Table 1.
Summary of known characteristics of LEE-encoded genes and their associated proteins, with novel homology-based functional predictions. New names as suggested in body text of this article. Summary of effects on gene expression, type-III secretion and virulence in mice drawn from Deng et al [33]. Yeast two-hybrid results drawn from Creasey et al [145]. Predictions drawn from combination of homology data and cited works. T3S: involved in type-III secretion.
| Gene (new name) | Effect of deletion mutation on secretion | Effect on pedestal formation / virulence | Known interactions | Homologues | Domains | Known functions | New functional prediction |
| rorf1 | + | +/+ | EspD | YjiK | SdiA-regulated domain (NHL repeats) | SdiA-regulated? | |
| espG | + | +/+ | VirA | Translocated effector | |||
| ler | No expression | -/- | H-NS, StpA | Positive regulator | Might form heterodimers with H-NS, StpA | ||
| orf2 (escE) | - | Orf29 | YscE, PscE, SsaE, CV2595, YPO0259 | T3S | Interacts with C-terminus of SepL; Functionally important conserved residues can be identified by scrutiny of homologues | ||
| cesAB | ± EspA, EspB | -/- | EspA, EspB | none | Chaperone for EspA and EspB | ||
| orf4 | - | -/- | YPO0264, SsaK, CV2589 | T3S | Functionally important conserved residues can be identified by scrutiny of homologues | ||
| orf5 (escL) | - | -/- | YscL, FliH | T3S | Binds to and regulates activity of ATPase EscN | ||
| escR | - | -/- | EscR, EscS, EscU, SepZ EspD | YscR, FliP | PF00813 | T3S | |
| escS | - | -/- | EscR, EspD | YscS, FliQ | PF01313 | T3S | |
| escT | - | -/- | YscT, FliR | PF01311 | T3S | Physically associated in the basal body with EscU in a 1:1 ratio; C-terminus is cytoplasmic [158] | |
| escU | - | -/- | EscrR, EscI, EspD | Yscu, FlhB | PF00771 | T3S | Physically associated in the basal body with EscT in a 1:1 ratio [158]; cleaved at NPTH motif [159]; regulates substrate specificity of secretion system [160]. |
| rorf3 (etgA) | ± | ±/± | EscI | lytic transglycosylase IagB, IpgF | Lytic transglycosylase needed to open gap in peptidoglycan for assembly of secretion system [58]; potential drug target | ||
| grIR | + | +/++ | GrlR/GrlA | Bongori regulator | Negative regulator | Will work in concert with GrlA | |
| grIA | No expression | -/- | GrlR | Bongori regulator, CaiF | Positive regulator | Will work in concert with GrlR | |
| cesD | -/EspD | ±/- | Other TPR chaperones | Chaperone for EspD | TPR chaperone [115] | ||
| escC | - | -/- | EscD | YscC, MxiD, InvG | T3S | Interacts with peptidoglycan [161], Dsb-dependent domain missing | |
| sepD | -/Translocators | -/- | SepL | None | Switches translocator/effector secretion | Works in concert with SepL | |
| escJ | - | -/- | YscJ, PrgK, FliF | PF01514 | T3S | EscD and EscJ form ring-like structure in inner membrane [66, 162, 163] | |
| rorf8 (escI) | - | -/- | EscU, rORF3 | PrgJ, MxiI, YscI | T3S | Forms inner rod within base of needle complex [65, 68-70]. | |
| sepZ | + | +/± | EscR | None | Translocated effector | ||
| orf12 | - | -/- | SsaM | T3S | Might play a role in switching translocator/effector secretion | ||
| escN | - | -/- | CesT, Tir [50] | YscN | T3S ATPAse | Forms hexameric complex | |
| escV | - | -/- | LcrD, FlhA | PF00771 | T3S | C-terminal cytoplasmic domain might play a role in gene regulation [164, 165]. | |
| orf15 | - | -/- | None | T3S | |||
| orf16 | ±/Translocators | ±/± | None | Secretion of translocators | FliK/YscP analogue? | ||
| sepQ (escQ) | - | -/- | YscQ, FliN | COG1887 | T3S | Forms ring within basal body [56]; interacts with EscL [54] | |
| espH | + | +/++ | Translocated effector | ||||
| cesF | ±/EspF? | +/+ | Chaperone for EspF | ||||
| map | + | +/++ | CesT | Translocated effector | |||
| tir | + | -/- | CesT Tir | Translocated effector | |||
| cesT | ±/Tir | -/- | Map, EspF, Tir, CesT | Many | Chaperone for Tir | Possible regulatory role, by analogy with ExsC? | |
| eae | + | -/- | Adhesin (intimin) | ||||
| escD | - | -/- | YscD, PrgH | YscD: FHA and BON domains | T3S | EscD and EscJ form ring-like structure in inner membrane [66, 162, 163]; BON domains mediate binding to phospholipids; FHA domain mediates protein-protein interactions and signalling | |
| sepL | -/Translocators | -/- | SepD | YopN, TyeA | Switches translocator/effector secretion | single protein mediating effects of YopN and TyeA; internal interaction between YopN- and TyeA-like moieties; also a translocated effector? | |
| espA | + | -/- | CesAB | flagellin | Translocator | Half-flagellin model (see text); dimerizes before polymerizes; lacks D0 and D3 domains | |
| espD | + | -/- | EspD, EscRSU, CesD, rORF1, SepZ | YopB etc | Translocator | ||
| espB | + | -/- | CesAB | YopD etc | Translocator | ||
| cesD2 | ±/EspD? | +/± | LcrR | Chaperone for EspD | LcrR will bind YopB | ||
| escF | - | -/- | YscF | Major needle component | |||
| orf29 | - | -/- | Orf2 | YPO0261, SsaI, H, CV2586 | T3S | Functionally important conserved residues can be identified by scrutiny of homologues | |
| espF | + | +/+ | Translocated effector |