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Department of Chemistry & Biochemistry, University of California—San Diego, La Jolla, California
SUMMARY INTRODUCTION TYPE III SECRETION VERSUS TRANSLOCATION TYPE III SECRETION SYSTEM APPARATUS Bacterial Surface Structures Needles. Filaments. Pili. Salmonella appendages. Conduits for translocation? Inner Membrane Ring Predicted Inner Membrane Proteins YscV and YscU. YscR, YscS, and YscT. ATPase. Outer Membrane Ring TRANSLOCATOR PROTEINS TARGETING EFFECTORS TO THE TYPE III SECRETION SYSTEM APPARATUS Nucleic Acid Signal Protein Signal Structures of N-Terminal Putative Secretion Signals TYPE III SECRETION SYSTEM CHAPERONES Structures Effector versus Translocator Chaperones Translocator chaperones. Promiscuous effector chaperones. Mode of Effector Binding by Chaperones Stoichiometry. Extended conformation in effectors. YopE Chaperone-Binding Site and Translocation Chaperones and Secretion Chaperones and Translocation Temporal Phases of Effector Transport MODELS OF CHAPERONE ACTION Passive Protection Secretion Competency Protein Unfolding in Transport Chaperone-Effectors as Targeting Motifs Hierarchy of transport. CONCLUSION AND FUTURE DIRECTIONS ACKNOWLEDGMENTS REFERENCES
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| INTRODUCTION |
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In the great majority of cases, proteins delivered into host cells by the TTSS, termed effectors, contribute to a pathogenic relationship between bacterium and host. The TTSS has been identified in many animal pathogens, such as Yersinia spp., Salmonella spp., Shigella spp., enteropathogenic and enterohemorrhagic Escherichia coli (e.g., O157:H7), Pseudomonas aeruginosa, Vibrio parahaemolyticus, Bordetella spp., and Chlamydia spp. (26, 90, 102, 108, 116, 147, 150, 184, 204, 248, 253). Certain bacteria, such as Salmonella enterica serovar Typhimurium, Yersinia pestis, and Y. enterocolitica, have been discovered to encode more than one TTSS (80, 103, 211). The TTSS has also been identified in plant pathogens, such as Pseudomonas solanacearum, P. syringae, Erwinia spp., and Xanthomonas spp. (21, 74, 186, 236). The distribution of the TTSS is not limited exclusively to pathogens; certain endosymbiotic bacteria also encode TTSSs (45, 46, 75).
The arsenal of effectors translocated into host cells varies widely across bacteria, being tailored to fit the life-style demands of a particular bacterium within a particular host. In contrast, many components of the TTSS apparatus used to transport effectors are conserved in sequence among bacteria, and some of these components are also functionally interchangeable. For example, the Yersinia effector YopE is secreted into the extracellular medium by the TTSS of S. enterica serovar Typhimurium, Xanthomonas campestris, and Erwinia chrysanthemi (5, 195, 197). YopE can also be translocated into HeLa cells by S. enterica serovar Typhimurium, as determined by the characteristic rounding up of HeLa cells brought about by YopE action (195). Likewise, the Yersinia TTSS is capable of secreting the P. syringae effectors AvrB and AvrPto (5). The efficiency of secretion of these heterologous substrates by Yersinia was shown to be similar to that of the autologous Yersinia substrate YopE (5, 31). However, limits to functional complementarity are also observed. As evidence of this, the S. enterica serovar Typhimurium TTSS inner membrane protein InvA (Table 1) is complemented, at least partially, by its S. flexneri homolog MxiA but not by its Yersinia homolog YscV (also called LcrD) (93). Therefore, while functional generalizations across different TTSSs are often informative, it should be kept in mind that there are limits to these generalities.
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| TYPE III SECRETION VERSUS TRANSLOCATION |
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In contrast to secretion, translocation is strictly dependent on the TTSS and does not occur through the flagellar apparatus (135). Translocation is triggered by an unknown mechanism by bacterial contact with host cells (196) and is more experimentally difficult to study than secretion. One of the major breakthroughs in studying translocation was the use of a host cell-activated reporter, a 
400-residue portion of Bordetella pertussis calmodulin-activated adenylate cyclase (Cya) (214). The enzymatic function of Cya is activated only in mammalian cells, due to the dependence of this enzyme on calmodulin. Other reporters specific to mammalian cells have been used as well, including a short protein sequence that is phosphorylated by mammalian kinases (52) and one that specifically binds biarsenical fluorescent reagents, such as FIAsH (29). FIAsH is not strictly a mammalian cell-specific reporter, but it is taken up more efficiently by mammalian cells than by bacterial cells (99). A potential problem in these experiments is that fusion proteins or peptides are not always innocuous and noninterfering reporters but sometimes give rise to unintended consequences for protein folding or stability. To avoid this problem, a number of researchers have examined translocation of untagged effectors, using biochemical separation to discriminate between host cell internalized (i.e., translocated) and intrabacterial pools of effectors (87, 129, 136, 196). This has generally relied on the use of detergents that lyse mammalian cells but not bacteria and on the detection of translocated proteins in the soluble fraction of lysed cells by Western blot analysis or immunofluorescence. Biochemical separation also has its potential shortcomings, centered mainly around whether various detergents (e.g., digitonin) provide the intended discrimination between translocated and intrabacterial effectors (167). Although results sometimes depend on whether a native or tagged version of an effector is used, the combination of reporter fusion and biochemical methods has generally proven powerful and illuminated many features of the type III secretion process.
| TYPE III SECRETION SYSTEM APPARATUS |
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The Yersinia needle is formed by the small protein YscF (9 kDa) (Table 1) (107). The Shigella and Salmonella needles are composed of MxiH (9 kDa) and PrgI (9 kDa) (Table 1), respectively, which are related in sequence to YscF (both with 26% identity to YscF) (107, 123, 131). MxiH polymerizes to form a helical superstructure, with 5.6 subunits per turn and a helical pitch of 24 Å, as revealed by electron micrographic reconstruction combined with X-ray fiber diffraction analysis (34). This arrangement is highly reminiscent of the bacterial flagellar filament and hook, which is surprising since MxiH has no appreciable sequence identity to proteins of the flagellar filament (FliC, flagellin, 52 kDa) or hook (FlgE, 42 kDa).
Overexpression of MxiH leads to needles as long as 1 µm. Disruption of the Shigella protein Spa32 (33 kDa) leads to even longer needles, longer than 5 µm (146, 221, 222). Spa32 is not found in most other TTSSs but appears to be distantly related to the Salmonella protein InvJ (36 kDa), whose deletion also leads to micron-length needles (131). The long-needle phenotype of Spa32 and InvJ mutants is much like that reported for the flagellar protein FliK (42 kDa; Table 1), which provides control over the length of the flagellar hook structure in the hook/basal-body complex (161). However, neither MxiH nor InvJ appears to be related in sequence to FliK. Knowledge of the three-dimensional structures is required to ascertain whether a deeper relationship exists among these functionally similar proteins.
In Yersinia, YscP (50 kDa) sets the length of the needle. Remarkably, it has been found that the number of residues in engineered variants of YscP correlates linearly with needle length; the metric is 1.9 Å of needle length per YscP residue (120). These data suggest a model in which YscP is tethered at one end to the base of the TTSS apparatus and at the other end to the growing end of the needle. The needle is thought to keep growing until YscP is fully stretched (120). YscP is not related in sequence to Salmonella InvJ, Shigella Spa32, or the flagellar protein FliK (131, 146, 221, 222).
While the external diameter of needles is estimated to be a spacious 60 to 130 Å (107, 130, 210, 221), electron micrographic reconstructions of negatively stained S. flexneri needles reveal an inner diameter of only 20 Å (19). Similar observations have been made on negatively stained Y. enterocolitica needles (107). Folded protein domains often have diameters of 20 to 30 Å, suggesting that if effector proteins were transported through the interior of the needle, they would need to be partially or fully unfolded, as discussed below.
The inner channel of the flagellum is also found to have a diameter of 20 Å, as deduced from an atomic model of the flagellar filament (203, 250). This model reveals that the inner surface of the flagellar channel consists mainly of polar residues, which may be advantageous for transport of unfolded proteins through the flagellum during its assembly. A polar surface would prevent association between the filament walls and exposed hydrophobic residues of potentially unfolded proteins in transit through the flagellum.
Filaments.
A variation on the needle is seen in pathogenic E. coli strains, which have a long filament that appears to be attached to the end of the needle distal to the bacterial cell. The E. coli needle is composed of the protein EscF (8 kDa), which is related in sequence to YscF (23% identity), and the filament is composed of the protein EspA (20 kDa) (244), which is not found in most TTSSs (Table 1). An EspA-related protein, SseB, has been identified in the SPI-2 TTSS of S. enterica serovar Typhimurium (106), although the existence of SseB filaments has not been demonstrated.
EspA filaments are helical tubes with an outer diameter of 120 Å and an inner diameter of 25 Å, which is as constricting as the inner diameter of needles (48). The presence of a central channel in the filament and the observation that the filament is required for delivery of the EspB protein suggest that the filament serves as a continuation of the needle for protein transport (59, 124). Consistent with this hypothesis, the needle subunit EscF is found to bind the filament subunit EspA (48, 244). Filaments can be as long as 700 nm but are most frequently between 40 and 140 nm (with an average of 90 nm) (47, 210), suggesting that the length of the filament is not under tight control. The filament may need to be lengthy for pathogenic E. coli to attach to host intestinal epithelial cells through the thick, overlaying glycocalyx layer.
Pili.
Rather than having a needle or filament, bacterial phytopathogens have a pilus-like structure termed the Hrp pilus. The Hrp pilus has an 80-Å outer diameter, similar to that of needles, but its length of 2 µm is much greater than that of wild-type needles (192, 237). Additionally, pili appear to be flexible whereas needles appear to be rigid. The length of the Hrp pilus is probably an important attribute in traversing the thick (>100-nm) cell wall of plant cells to reach the cytoplasmic membrane. Unlike needles, which are dispersed over the entire bacterial surface, the Hrp pilus of Ralstonia solanacearum is seen to emanate only from one pole (237). In P. syringae, the small protein HrpA (11 kDa) is necessary and sufficient to form the Hrp pilus (Table 1) (191, 192). The sequence of HrpA varies among bacterial pathovars. For example, HrpA from P. syringae pv. tomato strain DC300 has only 30% identity to HrpA from P. syringae pv. syringae or phaseolicola. HrpA from these pathovars have 18 to 21% sequence identity to YscF, which is slightly but not substantially lower than the identity of MxiH, PrgI, or EscF to YscF. It will be interesting to see whether needle and pilus subunits are structurally related despite their low sequence identity (57).
Salmonella appendages.
Surface appendages much larger than needles and filaments have been observed for invading S. enterica serovar Typhimurium (94). These appendages have diameters of 60 nm and lengths of 0.3 to 1.0 µm. Unlike needles, the existence of these appendages does not depend on InvA, a conserved putative inner membrane TTSS protein; however, like needles, it does depend on certain conserved TTSS components, such as the TTSS ATPase InvC and the secretin InvG (Table 1) (94). The relationship of these surface appendages to TTSS needle-like structures is unclear.
Conduits for translocation? The tube-like morphology of type III needles, filaments, and pili suggests an obvious and appealing mechanism for protein transport involving transit through the central, hollow channel of these structures. Consistent with this model, effector secretion requires assembly of needles (131). Although there is no direct experimental evidence for protein transport through the center of the needle, evidence does exist for egress of effectors from the distal ends of Hrp pili (117, 138). Electron micrographic images of P. syringae in the process of secreting the effectors AvrPto and HrpZ demonstrate localization of these proteins to the distal tip of the Hrp pilus (117, 138). However, the resolution of the method used for visualization, involving immunolabeling with 10 to 20-nm gold particles, is insufficient to define the path of transport of these effectors. While the electron micrographic images are reasonably interpreted to mean that effectors reach the end of the pilus by traveling through its center, it should be kept in mind that other paths for effector transit remain formally possible.
Flagellar subunits are also thought to travel through the center of the flagellum. This model derives from two findings. First, flagellin is found to add to the distal end of the flagellum during growth, and second, flagellin subunits appear not to be released extracellularly before adding to the flagellum (65, 112). The first point was established directly through electron micrographic visualization of flagella belonging to bacteria grown in normal media and then pulsed with a radiolabeled amino acid (65). Flagella containing segments of unlabeled and labeled flagellin were observed to contain the radiolabel only at the distal end. The second point was established indirectly, through an experiment in which an S. enterica serovar Abortusequi mutant that produces curly flagella was grown together with a wild-type strain that produces normal flagella (112). While flagellin subunits of these two strains were known to copolymerize, it was found that, despite the two strains having been grown together, flagella were either all curly or all normal over their entire length. This result suggests that flagellin subunits are not secreted into the extracellular medium before adding to the distal ends of the flagellum, otherwise flagella containing mixed normal and curly segments should have been found. Again, these results are reasonably interpreted to mean that flagellin travels through the central channel of the flagellum to add to the distal end, but direct evidence is lacking. With knowledge of the structure of unassembled and assembled flagellin now available (203, 250), it may be possible to devise direct experiments to test this notion.
The identities of proteins that make up the inner membrane ring in Salmonella and Shigella are known, with these proteins having been partially purified from bacterial spheroplasts as parts of needle-containing protein complexes (19, 130, 131, 221). In Salmonella the inner membrane ring is formed by the proteins PrgK (28 kDa) and PrgH (44 kDa), and in Shigella it is formed by the proteins MxiJ (28 kDa) and MxiG (43 kDa) (Fig. 1B; Table 1).
PrgK and MxiJ are related in their N-terminal regions to the flagellar protein FliF (61 kDa). FliF forms part of the flagellar MS ring (220), which is localized to the inner membrane and functions as the passive core of the flagellar rotor. While it is estimated that 26 FliF monomers assemble to form the MS ring (118), the stoichiometries of PrgK and MxiJ are unknown. PrgK, MxiJ, and the related Yersinia protein YscJ (25 kDa) are predicted to be lipoproteins, containing an N-terminal cysteine that is lipid acylated following cleavage of a signal sequence. These proteins are also predicted to have a 200-residue periplasmic domain followed by a C-terminal transmembrane region (Fig. 1B).
In contrast to PrgK and MxiJ, PrgH and MxiG are not related to flagellar proteins or, indeed, broadly conserved across TTSSs, but they are related to one another in their C-terminal regions. The topologies predicted for PrgH and MxiG resemble the topology predicted for Yersinia YscD (47 kDa), with a small N-terminal cytoplasmic domain, a single transmembrane region, and a large periplasmic domain (Fig. 1B) (153, 183).
The diameter of the TTSS inner membrane ring is considerably wider than that of the needle. Outer and inner diameters of 210 and 120 Å, respectively, are observed for the Salmonella inner membrane ring (123), and the Shigella ring has been observed to have a 260-Å outer diameter and a height of 110 Å (19, 221). PrgH alone has been observed to form defined tetrameric structures, suggesting that PrgH oligomers may represent an early intermediate in the assembly of the inner membrane ring (123). However, the stability of the inner membrane ring is seen to require both PrgH and PrgK (218).
YscV and YscU.
Among conserved integral inner membrane proteins, Yersinia YscV (78 kDa, also called LcrD) (181) is one of the few predicted to have a large cytoplasmic domain that could serve as a possible receptor site for interaction with translocation substrates (Fig. 1C; Table 1). YscV influences effector secretion, with low-level but not high-level expression of YscV promoting secretion (133). YscV is related in sequence to the Salmonella inner membrane flagellar protein FlhA (75 kDa). By using Hidden Markov Models (152), both YscV and FlhA are predicted to have seven transmembrane regions and an N-terminus located in the cytosol. However, this assignment places the 400-residue C-terminal domain of these proteins in the periplasmic space and contradicts experimental data supporting a cytoplasmic location of the FlhA C-terminal domain (158). A model containing six (or possibly eight) transmembrane crossings is more likely (Fig. 1C).
FlhA associates with the MS ring protein FliF (122) and the flagellar inner membrane protein FlhB (42 kDa) (257). The Yersinia protein YscU (40 kDa) is related to FlhB, and YscU and YscU-like proteins represent a second candidate for a signal receptor since they also have predicted, sizeable cytoplasmic domains (Fig. 1C; Table 1). YscU, like FlhB, is predicted to have four transmembrane regions followed by a 150-residue cytoplasmic domain, with topology experiments using alkaline phosphatase confirming this prediction (4). FlhB controls the choice between secretion of flagellar rod-hook proteins and secretion of flagellar filament proteins (86). Genetic evidence suggests that YscU has a similar function in the TTSS (60).
YscU appears to control the choice between secretion of the needle subunit YscF and secretion of effectors (60). Overexpression of the cytoplasmic domain of YscU in wild-type Yersinia increases effector secretion (133). Control of YscU over secretion substrates occurs in conjunction with the TTSS protein YscP, which is involved in controlling needle length (Table 1) (60, 120, 177). Deletion of YscP leads to enhanced secretion of YscF, with this phenotype being suppressed by mutations in the cytoplasmic domain of YscU (60). For FlhB, the C-terminal cytoplasmic domain is seen to undergo proteolytic (possibly autocatalytic) cleavage, enabling the switch between secretion substrates (156). The cleaved fragments remain associated (156), perhaps in a different conformation from the uncleaved C-terminal domain. The C-terminal cytoplasmic domain of YscU has also been observed to undergo proteolytic cleavage, but this cleavage is unnecessary for secretion of effectors (133).
The FlhA and FlhB cytoplasmic domains associate both homotypically and heterotypically (257). These domains also bind the flagellar ATPase Flil and FliH, the negative regulator of Flil (Table 1). In addition, the cytoplasmic domain of FlhA binds the soluble flagellar protein FliJ (85). FliJ appears to have chaperone-like function in preventing the aggregation of flagellar rod-hook and filament proteins (158). FliJ is related to Yersinia YscO (19 kDa), which plays a role in effector secretion (176). YscO also partitions into both soluble and membrane-bound fractions, suggesting a role in shuttling proteins between the bacterial cytosol and the membrane-embedded TTSS apparatus (176).
YscR, YscS, and YscT.
Yersinia YscR (24 kDa), YscS (10 kDa), and YscT (28 kDa) are conserved across TTSSs and are also related to the flagellar proteins, FliP, FliQ, and FliR, respectively (Fig. 1C; Table 1) (14, 76). Little is known about the function of these proteins, which are predicted to be inner membrane proteins with multiple transmembrane regions and no appreciable cytoplasmic or periplasmic regions. An exception is the 80-residue cytoplasmic segment predicted for YscR. The E. coli YscR-related protein EscR has been found by yeast two-hybrid analysis to interact with itself, with the YscS-related protein EscS, and with the YscU-related protein EscU (43). The genes for fliR and flhB are fused in Clostridium, and a similar fusion construct engineered in Salmonella has been found to be functional (234). This result provides indirect evidence for association between FliR and FlhB in the MS ring and suggests that YscR may interact with YscU in the inner membrane protein assembly of the TTSS.
ATPase. The ATPase Flil (49 kDa) is an essential component of the flagellar apparatus, providing energy for assembly, and is peripherally associated with the inner membrane (145). ATPases related to Flil have been identified in the TTSS and are essential to protein secretion (Fig. 1A; Table 1) (63, 221, 245). These ATPases are also related to the ß-subunit of the F0F1-ATP synthase. The mechanism by which energy from ATP hydrolysis is transduced to drive protein transport in the flagellar system or the TTSS is not known.
In the presence of ATP, Flil forms a sixfold symmetric, ring-like structure with an external diameter of 100 Å and a central cavity of 25 to 30 Å (33). The ATPase activity of Flil displays positive cooperativity, and both oligomerization and positive cooperativity are enhanced by phospholipids (33). The TTSS ATPase HrcN (48 kDa) from P. syringae pv. phaseolicola forms both monomers and oligomers, with the oligomeric form most probably being hexameric (185). As with Flil, oligomerization of HrcN is favored by its association with the membrane, and the oligomeric form of HrcN has significantly more ATPase activity than the monomeric form does. Hexameric association of secretion-related ATPases has been visualized by X-ray crystallography for ATPases involved in type IV bacterial secretion and in bacterial conjugation (95, 205, 249).
Both Yersinia and Shigella TTSS ATPases are parts of multiprotein complexes: The Yersinia ATPase YscN (48 kDa) (245) appears to be part of a complex containing at least YscQ and YscL, as detected by yeast two- and three-hybrid experiments (Table 1) (114). Similarly, the Shigella TTSS ATPase Spa47 is found by yeast two-hybrid and immunoprecipitation experiments to interact with Spa33 and MxiK, which are the Shigella versions of YscQ and YscK (119).
YscQ (34 kDa) is related at its C-terminal end to the flagellar proteins FliN (15 kDa) and FliM (38 kDa), which are structural components of the flagellar C-ring, a cup- like structure attached to the cytoplasmic surface of the flagellar MS ring (58). The X-ray crystal structure of a 80-residue C-terminal fragment of HrcQB (15 kDa), the P. syringae homolog of YscQ, has been determined (71). Unlike FliM and FliN, which are estimated to have stoichiometries of 37 and 111 (255, 256), respectively, the C-terminal fragment of HrcQB is found to form a dimer of dimers. It is hypothesized that the interfaces found in the tetramer might correspond to sites of association of HrcQB with the highly related protein HrcQA (26 kDa) in forming a C-ring-like structure.
YscL (24 kDa) (153) is related to the flagellar protein FliH (26 kDa), the negative regulator of the ATPase Flil. FliH and Flil form a heterotrimeric FliH2-Flil complex (12, 157), and both proteins interact with C-terminal cytoplasmic domains of FlhA and FlhB (257).
Secretins associate as oligomers, as seen by the 14-subunit multimer formed by the secretin pIV (46 kDa), which is involved in phage extrusion (170). The pIV multimer forms three discernible rings and is 120 Å long, with an outer diameter of 135 Å and an inner diameter varying from 60 to 88 Å (170). The channel in the pIV multimer appears to be blocked, raising the possibility that secretins are gated (170). The secretin PulD from Klebsiella oxytoca, which is involved in type II secretion of pullulanase, has also been found to be oligomeric but is reported to have 12-fold rather than 14-fold symmetry (168, 169).
The TTSS secretins YscC (67 kDa) from Yersinia and InvG (62 kDa) from Salmonella also form ring-shaped structures. YscC rings have external and internal diameters of 200 and 50 Å, respectively (125), and InvG rings have external and internal diameters of 150 and 70 Å, respectively (41). Ysc rings have 13-fold symmetry (25). The localization of InvG to the outer membrane is promoted by the TTSS outer membrane lipoprotein InvH (16 kDa) (41, 218). However, InvH does not form a complex with InvG and is not required for type III secretion. InvH is not related to flagellar proteins and is not widely conserved across TTSSs. The Yersinia lipoprotein YscW (15 kDa) also plays a role in proper localization of the secretin YscC to the outer membrane (125), but YscW is not related to InvH and is not widely conserved across TTSSs. Mutation of the P. syringae pv. syringae 61 secretin HrcC leads to accumulation of the effector HrpZ in the periplasm, consistent with the role of TTSS secretins in promoting the transport of effectors across the outer membrane (30).
| TRANSLOCATOR PROTEINS |
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As would be expected for pore-forming proteins, YopB and YopD form ion channels in planar lipid bilayers, with these channels having a conductance of 105 pS (223). Ion channels are observed in the absence of YopD, but channels formed by YopB alone have ill-defined conductance characteristics (223). Pores formed by YopB and YopD have a defined size, being permeant to Lucifer yellow CH (443 Da) but not to Texas Red-X phalloidin (1490 Da), indicating a narrow pore size (163). Pores formed in mammalian membranes by enteropathogenic E. coli have been visualized (111). These pores have an inner diameter of 30 to 50 Å and are presumably formed by the YopB-related protein EspB and the YopD-related protein EspD (111). EspB binds EspA, the filament component, suggesting that a continuous path exists between the filament and the host cell for polarized and direct translocation (104). EspA also binds host cell membranes in the absence of EspB, indicating that the filament may make initial contact with host cells before EspB inserts into membranes. Pores formed by E. coli are highly asymmetric, rising about 150 to 200 Å above the membrane plane, although it is uncertain whether this represents the external or cytoplasmic face of the pores. The YopB- and YopD-related proteins from P. aeruginosa, PopB and PopD, respectively, also form similar pores, with outer and inner diameters of 80 and 40 Å, respectively (207). The P. aeruginosa pores are not as asymmetrically disposed as the E. coli pores (207).
The YopB-related proteins SipB from Salmonella and IpaB from Shigella integrate into the mammalian cell plasma membrane without causing membrane disruption or lysis (105, 110). SipB forms trimers and hexamers, whereas IpaB forms only trimers (105, 110). Trimerization appears to occur through a sequence that has the potential to form a triple-stranded coiled coil (105). Labeling studies in combination with liposome protection experiments suggest that IpaB and SipB each have two transmembrane crossings (151).
In contrast to the hypothesis that translocation across the host cell membrane occurs through translocator pores, it has been suggested that the TTSS needle directly punctures the host cell membrane to deliver effectors (107). This is based on electron micrographic visualization of Yersinia needles that appear to be inserted into membranes of red blood cells that had been incubated with Yersinia (107). However, in another study the Yersinia needle was found to be insufficient to form pores in macrophage membranes, with this activity requiring at least YopB and YopD (148).
| TARGETING EFFECTORS TO THE TYPE III SECRETION SYSTEM APPARATUS |
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In contrast to the easily discernible signal sequences of proteins secreted by the sec-dependent pathway (166), no consensus signal sequence has been identified for proteins secreted or translocated by the TTSS. What is certain for type III-secreted proteins is the location of the signal sequence. What remains controversial is the molecular composition—mRNA or protein—of this signal.
The type III secretion signal has been localized to the first 15 mRNA codons or amino acids of secreted or translocated proteins. Fusion of the first 15 codons of the effector YopE to the N terminus of Cya (398 amino acids) or neomycin phosphotransferase II (NPT) (262 amino acids) is sufficient to drive type III secretion of these fusion proteins (Fig. 2) (7, 206, 213). This signal, however, is not sufficient to drive translocation, at least in a wild-type genetic background (23, 213). The first 15 codons or residues of other effectors besides YopE drive the secretion of fusion partners as well. These include the TTSS effectors Yersinia YopH, P. syringae AvrB and AvrPto, and X. campestris AvrBs2, as well as the secreted but not translocated proteins Yersinia YopN and YopQ and Salmonella InvJ (5, 7, 115, 160, 188, 189, 200, 213). In addition to Cya and NPT, fusion partners for these studies have included the 
-peptide of ß-galactosidase, E. coli alkaline phosphatase, green fluorescent protein (GFP) ubiquitin, and dihydrofolate reductase (DHFR) (73, 115, 135, 137, 153). However, it has also been found that not all heterologous proteins are competent substrates for secretion by the TTSS (73, 137).
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The most compelling evidence for an mRNA signal derives from experiments examining the secretion signal of the Yersinia type III-secreted but not translocated protein YopQ (189). A single synonymous base change in codon 3 of YopQ was found to destroy the ability of YopQ codons 1 to 10 to promote the secretion of an NPT fusion (189). The synonymous base change preserves the identity of the encoded amino acid, as was confirmed through protein sequencing. This clearly suggests a signal sequence composed of mRNA. However, it was also found that frameshifting destroys the secretion signal in YopQ codons 1 to 10, which suggests a protein-based signal. How might this work? The authors reconcile these findings by positing that the secretion signal does indeed reside in the mRNA, which explains the effect of synonymous base changes, but that the signal also requires the interaction of specific tRNAs with the mRNA, which accounts for the frame being important (189). Complicating the picture a bit further, it was also found that codons 11 to 15 of YopQ act to suppress mutations introduced into codons 1 to 10. The suppressor activity of codons 11 to 15 was found to be sensitive to synonymous base changes but not to frameshifting. It is not known yet whether these results extend to other type III secretion substrates, and no consensus RNA sequence or secondary structure is apparent as a secretion signal.
The degeneracy of a putatively protein-based signal has been confirmed in studies using synthetic secretion signals for YopE. A sequence encoding alternating serines and isoleucines at residues 2 through 8 of YopE (i.e., SISISISI replacing the wild-type KISSFIS) is sufficient to act as a secretion signal (142). These studies also provide some of the best evidence for a protein-based signal (143). Seven cases of single amino acid substitutions in YopE synthetic signals were found that affect secretion efficiency, with six of these substitutions increasing the amphipathic character of the sequence. For example, the YopE sequence ISIISSS (residues 2 to 8) was found to be unable to confer secretion, but substitution of residue 4 with Ser (changing the sequence to ISSISSS) restored secretion (143). Since these substitutions alter the mRNA only slightly, these results favor the idea of a protein-based signal.
As with the mRNA hypothesis, no clear consensus sequence is apparent at the amino acid level. Systematic variation of YopE amino acids 2 to 8 with serines or isoleucines (128 different sequences) reveals that sequences containing four or five serine residues have the greatest likelihood of promoting secretion (143). Multiple linear-regression analysis indicates that the most favorable secretion sequence in YopE residues 2 to 8 is Ile-X-Ser-Ser-Ile-Ser-Ser (143). Analysis of predicted N-terminal secretion signals of effectors from Yersinia, Salmonella, Pseudomonas, enteropathogenic E. coli, Shigella, and Xanthomonas demonstrates enrichment in Ile, Ser, Asn, and Thr (143). Cys and Trp are absent in this region (143). Analysis of the first 50 amino acids of effectors from P. syringae reveals a statistically significant enrichment of Ser and a paucity of Asp, Leu, and Lys (100). Lastly, analysis of the first 50 amino acids of S. enterica effectors reveals a similar statistically significant enrichment of Ser and a paucity of Asp (100).
-helix (1) in the structure of a fragment of YopH (YopH-N, residues 1 to 130 of 468 total) (68, 212). The 1 helix is not an independent structural element but, instead, wraps against the globular body of YopH-N (Fig. 3A). The existence of structure at the N terminus of YopH may represent a special case, however, in that this region has multiple functions. The N terminus of YopH serves not only as a putative secretion signal but also as part of a phosphotyrosine binding site (17, 159). This latter function increases the efficiency of the tyrosine phosphatase activity of YopH by aiding in substrate recognition (17, 55). Alternative functions for the putative N-terminal secretion signal regions of other effectors have not been described.
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-helix in YopH, the putative secretion signal in YopE shows no requirement for sequences that can form amphipathic -helices (143). Indeed, the Ser-Ile repeat found to confer secretion for YopE has the correct periodicity to form an amphipathic ß-strand rather than an -helix. In further contrast to YopH, the putative secretion signal in YopM, which has been mapped to within the first 40 residues, is mostly flexible and disordered, with only residues 34 to 40 being structured (Fig. 3B) (22, 66). Therefore, the putative N-terminal secretion signal is not defined by any particular structural element, at least in its isolated state. It is possible that it is induced to adopt a specific structure in association with a receptor.
Structural evidence is also available for a potential secretion signal in the flagellar protein FlgM, which is secreted through the flagellar basal-body/hook and filament. As with the TTSS, no clear signal sequence has been identified for flagellar proteins. Residues 7 to 25 of FlgM are essential for transport and are found by nuclear magnetic resonance (NMR) spectroscopy to be unfolded in free FlgM or when FlgM is bound to the protein 
28 (51). While the unfolded nature of these protein segments may be useful in transport through needles or flagella, it is unlikely that the lack of structure serves as a signal for a putative receptor (51). An unstructured element, by definition, adopts a very large number of conformations. It is difficult to envision the physical properties of a receptor that can recognize a multitude of conformations with enough specificity and affinity to achieve discrimination between substrates and nonsubstrates.
| TYPE III SECRETION SYSTEM CHAPERONES |
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TTSS chaperones function in dedicated fashion, with an individual TTSS chaperone usually promoting translocation of just a single cognate effector. For example, the Yersinia TTSS chaperone SycE (15 kDa) promotes the translocation of YopE (23 kDa) but not of other effectors (239). Likewise, the Yersinia TTSS chaperones SycH (16 kDa) and SycT (15 kDa) are required for translocation of their cognate effectors, YopH (51 kDa) and YopT (36 kDa), respectively (Fig. 2) (113, 239). SycE, SycH, and SycT have only 14% sequence identity, which is representative of sequence conservation across the large family of TTSS chaperones (15). Despite the low sequence conservation, TTSS chaperones are remarkably similar in structure (Fig. 4), suggesting a common mechanism of action (15, 70, 144, 215, 229, 235).
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ß sandwich fold that is unique to TTSS chaperones. The chaperones are homodimeric, with large surface areas buried at the dimer interface (2,190 Å2 in SigE, 2,100 Å2 in SicP, and 2,400 Å2 in SycE), indicative of constitutive dimerization (15, 70, 229). CesT forms a domain-swapped dimer that is likely to be an artifact of high protein concentrations used for crystallization, as discussed below. The domain-swapped CesT dimer is related to the other chaperone dimers by a swap of the first helix and strand of CesT (144). The Yersinia chaperone SycT has also been found by X-ray crystallography to resemble these other chaperones (Z. Xu and J. Dixon, unpublished data). Likewise, the structure of the S. flexneri chaperone Spa15 has been determined (235), revealing that it is homodimeric and has a protein fold observed for these other TTSS chaperones. However, Spa15 is the least like these other chaperones, in that Spa15 monomers are rotated 30° with respect to one another, in contrast to the roughly parallel orientation of monomers seen for the SycE, SicP, SigE, and CesT dimers (Fig. 4).
The specificity for homodimerization in TTSS chaperones appears to be conferred by the 2 helix, with the 2 helix from one monomer pairing with the 2 helix from a second monomer (Fig. 4). This helix contains residues that are unique to particular chaperones and are not broadly conserved, consistent with a role for this helix in guiding homodimerization specificity. An exception to chaperone homodimerization comes from the Yersinia chaperones SycN and YscB (54). These chaperones are not involved in the translocation of effectors but, rather, in the secretion of YopN, which is not translocated and whose function is necessary to prevent premature release of effectors. SycN and YscB associate in simultaneous fashion with YopN, consistent with the existence of a possible SycN-YscB heterodimeric chaperone, although the stoichiometry of the complex is not yet known (54).
Most significantly for function, TTSS chaperones have hydrophobic surface patches that are formed by residues broadly conserved among chaperones (15, 144, 215). These patches act as effector-binding sites, as shown through direct structural examination (16, 215). There are two different hydrophobic patches, called patch 1 (or helix-binding groove) and patch 2 (15, 16, 215). Patch 1 is found at the dimer interface and includes residues from the 2 helix and adjacent ß-strands (ß3 and ß5) (Fig. 4). Patch 2 is formed by the amphipathic 1 and 3 helices, which are found at the N and C termini, respectively, of TTSS chaperones. The 1 and 3 helices are positioned roughly perpendicular to one another and are positioned on the central ß-sheet of TTSS chaperones, with the ß1 and ß2 strands of the sheet also contributing hydrophobic residues to patch 2. Since the chaperone is a dimer, patch 1 and 2 occur as pairs, giving rise to a total of four exposed hydrophobic patches. As the broad sequence conservation of these hydrophobic patches suggests, these sites confer overall binding energy but little in specificity to effector association (16, 215). For example, one of the patch 1 regions in SycE forms a binding site for a tyrosine, leucine, and alanine of YopE, and the other forms a binding site for two phenylalanines of YopE (16).
Most but not all chaperones are negatively charged, but the functional implication of this is unclear. The structures reveal that the negative charge is conserved in character but the primary sequence position of negatively charged residues is not strictly conserved (15). There is no obvious candidate for a positively charged TTSS protein that would interact electrostatically with chaperones.
Translocator chaperones.
No structure of a SycD-like translocator chaperone exists, but these proteins are predicted to have a tetratricopeptide-like repeat fold within their central region, which is unrelated to the fold found in the SycE-like family of effector-chaperones (Fig. 4) (172). A hydrophobic groove is proposed to exist in the tetratricopeptide-like repeat-like domain of SycD that binds an amphipathic -helix of the translocator YopD (172, 224). YopB does not appear to have a discrete, single SycD-binding region, since no single deletion in YopB has been found to abrogate association with SycD (164). Phylogenetic analysis is consistent with effector chaperones of the SycE class being distinct from translocator chaperones of the SycD class (Fig. 5). Furthermore, the mechanism of action of effector chaperones is likely to differ from that of translocator chaperones. Indeed, proteins belonging to the SycD-like family of translocator chaperones play regulatory in addition to secretory roles (6, 27-29, 49, 50, 81, 128, 149, 179, 232, 242).
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The E. coli chaperone CesT also binds at least two effectors, Tir and Map (Fig. 4) (1, 42, 64). CesT has been reported to bind within the N-terminal 100 residues of the effector Tir (1), although another report suggests that additional portions of Tir are required for association, based on yeast two-hybrid assays (64). CesT is also reported to bind within the N-terminal 101 residues of the effector Map (42). Since Tir and Map are not related in sequence, CesT may also be considered a promiscuous chaperone. The basis for promiscuity is unknown for CesT and Spa15 and awaits structural studies of chaperone-effector complexes for these or other promiscuous chaperones.
The effector chaperone family also appears to include members that bind target proteins that are not secreted or translocated. YscG (13 kDa) belongs to the SycE class of effector chaperones but has been identified to bind YscE (7 kDa), a protein that is not transported out of Yersinia (53).
For simplicity, in this review the term "chaperone" will continue to refer to the SycE class of effector chaperones and not to the SycD class of translocator chaperones.
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