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Signal Peptides 297
1. In the cytosol, the ribosome binds mRNA regardless of whether it codes
a secretory protein.
2. The ribosome begins to synthesize the polypeptide according to the bound
mRNA.
3. When about 80 amino acid residues protrude from the ribosome, the
peptide can interact with the signal recognition particle (SRP). If the
polypeptide includes an N-terminal signal peptide, the SRP recognizes it
and transiently stops translation of the polypeptide.
4. The SRP–ribosome complex moves to the ER membrane and the SRP
binds to the membrane-bound SRP receptor. Then, the translation restarts.
5. The ribosome binds to the translocon channel on the ER membrane.
6. The gate of the translocon opens and the ribosome pushes the elongated
polypeptide into the pore of the channel.
7. During or after translation, a signal peptidase cleaves the signal sequence.
8. When the completed protein is released, the complex is dissociated and
the channel pore closes.
This hypothesis can also explain the assembly process of integral membrane
proteins in which signal or signal-like hydrophobic segments start transfer across
the membrane while other hydrophobic segments serve as the stop-transfer signal. 6-9
The validity of the signal hypothesis has been verified by many later experiments.
Its basic idea also holds for translocation in prokaryotes; furthermore, proteins
destined to other compartments such as mitochondria and chloroplasts also have
specific sorting signals.
Because the signal hypothesis was so beautiful, people believed in a quite simple
dogma based on it: although there is no simple consensus sequence pattern between
amino acid sequences of signal peptides, they are believed to code a common
function. Namely, the signal peptide cotranslationally directs the protein to the SRPdependent
pathway in eukaryotes while it post-translationally directs the protein to
the Sec system (the protein translocation system dependent on SecA/SecYEG) in
prokaryotes. 10 However, recent studies have begun to clarify that the real situation
is a little more complex. Thus, the main purpose of this review is to introduce recent
developments in the study of protein translocation, including computational and
genome-wide studies.
14.2 PROTEIN SECRETION PATHWAYS IN BACTERIA
Early studies of protein secretion in bacteria were focused on genetic studies because
of the difficulty of construction of in vitro translocation assay. At first, the parallelism
between prokaryotic and eukaryotic systems was recognized; namely, that SecB
protein and SecYEG channel were analogous to SRP and translocon, respectively,
although this translocation process occurs post-translationally in prokaryotes. However,
it turned out that there are several other translocation pathways, including the
cotranslational SRP-dependent pathway, in bacteria (Figure 14.1). The translocation
pathways of archaea are recently described elsewhere. 11,12