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Signal Peptides 301
more important structure, the finger-loop structure, was observed. Furthermore, it
was found that the proposed signal peptide-binding groove lies alongside the RNA
backbone. Thus, it is likely that RNA and protein constitute a signal peptide-binding
site. 62
This hypothesis is consistent with an observation that RNA increases the affinity
of Ffh for signal peptides. 64 In fact, signal peptides bind the RNA component of
SRP. 65 It seems that the 4.5S RNA stabilizes the hydrophobic finger loop, 66 thus
catalyzing the assembly of Ffh and the FtsY receptor. 67 Then, SRP binds the ribosome-nascent
chain complex (RNC) and targets it to the membrane-bound FtsY.
14.2.2.2 FtsY
FtsY, the receptor of bacterial SRP, is homologous to eukaryotic SRα. Its structure
is roughly divided into two domains: the NG-domain, which has GTPase and Ffh
binding activities, and the N-terminal domain (A-domain in E. coli), which is not
well conserved across species but responsible for its membrane targeting. In the
eukaryotic system, the signal receptor (SR) is bound by SRβ, an integral membrane
protein. Since the homolog of SRβ has not been discovered in bacteria, how FtsY
binds the membrane is not known.
A crystallographic structure of the E. coli NG domain was determined. 68 Interestingly,
the structure of the NG domain of FtsY is similar to the NG domain of
Ffh, although its meaning is not well understood. Anyway, in a GTP-dependent
manner, RNC is released from the SRP/FtsY complex to the SecYEG complex, 69
although some inner membrane proteins containing long periplasmic loops do not
require the Sec-translocase. 70,71 Then, the ribosome restarts the translation, leading
to cotranslational translocation of the nascent polypeptide; however, the details of
each step are not known. SRP may operate downstream of SR-mediated targeting
of ribosomes to the inner membrane in E. coli. 72 SecA is necessary for this pathway,
but its role is still under investigation. 73 It has been reported that SecA is not
necessary for the targeting but is required for subsequent translocation of multispanning,
hydrophobic membrane proteins. 74
14.2.3 TAT-DEPENDENT PATHWAY
In this chapter the word “Tat” means not the Tat protein of HIV (as in Chapter 1)
but the twin arginine translocation pathway of proteins. Recent studies have clarified
that bacteria have another protein translocation pathway independent of the general
secretory pathway for a subset of periplasmic proteins. 75,76 The pathway was named
Tat protein export pathway because the signal peptides that direct joined proteins to
this pathway are similar to usual signal peptides but have a characteristic twinarginine
translocation motif (see Section 14.4.3.1); the system was also called Mtt
for membrane targeting and transport. 77-80 Although not all bacteria use this translocation
system, it is analogous to the ∆pH-dependent pathway across the thylakoid
membrane of plant chloroplasts. 81-83 The most intriguing feature of the Tat-dependent
pathway (and the ∆pH-dependent pathway) is that it can translocate folded proteins
directly. Thus, it makes sense that many of the substrates of this pathway are