
(13, 15) , the probable capsid protein (CA). PR also
processes the TYA- TYB polyprotein of Ty 1,
releasing three polypeptides: reverse transcriptase/RNase H (RT/RH, 60
kDa), integrase (IN, 90 kDa), and PR itself (23 kDa)
(14, 44) .
The defect of the PR-mutant VLPs appears to be that
cDNA synthesis is much reduced. Mutant Ty 3 particles had
background levels of reverse transcriptase, suggesting that processing
is essential for enzyme activity
(46) . This was, however, not
true for the unprocessed Ty 1 polyprotein. Though reverse
transcriptase was present, endogenous cDNA synthesis was reduced to
background levels
(16) . The VLPs contain about 10-fold less
RNA, either because of defective packaging or degradation, though it is
not clear how a 10-fold reduction could eliminate transposition.
Perhaps the VLPs also lack other required factors ( e.g. primer
tRNA
Sandmeyer
(17) has explained the inability of PR mutants to complement
differently by considering the need for PR to dimerize to become
activated
(52) . If PR is only active as a dimer then the PR
mutants could have a dominant negative effect (Fig. 3
).
However, dimerization is probably not sufficient to activate PR.
Mutations that fuse the TYA and TYB genes into one
open reading frame express only the TYA-TYB fusion protein. In both
Ty 1(37) and Ty 3(38) the expressed
polyprotein remained unprocessed, and neither protein would form VLPs.
In both cases, wild-type processing and transposition were restored by
expressing the capsid protein (CA). This demonstrates that the fusion
protein is not defective but rather that its processing requires CA.
Therefore, rather than concluding that PR activity is rate-limiting for
formation of transpositionally competent VLPs, Sandmeyer concludes that
VLP formation rather may be rate-limiting for activation of PR
(17) .
It is not clear how activation might depend on VLP
assembly. Three types of formal models might explain this dependence.
First, there could be a true allosteric interaction in which
association between a TYA-TYB dimer and TYA monomers induces a change
in the structure of PR that activates it. Second, PR may actually be
activated in the dimer, but its low concentration in the cell might
make it unable to process significant amounts of substrate. In a VLP
the effective concentration of PR and its substrates would be very
high, accelerating processing. Third, VLP formation may occur in
competition with some other fate, for example proteolytic degradation.
This would both limit the amount of the protein which could accumulate
so that even though PR might be activated by dimerization the low
concentration of protein would reduce the rate of processing. No data
on the stability of the Ty 1 fusion protein when not assembled
into VLPs has been published, but in the Ty 3 fusion appears to
be unstable
(38, 46) .
Dinman and
Wickner
(33) explain the effect of altering stoichiometry as
interfering with particle assembly. They believe that a dimer of the
Gag-Pol fusion protein nucleates formation of the L-A particle
(33) and proposed that increasing the proportion of fusion
protein might result in nucleating too many particles, none of which
are completely formed, while decreasing the fusion protein may
drastically decrease dimerization, interfering with nucleation so that
fewer particles form.
Studies with Ty elements suggest that the
defect is actually at the processing of Ty-encoded proteins
(42) . Normally Ty 1 expresses TYA-TYB (p190) at 3% the
level of TYA (p58)
(42) . Transposition is blocked when the
levels of p190 and p58 are equal. At this ratio p190 is incompletely
processed
(42) ; about half of the TYA-TYB protein accumulates
as p160, created by cleavage at the N terminus of PR (see Fig. 4
). This phenotype is very different from that caused
by expression of p190 in the absence of p58, which eliminates all
processing, as described above. Apparently, the abnormal ratio of the
primary translation products does not inactivate protease but blocks
efficient processing of p190. This result is also consistent with the
hypothesis that activation of PR requires an association between p190
and p58 or p54. It may be significant that the cleavage that occurs
releases the PR, IN, and RT/RH activities from their association with
CA and thus their physical connection to the VLP.
The sensitive response of the transposition to
the p190:p58 ratio suggests that Ty elements might use frameshift
efficiency to sense changes in cellular physiology. One would predict
that since frameshifting is very sensitive to the availability of the
particular slowly decoding aminoacyl-tRNAs, changes in aminoacylation
should reduce the likelihood of transposition. Balasundaram et al.(54, 55) have demonstrated that changing the
relative intracellular concentrations of the polyamines spermidine and
putrescine interferes both with +1 frameshifting on a
Ty 1-derived site and with transposition of Ty 1. The
mechanism of this interference is unclear, though changing the
polyamine pools could have a direct effect on ribosome structure
(altering rRNA structure? rearranging ribosomal proteins?) or could act
indirectly by interfering with tRNA aminoacylation. It is not clear if
the ability of Ty 1 to respond in this fashion to changes in
polyamine pools has any evolutionary significance or if it is merely
the unavoidable effect of the element depending on an unusual
translational event for its propagation.
Ty transposition is controlled at several
post-transcriptional steps: translational elongation, proteolytic
processing, and phosphorylation. Since transposition depends on several
other post-transcriptional events (packaging of tRNA primers, creation
of a cDNA copy of the Ty mRNA, insertion of the cDNA copy into a new
chromosomal location) it is likely that we will find that other
post-transcriptional events regulate transposition. The existence of
Ty 5 demonstrates that at least one other post-transcriptional
process can regulate transposition in yeast. Since Ty 5 encodes
all of its products from a single open reading frame, it cannot
regulate the critical ratio of structural and enzymatic products by
translational frameshifting. In this Ty 5 resembles both the
elements Tf 1 of Schizosaccharomyces pombe(56) and copia of Drosophila(57) . It
remains to be seen how Ty 5 adjusts the concentration of its
gag and pol analogs. copia does so by
alternative splicing
(58) , while Tf 1 appears to
degrade excess enzymatic proteins to adjust the gag: pol ratio.
Thanks to Dr. Dan Votyas and Dr. Henry Levin for
communicating results before publication and to Dr. Suzanne Sandmeyer
for critical reading of the manuscript.
ABSTRACT
INTRODUCTION
Structure of Ty Elements
Programmed Translational Frameshifting in Ty Elements
Relevance of Frameshifting to the Ty Life Cycle
Proteolytic Processing and Morphogenesis of the
Virus-like Particle
Summary and Perspectives
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
(
)
Ty elements transpose through an RNA intermediate using the
same replication and integration strategy employed by the metazoan
retroviruses
(7, 8, 9) . Because of this
similarity, they provide an attractive model for virus-host interaction
in a genetically tractable eukaryote. Much of the work on Ty elements
has therefore focused on the transposition cycle and its regulation.
Since the Ty mRNA has two roles, as messenger for Ty-encoded proteins
and as substrate for reverse transcription, alterations in the level of
Ty mRNA can drastically affect the efficiency of transposition
(10) . However, much of the regulation of transposition occurs
post-transcriptionally, including translational control (programmed
translational frameshifting
(11, 12) ) and
post-translational control (proteolytic processing
(13, 14, 15, 16) ). This review will
focus on recent advances in our understanding of post-transcriptional
regulation of transposition of Ty elements.
(
)
(Fig. 1
) (for a review see Refs. 17-19).
Transcripts of the Ty 1, Ty 2, and Ty 3 initiate in the 5`-LTR and terminate in the 3`-LTR, generating an
RNA with a short terminal duplication, a structure essential to the
process of reverse transcription. Like metazoan retroviruses, they
express one of their primary translation products by an unusual
mechanism. Ty elements include two open reading frames, TYA and TYB, which are analogous to the retroviral gag and pol genes, respectively.
(
)
As
expected for a eukaryotic mRNA, the first potential initiator codon in
the mRNAs of Ty elements is the AUG at the 5`-end of the TYA gene. One would predict that this RNA would express only the TYA
protein. This leaves open the question of how the TYB gene is
expressed since there is no subgenomic RNA that could be normally
translated to express TYB. In the mid-1980s it became clear that in Ty
elements
(20, 21, 22) , as in certain
retroviruses
(23) , expression of the downstream TYB gene occurred by translational frameshifting. The mechanism used
by Ty elements had to be different, since in retroviruses the pol gene overlaps the end of gag in the -1 frame, while
in Ty elements TYB overlaps the 3`-end of TYA in the
+1 frame. This difference in sign in turn reflects a profound
difference in mechanism between the two (reviewed in Refs. 24 and 25).
Figure 1:
The
structure of the five classes of Ty retrotransposons in S.
cerevisiae . Ty elements consist of an internal region
( openboxes) flanked by direct repeats
( triangles). The classes of elements can be distinguished by
the identity of the direct repeats: delta elements ( redtriangles), sigma elements ( bluetriangles), tau elements ( greentriangles), and pseudo-X elements ( purpletriangles). Each element encodes structural (CA and
nucleocapsid ( NC)) and enzymatic proteins (PR, IN, RT, and
RH). Ty 1, Ty 2, Ty 3, and Ty 4 each
include two open reading frames, TYA ( lightbluerectangle) encoding the structural protein(s) and TYB ( orangerectangle), encoding the enzymatic
activities. Note that for members of the Ty 1/ copia group (Ty 1, Ty 2, and Ty 4) the order of
enzymatic activities is PR-IN-RT/RH, while for Ty 3 (which
defines the Ty 3/ gypsy group) the order is
PR-RT/RH-IN. Ty 5 encodes only one protein ( violetrectangle; D. Voytas, personal communication); the order
of enzymatic activities encoded has not been reported. kb,
kilobase.
Frameshifting Induced by tRNA Slippage
Though this
experiment essentially settled the issue of whether a translational
mechanism were involved, it left open the question of the nature of the
mechanism. The first mechanism to be extensively studied was that of
Ty 1(11) . The first surprise was that a very short
nucleotide sequence promoted efficient frameshifting. A sequence of
only seven nucleotides, CUU-AGG-C (shown as codons of the upstream
TYA gene) is sufficient to induce maximal levels of
frameshifting (Fig. 2A). How could such a short
oligonucleotide sequence cause up to 40% of ribosomes to change reading
frame? The answer turns out to be a simple one. A ribosome that has
decoded the CUU codon and has a peptidyl-tRNA bound to
that codon in the ribosomal P site pauses because of the low
availability of the AGG-decoding tRNA
.
During the pause, peptidyl-tRNA
slips
+1 onto the overlapping Leu codon (UUA). After peptidyl-tRNA
slippage translational elongation resumes in the new +1 reading
frame, leading to the expression of the TYA-TYB fusion peptide.
Figure 2:
Ty
elements employ two distinct +1 frameshift mechanisms. The TYB gene is expressed as a translational fusion to the upstream
TYA gene by a process of translational frameshifting.
A, frameshifting in Ty 1, Ty 2, and Ty 4 elements. The ``slippery''
tRNA is pictured in blue,
recognizing its cognate codon CUU by two-out-of-three decoding (32).
Normal decoding of the in-frame AGG codon ( red) occurs slowly
because of the low availability of its cognate tRNA
tRNA
( red). During a translational
pause caused by the slow recognition of AGG,
tRNA
( violet) probably transiently
binds to the +1 frame codon GGC, followed by slippage of
tRNA
+1 to the UUA codon (11, 74).
B, frameshifting in Ty 3 elements (12). After
recognition of the GCG codon by tRNA
(both
in blue), the slow recognition of AGU by
tRNA
(both in red), allows
recognition of the +1 frame codon GUU by
tRNA
(both in violet). The
presence of peptidyl-tRNA
allows the
out-of-frame tRNA to be accepted by the ribosome, allowing peptide
transfer to occur, shifting reading into the +1 frame (30,
59).
This
mechanism is stochastic. The translational pause induced by slow
recognition of the AGG codon allows sufficient time for a proportion of
paused ribosomes to shift into the new frame. The probability that an
individual ribosome will shift reading frame depends on the length of
the pause and on the propensity for the tRNA to slip. Curran has shown
in Escherichia coli that the ``slipperiness'' of a
tRNA is related to the stability of its interaction in the shifted
frame
(29) . The results of mutagenesis of the Ty 1 frameshift site were generally consistent with this conclusion
(11) . Unexpectedly, though this feature seems to be sufficient
to predict frameshift efficiency in E. coli, it is not
sufficient in yeast. Clearly, there is something about frameshifting in
yeast that is unlike frameshifting in E. coli.
Unconventional Frameshifting without tRNA
Slippage
An understanding of this difference emerged only after
a detailed analysis of the Ty 3 frameshift expression of the
GAG3-POL3 fusion protein
(12) . The minimal frameshift site in
Ty 3 is a 21-nucleotide region of the GAG3- POL3 overlap shown in Fig. 2B. However, again a
7-nucleotide region, GCG-AGU-U, is essential for frameshifting; the
other 15 nucleotides, a downstream ``context,'' stimulate
frameshifting 7.5-fold but are not essential. Frameshifting occurs
while tRNA is bound to the GCG codon by
reading of the +1 frame Val codon, GUU. Frameshifting again is
stimulated by a slowly decoded codon, AGU, in the ribosomal A site.
Unexpectedly, though, frameshifting must occur without peptidyl-tRNA
slippage since the tRNA
cannot base pair
with the +1 frame CGA codon. More recently, saturation mutagenesis
of the Ty 3 frameshift site has shown that there is no
correlation between that ability of the peptidyl-tRNA to slip and the
efficiency of frameshifting
(30) . It appears that some other
feature(s) of some tRNAs allows them to promote frameshifting by
directing out-of-frame binding of incoming aminoacyl-tRNA. What those
feature(s) are remains to be determined.
, is present within the gag gene, which
directs insertion of the mRNA into the forming viral core
(35) .
If the Gag-Pol fusion were made by some pretranslational mechanism, an
mRNA would be produced in which the two genes would be in-frame and
which could be packaged into core particles
(36) . An element in
which the gag and pol genes are fused is not capable
of futher replication
(37, 38, 39, 40) .
Thus, the putative gag- pol splice would lead to
generation of defective particles. Thus frameshifting provides a
morphogenetic tool while avoiding a potential genetic problem.
caused a drastic decrease in
transposition. Kawakami et al.(41) later identified a
strain deleted for the only gene encoding
tRNA
, termed HSX1. Surprisingly,
the
hsx1 strain is viable, presumably because AGG
continues to be decoded by the near-cognate tRNA specific for AGA.
However, in the
hsx1 strain frameshifting at the Ty 1 site was dramatically increased, and concomitantly, transposition
of Ty 1 was drastically reduced
(42) . The defect
appears to be at the level of proteolytic processing
(42) , as
described below in detail. Thus, changes either increasing or
decreasing the efficiency of frameshifting can have a profound effect
of transposition of the element by altering the very sensitive
stoichiometry of Ty 1 gene expression.
Figure 3:
Proteolytic
processing of Ty1-encoded proteins and the effect of TYB mutations. Ty 1-encoded activities are depicted: bluecircles, capsid; orangecircles,
protease; greenroundedrectangle,
integrase; and violetroundedsquare,
reverse transcriptase/RNase H. Normal processing is shown of the
TYA product (p58 p54) and the TYB product
(p190
p54 + p160; p160
p23 + p140; p140
p90 + p60). The proposed activation of PR by dimerization is
indicated by the presence of a stylized mouth. Normal processing of an
RT/RH mutant form of the TYB product when complemented by
endogenous wild-type (WT) protein is shown; monomers of p60 that are
released by proteolysis presumably may dimerize within the VLP.
Abnormal processing of a PR mutant form of TYB is shown. All
processing is blocked by this mutant, even in the presence of
endogenous wild-type proteins. Normally processed forms that are not
found are shown stippled.
Processing of the Ty 3 GAG3 and
GAG3- POL3 products is grossly similar. Processing of
the POL3 product produces mature PR (16 kDa), RT/RH (55 kDa),
and IN (alternative products of 58 and 61 kDa), while processing of the
GAG3 product yields capsid (CA, 26 kDa) and nucleocapsid (9 or
11 kDa) proteins
(45, 46, 47) . Ty 3 VLPs also include smaller amounts of three more products derived
from GAG3: an N-terminal 31-kDa fragment, the 38-kDa primary
translation product of GAG3, and a 39-kDa product apparently
derived from the GAG3- POL3 fusion
(38, 46) . The precise locations of the processing sites
in the Ty 3 polyprotein identified a consensus hydrophobic
region apparently recognized by PR
(46) .
Blocking Processing Interferes with
Transposition
Proteolytic processing of the TYA- TYB polyprotein is essential for transposition by Ty 1 and
Ty 3. Mutant Ty 1 elements with either short
oligonucleotide insertions into or deletions of PR appeared to abolish
transposition
(16) . Mutating a conserved active site residue of
the Ty 3 PR had the same effect
(46) . All of the
mutants produced morphologically abnormal VLPs containing unprocessed
primary translation products. A processed POL3 product of 115
kDa, which accumulated in the Ty 3 mutant, probably
corresponding to a fusion of IN and RT/RH, could have been generated by
the action of endogenous PR (from cellular elements) or by the action
of another protease
(46) , though similar protease-independent
processing of Ty 1 proteins appears to have been artifactual
(48) .
). It is still not clear though why reverse
transcriptase activity in Ty 3 requires processing while
processing is irrelevant for the Ty 1 enzyme. The Problem of Transpositional Dormancy: Why Don't Ty Elements
Jump?-The longest standing conundrum in Ty 1 phenomenology is the fact that a modest increase in transcription
of Ty 1 elements, as when a Ty driven by an active heterologous
promoter is introduced into cells, yields a disproportionate increase
in transposition
(7) . Two models have been proposed to explain
this problem
(49) . First, defective Ty elements could interfere
with transposition either by accumulating in place of active elements
or by interfering in trans with the transposition of active
elements, a dominant negative effect. Since most Ty 1 and
Ty 2 elements are transpositionally competent
(49, 50) this cannot be the case. Second, an endogenous
transpositional inhibitor might block protein synthesis, or processing,
or interfere with Ty-encoded enzymatic activities. Overexpressing a Ty
transcript in this model would titrate the inhibitor. The inhibitor
cannot be a translational repressor since overexpression causes only
the expected proportional increase in translation
(51) .
Inefficient Protein Processing Causes Transpositional
Dormancy
If transpositional dormancy is not a genetic effect of
defective elements or an effect of reduced translation, then it must be
a post-translational effect. Overexpression of a Ty element causes a
large increase in production of VLPs. The effect is not limited to the
overexpressed element since transposition of endogenous elements also
increases. Overexpression can be thought of as complementing the
transpositional dormancy of endogenous elements. Surprisingly,
complementation works both ways since genomic elements can complement
overexpressed mutant elements. Curcio and Garfinkel
(51) showed
that endogenous elements can complement all introduced RT/RH mutants
and most IN mutants. However, all PR mutants and some IN mutants (those
with an apparent partial PR defect) could not be complemented. They
concluded that though endogenous elements express sufficient RT/RH and
IN activity to support transposition, the lack of sufficient endogenous
PR activity may block efficient transposition. The idea that
transpositional dormancy involves a lack of PR is validated by the fact
that endogenous proteins are not completely processed and that
overexpression enhances processing
(51) .
Altering the Stoichiometry of Ty-encoded Proteins
Interferes with Proteolytic Processing
The ratio of TYA to
TYA-TYB is crucial to efficient transposition. Changes in frameshift
efficiency, which either increase
(37) or decrease
(42) the ratio of TYA-TYB to TYA, reduce transposition.
Replication of the endogenous yeast virus L-A also strictly depends on
the efficiency of frameshifting between its gag and pol analogs
(33) . The effects of changes in stoichiometry were
particularly acute for L-A virus. L-A also employs translational
frameshifting in its gene expression
(53) . Propagation of
M, a satellite form of this RNA, depends on expression of
the L-A gene products. Its maintenance is exquisitely sensitive to
alteration in frameshift efficiency
(33) . The stringency of the
assay used may overestimate the effect on transposition. It may be that
the M
satellite is eventually lost even if the efficiency
of its replication is reduced by such a small amount.
Figure 4:
The effect of an increased ratio of
TYB to TYA products caused by overexpression of
TYB . Processing of Ty 1-encoded proteins is
pictured as in Fig. 4. Overexpression of TYB (as the TYA-TYB
fusion p190) relative to TYA (p58) results in abnormal
proteolytic processing. The only processing observed is p58 p54
and p190
p54 + p160; note that both of these events involve
cleavage at the same site, between CA and PR. Again, those forms not
found are shown stippled.
The model of
Dinman and Wickner
(33) predicts that overexpressing the
TYA-TYB fusion p190 should result in incompletely formed VLPs. Kawakami
et al.(42) show that partially processed proteins
accumulate in the VLP fraction (data not shown), but they do not report
whether the VLPs are normal or aberrant. It is not clear why partial
assembly of VLPs should result in completely processed TYA protein (to
p54) and incomplete processing of p190. It will be interesting to see
if the processing efficiency increases continuously with a decreasing
p190:p58 ratio. This would indicate that titrating p190 progressively
reduces some unknown block to processing, allowing a gradual increase
in the efficiency of each processing step. Alternatively, as the ratio
approaches the wild type the fully processed proteins may accumulate
without any other processing intermediates. This would suggest that
excess p190 causes the formation of an alternative structure, which
processes improperly, and that as the ratio declines a greater
proportion of wild-type VLPs accumulate in which the proteins are
properly processed.
(
)
Use of yeast genetics should allow
the identification of host-encoded factors responsible for
post-transcriptional control of transposition.
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.