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Department of Animal and Dairy Sciences, Program in Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849-5415;
Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands; and
Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154 .
**
*
3To whom correspondence should be addressed. E-mail: jwower{at}acesag.auburn.edu
 |
ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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KEY WORDS: • 10Sa RNA • SsrA RNA • tmRNA • trans-translation • peptide tagging
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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). Such a high level of
precision is achieved by intricate surveillance mechanisms of the gene
transcription into messenger RNA
(mRNA)4
and its translation into a protein molecule. Translation requires
sophisticated protein synthesis apparatus (the ribosome), and consumes
up to 50% of the energy generated by rapidly growing bacteria
(2
). Not only protein synthesis is regulated
(3
), but also aminoacylation of tRNAs (4
, 5
).
Initiation of translation is the rate-limiting step of protein
synthesis and is tightly regulated (6
). Less is known
about the control of elongation, a process viewed as the orderly
incorporation of amino acid residues into a growing peptide chain
according to the trinucleotide code of mRNA. There is evidence that
protein elongation is also carefully monitored. For instance, the
elongation rate appears to be variable and the ribosome may pause
because of rare codons, a limited supply of certain aminoacyl-tRNA
species, or the formation of stable structures in certain regions of
the mRNA. These factors might induce binding of noncognate
aminoacyl-tRNAs to mRNA-programmed ribosomes, frameshifting,
and sliding of the peptidyl-tRNA:ribosome complex over a 5–50
nucleotide-long segment of mRNA to resume translation further along
the decoded message (7
). When no stop codon is
encountered, elongation ceases and the peptidyl-tRNA:ribosome complex
is trapped at the 3' end of mRNA. Recent studies indicate that stalled
ribosomes are rescued by a surveillance and quality-control process
called trans-translation (8
). Although the
details of trans-translation are not yet fully understood,
it requires two adaptor molecules, tRNA and tmRNA (previously called
10Sa RNA). tmRNA resumes elongation by accepting the truncated
polypeptide from peptidyl-tRNA and provides an open reading frame
followed by two stop codons. The open reading frame encodes a short
peptide that signals a number of proteases to digest the truncated
tagged protein. tmRNA forms a ribonucleoprotein complex, the tmRNP,
with the elongation factor Tu (9
), protein SmpB
(10
), and ribosomal protein S1 (11
, 12
). It is
this particle that provides a mechanism for the resumption of
translational elongation, possibly through "hopping" or
"sliding" (13
).
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tmRNA sequences |
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TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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, 15
). Transcription of
ssrA is controlled by a s70-type promoter and a
r-independent terminator to yield a 457-nucleotide precursor
(16
). Trimming of this precursor molecule at its 5' end is
carried out by RNase P (16
). The 3' end of mature tmRNA
(363 nucleotides in E. coli) is generated by RNase III
(17
) and also requires RNases E, T and PH
(18
, 19
).
Most tmRNA sequences have been derived from bacterial and plastid
genome sequences (20
, 21
). Initially, tmRNA was believed to
be absent in the 
-subdivision of the proteobacteria
(22
), but has been found recently in the
-proteobacterium Caulobacter crescentus and the
mitochondrial genome of Reclinomonas americana
(23
). These two tmRNA sequences, as well as those of
cyanobacteria Prochlorococcus marinus and
Cyanobium PCC6307, are transcribed from a circularly
permutated ssrA gene. Although the biological significance
of this particular gene arrangement is unknown, excision of internal
sequences from the precursor of the Caulobacter 10Sa RNA
yielded a functional, two-piece 10Sa RNA molecule. In contrast, the
R. Americana tmRNA is likely to represent an evolutionary
fossil, which due to attrition of its mRNA-like domain and
pseudoknots, may no longer be able to facilitate peptide tagging
(Fig. 1
).
|
|
tmRNA: a hybrid of tRNA and mRNA |
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TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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–26
). E. coli tmRNA
contains twelve helices. Helices 1, 2a, and 12 form the tRNA-like
domain as originally suggested by Komine et al. (16
).
Other regions participate in the formation of four pseudoknots (pk1 to
pk4). The open reading frame for the tag peptide is flanked by pk1 and
pk2 (Fig. 1)
.
Sequence comparisons were useful also in preliminary determinations of
the three-dimensional structure of tmRNA (27
). Helices
2b/2c, 2d/3/4, 5a/5b, 6a/6b/6c/7, 8b/9, 10a/10b10c/11b/11a and 1/12 are
likely to be coaxially stacked. Coaxial stacking of helices
participating in the formation of pseudoknots pk1-pk4 has already been
confirmed by NMR studies (28
).
tRNA-like portion of tmRNA folds into three-dimensional tRNA motif.
The 3' and 5' termini of all tmRNAs are base-paired to mimic
pairings found in alanyl-tRNAAla
(16
). The resemblance is most striking in the acceptor
stem and the T arm of tmRNA. These highly conserved motifs are a
G3·U357 wobble base pair (numbered according to the E.
coli tmRNA), 5-methyluridine at position 341, and two
pseudouridines at positions 342 and 347 (29
). A likely
candidate for methylation of U341 is tRNA
(m5U54)-methyltransferase (30
).
Conversion of U342 and U347 to pseudouridine may be carried out by
E. coli pseudouridine synthetase I, which modifies an
analogous U residue in canonical tRNAs (31
). The same
enzyme may also modify U347. However, the analogous position in tRNA
has never been found to be occupied by pseudouridine (32
).
Felden et al. (25
) suggested that T341 and A345 form a
reverse-Hoogsteen base pair. Additional stabilization of the T loop
may occur by hydrogen bonding of the anionic oxygen in the phosphate
347 to both the O2' of A345 and the amino group of C348
(33
).
The region between helices 1 and 2 (equivalent to the D-domain of tRNA)
is reduced considerably (25
, 26
). Thus, six of the nine
long-range interactions that contribute to the L-shape of canonical
tRNA are missing. UV irradiation of both free and ribosome-bound
E. coli tmRNA induces cross-links between nucleotides
U9/U10 and C46/U347 providing evidence for proximity between the D- and
T-domains and indicating that the 3'- and 5'-terminal segments of
E. coli tmRNA closely resemble the L-shaped
structure of canonical tRNAs [Fig. 2
; (34
)]. Because of an additional degree of flexibility in
the "elbow" region of the tmRNA molecule, the interstem angle may
be 10–20o larger than the corresponding angle in
the crystal structure of yeast tRNAPhe. This
suggestion is supported by transient electric birefringence
measurements of the E. coli tmRNA (35
).
|
All known tmRNAs of bacterial and plastid origin contain short open
reading frames that begin with the "resume" codon, are terminated
with two stop codons and encode peptides ranging in size from 10 to 27
amino acids. The C-termini of these peptides contain nonpolar
(Y/A)A(L/V)AA sequences which constitute relatively promiscuous signals
recognized by periplasmic protease Tsp, cytosolic protease complexes
ClpXP and ClpAP, and membrane-anchored protease HflB
(24
, 36
).
|
Trans-translation: A model for tmRNA-dependent tagging of incomplete proteins |
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TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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), its
function was elusive until 1996. The first clue to its role came
serendipitously from expression studies of recombinant interleukin-6.
An 11-amino acid tag (AANDENYALAA), attached to the C-terminus of
truncated interleukin-6, was shown be a signal for proteolytic
destruction (38
). The tag peptide was found to be encoded
in tmRNA and a new mechanism, now called trans-translation,
was proposed. Keiler et al. (8
) suggested that
aminoacylated tmRNA binds to the A site of ribosomes stalled at the 3'
end of truncated mRNA, accepts incomplete polypeptide from tRNA bound
to the P site and, after translocation to the P site, provides an open
reading frame (Fig. 3
). The molecular details of the trans-translation model are
under vigorous investigation.
|
|
Roles of tmRNA in trans-translation |
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TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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Komine et al. (16
) and Ushida et al. (39
)
demonstrated that E. coli, B. subtilis and
M. capricolum tmRNAs can be alanylated in vivo or in vitro.
Replacing G3-U357 with a G-A or G-C pair inactivated charging
of E. coli tmRNA in vitro, and the
G3.A357 mutant could not accept alanine in vivo.
These findings suggested that G3·U357 is equivalent to the wobble
base pair G3·U73, shown earlier by McClain and Foss (40
)
to be an identity element in tRNAAla. Given that
all known tmRNA sequences contain a wobble base pair equivalent to the
G3·U357 pair in E. coli tmRNA, one could expect that in
all organisms tmRNA is charged by alanyl-tRNA synthetase.
Interaction of alanyl-tRNA synthetase appears to be limited to the
acceptor-T arm (41
). Indeed, in vitro studies have
demonstrated that a minihelix corresponding to the acceptor stem and
the T arm functions as a substrate for alanyl-tRNA synthetase,
provided that it contains a single G.U base pair
(42
). Interestingly, switching the amino acid acceptor
identity of E. coli tmRNA from alanine to histidine did not
abolish peptide-tagging at least in vitro (28
).
Pseudoknots.
Little is known about the role of the tmRNA pseudoknots. According to
Nameki et al. (43
), three of the four pseudoknots in tmRNA
are interchangeable and can be substituted with single stranded RNAs
without substantial loss of peptide tagging activity in vitro. However,
pk3 recognizes ribosomal protein S1, which is essential for binding of
tmRNA binding to ribosomes (10
, 11
). Although pk1 is
missing in Mycoplasma tmRNA, its disruption prevents
synthesis of the tag peptide in vitro (28
).
mRNA-like domain.
In the course of trans-translation, ribosomes jump from mRNA
to the mRNA-like domain of tmRNA. While most studies have focused
on the switch that occurs when ribosomes reach the 3' end of truncated
mRNA, Karzai et al. (44
) demonstrated that ribosomes can
also abort translation and begin peptide-tagging when they
encounter a cluster of rare codons. An essential requirement for
aborting mRNA at an internal site is the lack of cognate tRNA, a
situation which can be caused, for example, by amino acid starvation.
Irrespective of what constitutes the abortive signal,
trans-translation begins at the resume codon, the first
codon of the tmRNA-coding domain, and continues until ribosomes
reach the stop codons. Muto et al. (45
) suggested that
correct registration of the trans-translation may be secured
by base-pairing interactions between nucleotides 68–125 in
E. coli tmRNA and the complementary region at the 3' end of
the 16S ribosomal RNA. However, this proposal was ruled out by recent
phylogenetic analyses of tmRNA sequences (26
). Recently,
Williams et al. (46
) determined that principal
determinants for initiating trans-translation at the resume
codon are located in a monotonic sequence 79-AAAAAAUAGUCG-89
between the pk1 and the resume codon.
|
Trans-translational protein factors |
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TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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tmRNA has been shown to bind to 70S ribosomes but not to ribosomal
subunits (39
, 47
), apparently in an
aminoacylation-dependent manner (48
, 49
). Since all
aminoacylated tRNAs enter the elongation cycle as ternary complexes
with elongation factor Tu and GTP (EF-Tu:GTP), it is reasonable to
assume that Ala-tmRNA uses the same mechanism to initiate peptide
tagging of truncated proteins (8
). This suggestion was
recently tested by Barends et al. (9
), who showed that the
association rate constant of Ala-tmRNA for the
EF-Tu.GTP complex is approximately 150-fold lower
than that of Ala-tRNAAla, whereas its
dissociation rate is about five-fold lower, indicating that additional
factors may facilitate interactions between Ala-tmRNA and the
EF-Tu.GTP complex and tmRNA delivery to the A
site.
SmpB protein.
Recently, Karzai et al. (10
) reported the discovery of a
small protein called SmpB in E. coli and demonstrated that
deletion of the smpB gene, located just upstream of the
ssrA gene for tmRNA, resulted in slower growth and delayed
recovery from carbon starvation. The same defects were observed earlier
in E. coli ssrA mutants (16
, 50
). Protein SmpB
is required for stable association of tmRNA with 70S ribosomes and,
after dissociation of ribosomes into subunits, remains associated with
tmRNA. The latter observation suggests that protein SmpB may not only
play a role in initiating peptide tagging, but may also stabilize
tmRNA-ribosome complexes. Purified SmpB protein binds tmRNA
specifically and with high affinity. In contrast to EF-Tu, these
interactions are not affected by the aminoacylation status of the tmRNA
molecule, although both molecules seem to bind primarily to the
acceptor stem-T arm segment of the tRNA-like domain of tmRNA.
Preliminary results of CD analysis of SmpB protein from T.
aquaticus indicate that it consists mostly of ß pleated sheets
(10
).
Ribosomal protein S1.
Ribosomal protein S1 forms complexes with tmRNA both on and off the
ribosome (11
, 12
) and does not require EF-Tu.
Interactions between S1 and tmRNA are restricted to the mRNA-like
region and pseudoknots pk2 and pk3, and, as in the case of protein
SmpB, are independent of the aminoacylation state of tmRNA. Since the
equivalent of the Shine-Dalgarno sequence, which facilitates mRNA
binding to the E. coli ribosome, has not been identified in
tmRNA, protein S1 would help to direct
Ala-tmRNA:EF-Tu.GTP:SmpB complexes to the
ribosome, and thereby initiate transpeptidylation. S1 may also play a
role in converting tmRNA from a tRNA analogue into an mRNA. Finally,
since association of S1 with the ribosome is weak, this protein might
facilitate the departure of tmRNA from the ribosome, probably in
concert with RF-1 (46
).
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CONCLUSION |
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TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
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ACKNOWLEDGMENTS |
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FOOTNOTES |
|---|
2 This work was supported by Grant GM58267 from
the National Institutes of Health and by the Upchurch Fund for
Excellence. B.K. was supported by the Council for Chemical Sciences of
the Netherlands Organization for Scientific Research (CW-NWO,
328–035).
4 Abbreviations used: RNP, ribonucleoprotein;
tmRNA, transfer-messenger RNA.
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LITERATURE CITED |
|---|
|
TOPABSTRACTINTRODUCTIONtmRNA sequencestmRNA: a hybrid of...Trans-translation: A model for...Roles of tmRNA in...Trans-translational protein...CONCLUSIONLITERATURE CITED |
|---|
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90o) and tRNA motif
(110o) are highlighted (34