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Signal Peptides 309
The specificity determinants for various pathways are not well understood. An
important question is how the distinction between the SecB-dependent pathway and
the SRP-dependent pathway is made. 59 The SRP-dependent pathway is utilized by
a subset of inner membrane proteins while the SecB-dependent pathway is utilized
mainly by proteins at periplasm and outer membrane. 58,69 It is considered that SRPdependent
signal peptides are more hydrophobic in their h-region. Increasing the
hydrophobicity of an SRP-independent signal peptide changed its SRP-dependence.
96 Only functional signal peptides were shown to bind and aggregate the RNA
component of SRP. 65 In addition, another factor — trigger factor — seems to play
an important role in the selection. 192
The presence of flanking charged residues also affects specificity of signal
peptides. The reason why the n-region often harbors positively charged residue seems
to be understood in terms of the positive-inside rule and the loop model. 8,41 Similarly,
in a Sec-independent translocation of membrane proteins, it was shown that the
effect of the proton motive force on positively or negatively charged residues
becomes more significant when hydrophobicity of the translocating segment is
low. 108,193 The longer the hydrophobic region becomes, the more N-terminal translocation
is favored. 194 The presence of flanking charged residues and the degree of
hydrophobicity seem to contribute additively to determination of the topology of
signal-anchor proteins. 195
Signal peptides for the Tat-dependent pathway are somewhat similar to typical
signal peptides, but their length is typically longer, due mainly to the extension of
the n-region. 17 In addition, their degree of hydrophobicity is lower than that of usual
Sec-type signal peptides. 196 However, the most conspicuous feature of the Tatdependent
signal is the unique twin-arginine motif that locates immediately upstream
of the h-region. The motif is represented as (S/T)RRXFLK, where X represents an
arbitrary residue. The arginine residues are invariant in chloroplasts 197,198 but only
one substitution of them into lysine seems to be tolerated to some extent in bacteria.
199,200 The phenylalanine (F) is also important but can be changed to leucine (L).
Surprisingly, the presence of the last lysine retards the transport. 199
Basically, signals for the Tat-dependent pathway seem interchangeable between
bacteria and chloroplasts. 201 However, in contrast to Sec-dependent signal peptides,
the Tat-dependent signal peptides may not be universally recognized across species.
202 Not all Sec-dependent signal peptides can be converted into Tat-dependent
by simply adding the motif, probably because of the nature of the bound proteins.
In addition, one or two lysine residues in the c-region can work as a “Sec-avoidance”
motif. 203 By increasing the hydrophobicity of a Tat-dependent signal peptide, the
signal containing the Tat motif could be converted into Sec-dependent, thus proving
the importance of low hydrophobicity of Tat-dependent signals. 196
14.4.3.2 Eukaryotic Signal Peptides
In eukaryotic cells also, it is most likely that SRP dependence of signal peptides is
determined by their own amino acid sequence; 150,204 their hydrophobicity seems to
be the major determinant of this dependency. Other factors such as their 3D structure