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234 Protein Synthesis
to selenocysteine by the enzyme selenocysteine synthase, 10Sa RNA) to remove the resulting partially synthesized
which uses selenophosphate as a donor. Elongation proteins and free the ribosomal subunits. The 5 - and
factor Tu does not bind Sec–tRNA Sec as it does other 3 -ends of this molecule resemble alanyl–tRNA, while
elongator AA–tRNAs; instead, a unique protein SELB the central portion encodes a peptide “tag.” Alanyl–tRNA
transports Sec-tRNA Sec to the ribosomal A-site. SELB is synthetase aminoacylates the tmRNA, which is then
specific for Sec–tRNA Sec , rejecting other AA–tRNAs transported to the stalled elongation complex by EF-Tu.
including Ser–tRNA Sec . The final novel feature of seleno- After attaching alanine to the end of the growing nascent
cysteine insertion is the mechanism of mRNA recognition. polypeptide, the ribosome switches from the truncated
The UGA triplet can be used in the same organism as mRNA to the tmRNA in a mechanism called trans-
either a selenocysteine or a stop codon. The sequence translation. The ribosome adds 10 additional amino acids
context determines its recognition as a selenocysteine totheendoftheproteinaccordingtothetmRNAsequence.
codon. The ternary complex SELB:GTP:Sec–tRNA Sec The resulting tagged protein is released and degraded, as
recognizes a stem-loop structure immediately 3 (down- the tag is a recognition signal for several proteases.
stream) from a UGA codon that is read as selenocysteine.
This structural feature of the mRNA is specifically
F. mRNA Surveillance
bound by the carboxyl-terminal portion of SELB, while
other regions of the protein are highly homologous Eukaryotes use a surveillance mechanism to identify
to EF-Tu as expected. Insertion of selenocysteine into mRNAs with mutations (typically premature termination
polypeptides therefore requires formation of a quaternary codons) or processing errors (such as incorrect splicing).
SELB:GTP:Sec–tRNA Sec :mRNA complex. This is in Once detected, the aberrant messages are degraded
contrast to all other elongation steps in protein synthesis, to prevent the synthesis of truncated proteins. Recent
which proceed through ternary complexes. evidence suggests that these mRNAs must be at least
partially translated to determine whether a stop codon is in
its proper context. In mammalian systems, the translating
D. Degradation of Incomplete Polypeptides
ribosome is proposed to measure the distance between
One consequence of the necessary accuracy in protein syn- the final splicing junction and the termination signal—if
thesis is the release of peptidyl–tRNA molecules repre- they are within 50 nucleotides of one another, termination
senting incomplete translation products. These products is allowed to proceed. If they are further apart, either
can be the result of ribosome stalling, a premature stop because of a misplaced stop codon within the mRNA
codon that is not suppressed, or detection by the ribosome reading frame or a splicing error, the mRNA is targeted
of noncognate tRNA present in the decoding center. It has for rapid degradation. How the ribosome recognizes this
been estimated that this “drop-off” might result in a trun- distance is not yet known. This mRNA surveillance is also
cated polypeptide chain approximately 10% as often as the called nonsense-mediated decay because the majority of
full-length protein. Not only is this a waste of amino acids mutational errors result in premature termination codons.
resulting in useless products but also tRNA molecules are
sequestered and unavailable for translation of other genes.
G. Accuracy Mechanisms
The incomplete peptidyl–tRNAs are substrates in bac-
teria and yeast for the enzyme peptidyl–tRNA hydrolase, Despite the types of translational errors described above,
which cleaves the ester bond between the tRNA and its mRNA-directed protein synthesis is remarkably accurate.
attached polypeptide. Peptidyl–tRNA hydrolase therefore How is it that the ribosome and translational factors are
removes the useless (and potentially harmful) protein frag- able to achieve such faithful transmission of genetic in-
ments and recycles the tRNAs. Interestingly, although the formation? One way to describe the specificity of cog-
initiatortRNA(fMet–tRNA fMet )mimicsapeptidyl–tRNA nate over noncognate AA–tRNAs is termed the “kinetic
by virtue of its N-formyl group, peptidyl–tRNA hydrolase proofreading” mechanism. One can imagine that selec-
does not recognize the initiator as a substrate. The hydro- tion of an EF-Tu:GTP:AA–tRNA ternary complex by the
lase bypasses fMet–tRNA fMet because of the presence of ribosome during elongation can be considered a “scan-
structural features unique to fMet–tRNA fMet . ning” step. Depending on the codon–anticodon interac-
tion, the AA–tRNA will either bind irreversibly in the ri-
bosomal A-site (in the case of the cognate AA–tRNA), or
E. A Dual-Function RNA
dissociate from the ribosome before or after GTP hydrol-
A particular challenge arises when an mRNA lacks in- ysis (noncognate AA–tRNA). In this model, the rate of
frame stop codons due to deletion or degradation. Bacteria EF-Tu-triggered GTP hydrolysis is the same for cognate
use a unique tRNA–mRNA hybrid (tmRNA, also called and noncognate substrates. However, because the cognate