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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.

From: Bioinformatics analysis of the locus for enterocyte effacement provides novel insights into 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