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Table 4 Conservation of Sakai virulence-related genes in EHECs and other sequenced pathogenic E. coli strains

From: Extensive genomic diversity and selective conservation of virulence-determinants in enterohemorrhagic Escherichia colistrains of O157 and non-O157 serotypes

     In silico* No. of strains conserved†
Gene Location Conservation in K-12 Common name/description CFT073 UTI89 536 APEC O157 (8) O26 (8) O111 (6) O103 (6)
Genes related to adhsion (not fimbrial genes)            
ECs0336 S-loop20 Partly conserved Putative invasin + + + + [8] [8] [6] [6]
ECs0350 S-loop23 Absent HmwA-like protein - - + - (7) 0 0 0
ECs0362 S-loop24 Absent AidA-I adhesin-like protein - - - - [8] [8] [6] [6]
ECs0548 S-loop43 Absent Saa-like protein - + - + [8] 0 0 0
ECs1360 SpLE1 Absent Iha adhesin + - - - [8] [8] [6] 2
ECs1396 SpLE1 Conserved AidA-I adhesin-like protein - - - - (7) [8] 0 [6]
ECs1772 Sp9 Absent Paa - - - - [8] (7) [6] 4
ECs2006 Backbone Absent BigA-like protein - - - - [8] 0 0 0
ECs2007 Backbone Absent BigB-like protein - - - - [8] 0 0 0
ECs2567 Backbone Conserved Putative adhesin + + + + [8] [8] [6] [6]
ECs3860 SpLE3 Absent Efa1 (interrupted) - - - - (7) [8] [6] [6]
ECs3861 SpLE3 Absent Efa1 (partial) - - - - (7) [8] [6] [6]
ECs4559 SpLE4 (LEE) Absent Gamma intimin - - - - [8] 0 0 0
ECs5290 S-loop288 Absent Putative invasin - - - - (7) 0 0 0
Genes confer resistance to host immune response            
ECs0218 S-loop14 Absent IcmF-like protein - - - - [8] [8] [6] [6]
ECs1236 Sp5 Absent Lom - - - - 5 1 2 0
ECs1312 SpLE1 Absent TraT - - - - (7) (7) 0 3
ECs1956 Sp10 Absent IrsA-like protein - - - + 5 1 (5) 1
ECs3850 SpLE3 Absent PagC-like protein - - - - [8] 0 [6] 2
RF001 Sp5, 8 Conserved Bor + + + + 6 [8] 1 5
RF098 Sp4, 10 Absent Copper/zinc-superoxide dismutase - - - - 4 1 (5) [6]
RF115 Sp3, 4, 8 - 12, 14, 15 Absent Lom - - - + [8] [8] [6] [6]
Toxins and activators            
ECs0541 S-loop42 Absent RTX-like protein - - - - [8] 0 0 0
ECs0542 S-loop42 Absent RTX-like protein - - - - [8] 0 0 0
ECs0814 Sp3 Absent SfpA (systemic factor protein A)-like protein - - - - [8] [8] [6] [6]
ECs1205 Sp5 Absent Shiga toxin 2 subunit A - - - - 4 1 2 1
ECs1206 Sp5 Absent Shiga toxin 2 subunit B - - - - 3 1 2 1
ECs1282 S-loop71 Absent Hemagglutinin/hemolysin - related protein - - - - [8] 0 0 0
ECs1283 S-loop71 Absent Hemolysin activator - related protein - - - - [8] 0 0 0
ECs1382 SpLE1 Absent HecB-like protein - - - - 5 (7) [6] 2
ECs1652 Sp8 Absent Putative catalase - - - - [8] 0 0 0
ECs1677 Backbone Conserved Hemolysin E - - - - [8] [8] [6] [6]
ECs2973 Sp15 Absent Stx1B - - - - 6 (7) [6] [6]
ECs2974 Sp15 Absent Stx1A - - - - 6 (7) [6] [6]
Regulators            
ECs1274 s-loop71 Absent GrvA - - - - [8] 0 0 0
ECs1388 SpLE1 Absent PchD + - - + 4 (7) 2 2
ECs1588 Sp7 Absent PchE - - - - (7) [8] 0 4
ECs3105 Backbone Conserved RcsD + + + + [8] [8] [6] [6]
ECs3106 Backbone Conserved RcsB + + + + [8] [8] [6] [6]
ECs3107 Backbone Conserved RcsC + + + + [8] [8] [6] [6]
ECs3720 ETT2 Absent EtrA - - - - [8] [8] 4 4
ECs3734 ETT2 Absent EivF - - - - [8] 0 0 0
ECs4577 SpLE4 (LEE) Absent GrlA - - - - [8] [8] 4 (5)
ECs4578 SpLE4 (LEE) Absent GrlR - - - - [8] [8] 4 4
ECs4588 SpLE4 (LEE) Absent Ler - - - - [8] [8] (5) [6]
RF132 Sp4, 11, 14 Absent PchA, B, C - - - - [8] (7) [6] [6]
Secretion machineries            
ECs0540 S-loop42 Absent CyaE-like protein - - - - [8] 0 0 0
ECs0543 S-loop43 Absent Putative RTX toxin secretion ATP-binding protein - - - - [8] 0 0 0
ECs0544 S-loop44 Absent Putative RTX toxin secretion membrane fusion protein - - - - [8] 0 0 0
ECs3716 ETT2 Absent EprK - - - - [8] [8] (5) (5)
ECs3717 ETT2 Absent EprJ - - - - [8] [8] 4 (5)
ECs3718 ETT2 Absent EprI - - - - [8] [8] (5) 4
ECs3719 ETT2 Absent EprH - - - - [8] [8] 4 (5)
ECs3721 ETT2 Absent EpaS - - - - [8] [8] (5) (5)
ECs3722 ETT2 Absent EpaR2 - - - - [8] [8] 4 4
ECs3723 ETT2 Absent EpaR1 - - - - [8] [8] (5) 4
ECs3724 ETT2 Absent EpaQ - - - - [8] [8] (5) (5)
ECs3725 ETT2 Absent EpaP - - - - [8] [8] 4 4
ECs3726 ETT2 Absent EpaO - - - - [8] 1 0 2
ECs3727 ETT2 Absent EivJ - - - - [8] 0 0 0
ECs3729 ETT2 Absent EivI - - - - [8] 0 0 0
ECs3730 ETT2 Absent EivC - - - - [8] 0 0 0
ECs3731 ETT2 Absent EivA - - - - [8] 0 0 0
ECs3732 ETT2 Absent EivE - - - - [8] 0 0 0
ECs3733 ETT2 Absent EivG - - - - [8] 0 0 0
ECs4551 SpLE4 (LEE) Absent Orf29 - - - - [8] 3 [6] (5)
ECs4552 SpLE4 (LEE) Absent EscF - - - - [8] [8] [6] [6]
ECs4553 SpLE4 (LEE) Absent CesD2 - - - - [8] [8] [6] [6]
ECs4555 SpLE4 (LEE) Absent EspD - - - - [8] 0 0 1
ECs4556 SpLE4 (LEE) Absent EspA - - - - [8] 1 0 1
ECs4557 SpLE4 (LEE) Absent SepL - - - - [8] [8] [6] (5)
ECs4558 SpLE4 (LEE) Absent EscD - - - - [8] 0 3 2
ECs4560 SpLE4 (LEE) Absent CesT - - - - [8] 6 [6] [6]
ECs4563 SpLE4 (LEE) Absent CesF - - - - [8] 0 0 0
ECs4565 SpLE4 (LEE) Absent SepQ - - - - [8] 0 0 1
ECs4566 SpLE4 (LEE) Absent Orf16 - - - - [8] 0 (5) 0
ECs4567 SpLE4 (LEE) Absent Orf15 - - - - [8] 6 (5) 4
ECs4568 SpLE4 (LEE) Absent EscN - - - - [8] 4 (5) 3
ECs4569 SpLE4 (LEE) Absent EscV - - - - [8] 6 (5) 2
ECs4570 SpLE4 (LEE) Absent Orf12 - - - - [8] 4 4 2
ECs4572 SpLE4 (LEE) Absent Rorf8 - - - - [8] 0 0 0
ECs4573 SpLE4 (LEE) Absent EscJ - - - - [8] 3 4 2
ECs4574 SpLE4 (LEE) Absent SepD - - - - [8] 0 4 2
ECs4575 SpLE4 (LEE) Absent EscC - - - - [8] [8] [6] 4
ECs4576 SpLE4 (LEE) Absent CesD - - - - [8] 5 4 3
ECs4579 SpLE4 (LEE) Absent Rorf3 - - - - [8] 1 4 2
ECs4580 SpLE4 (LEE) Absent EscU - - - - [8] (7) (5) 4
ECs4581 SpLE4 (LEE) Absent EscT - - - - [8] (7) 4 3
ECs4582 SpLE4 (LEE) Absent EscS - - - - [8] [8] (5) (5)
ECs4583 SpLE4 (LEE) Absent EscR - - - - [8] [8] 4 (5)
ECs4584 SpLE4 (LEE) Absent Orf5 - - - - [8] [8] [6] (5)
ECs4585 SpLE4 (LEE) Absent Orf4 - - - - [8] [8] 4 (5)
ECs4586 SpLE4 (LEE) Absent Orf3 - - - - [8] 6 [6] (5)
ECs4587 SpLE4 (LEE) Absent Orf2 - - - - [8] 3 1 2
T3SS effectors (LEE encoded)            
ECs4550 SpLE4 (LEE) Absent EspF1 - - - - [8] 0 0 0
ECs4554 SpLE4 (LEE) Absent EspB - - - - [8] 0 0 0
ECs4561 SpLE4 (LEE) Absent Tir - - - - [8] 0 0 0
ECs4562 SpLE4 (LEE) Absent Map - - - - [8] 0 0 2
ECs4564 SpLE4 (LEE) Absent EspH - - - - [8] [8] 0 [6]
ECs4571 SpLE4 (LEE) Absent SepZ - - - - [8] 0 0 0
ECs4590 SpLE4 (LEE) Absent EspG - - - - [8] 1 3 2
T3SS effectors (non-LEE encoded)            
ECs0061 Backbone Conserved EspY1 - - - - [8] 0 0 0
ECs0847 Sp3 Absent NleC - - - - [8] (7) 1 1
ECs0848 Sp3 Absent NleH1-1 - - - - [8] 1 0 3
ECs0850 Sp3 Absent NleD - - - - [8] 0 0 4
ECs0876 S-loop57 Absent EspX2 - - - - [8] 0 0 0
ECs1127 Sp4 Absent EspK - - - - [8] [8] [6] [6]
ECs1560 Sp6 Absent EspX7 - - - - [8] (7) [6] [6]
ECs1561 Sp6 Absent EspN - - - - [8] (7) (5) [6]
ECs1567 Sp6 Absent EspO1-1 - - - - [8] 0 [6] 1
ECs1568 Sp6 Absent EspR1 - - - - [8] [8] [6] [6]
ECs1810 Sp9 Absent NleG2-1 - - - - (7) (7) [6] 1
ECs1811 Sp9 Absent NleG2-1 - - - - (7) (7) 0 2
ECs1812 Sp9 Absent NleA/EspI - - - - (7) (7) 0 1
ECs1814 Sp9 Absent NleH1-2 - - - - 4 6 [6] [6]
ECs1815 Sp9 Absent NleF - - - - 4 6 [6] [6]
ECs1824 Sp9 Absent NleG - - - - [8] (7) [6] 0
ECs1825 Sp9 Absent EspM1 - - - - [8] (7) [6] 0
ECs2226 Sp12 Absent NleG7 - - - - [8] [8] [6] [6]
ECs2714 Sp14 Absent EspJ - - - - [8] 0 0 1
ECs3485 Sp17 Absent EspM2 - - - - [8] (7) [6] 2
ECs3486 Sp17 Absent NleG8-2 - - - - [8] (7) [6] 3
ECs3487 Sp17 Absent EspW - - - - [8] (7) [6] 3
ECs3855 SpLE3 Absent EspL2 - - - - [8] [8] [6] [6]
ECs3857 SpLE3 Absent NleB1 - - - - [8] [8] [6] [6]
ECs3858 SpLE3 Absent NleE - - - - [8] [8] [6] [6]
ECs4653 S-loop252 Absent EspY4 - - - - [8] 0 0 0
RF004 Sp4, 14 Absent Tccp, TccP2 - - - - [8] 1 2 4
RF067 Sp10, 11 Absent NleG2-2, NleG2-3 - - - - [8] [8] [6] 4
RF069 Sp10, 11, 17 Absent NleG6-1, NleG6-2, NleG6-3 - - - - [8] (7) [6] 3
RF070 Sp10, 11 Absent NleG5-1, NleG5-2 - - - - [8] (7) (5) 1
Plasmid encoded            
pO157_01 pO157 Absent Metalloprotease StcE - - - - [8] 0 0 0
pO157_02 pO157 Absent Type II secretion pathway related protein - - - - [8] 1 0 3
pO157_03 pO157 Absent Type II secretion pathway related protein - - - - [8] 1 0 3
pO157_04 pO157 Absent Type II secretion pathway related protein - - - - [8] 1 0 3
pO157_05 pO157 Absent Type II secretion pathway related protein - - - - [8] 0 0 2
pO157_06 pO157 Absent Type II secretion pathway related protein - - - - [8] 2 0 3
pO157_07 pO157 Absent Type II secretion pathway related protein - - - - [8] 1 0 3
pO157_08 pO157 Absent Type II secretion pathway related protein - - - - [8] 0 0 3
pO157_09 pO157 Absent Type II secretion pathway related protein - - - - [8] 1 0 3
pO157_10 pO157 Absent Type II secretion pathway related protein - - - - [8] 0 0 1
pO157_11 pO157 Absent Type II secretion pathway related protein - - - - [8] 1 0 3
pO157_12 pO157 Absent Type II secretion pathway related protein - - - - [8] 1 0 3
pO157_13 pO157 Absent Type II secretion pathway related protein - - - - [8] 0 0 1
pO157_14 pO157 Absent Type II secretion pathway related protein - - + + [8] 0 0 1
pO157_17 pO157 Absent Hemolysin C - - - - [8] [8] (5) 3
pO157_18 pO157 Absent Hemolysin A - - - - [8] (7) (5) 4
pO157_19 pO157 Absent Hemolysin B - - - - [8] (7) (5) 4
pO157_20 pO157 Absent Hemolysin D - - - - [8] (7) (5) 4
pO157_39 pO157 Absent Hemagglutinin-associated protein - + - - [8] 5 0 1
pO157_59 pO157 Absent Putative adherence factor, Efa1 homolog - - - - [8] 3 0 (5)
pO157_76 pO157 Absent KatP - - - - 6 6 (5) 2
pO157_79 pO157 Absent EspP - - - - [8] (7) [6] 4
pO157_80 pO157 Absent Putative polysaccharide deacetylase (ecf1) - - - - [8] (7) (5) 4
pO157_81 pO157 Absent Putative LPS-1,7-N-acetylglucosamine transferase (ecf2) - - - - [8] (7) (5) 4
pO157_82 pO157 Absent Putative membrane protein (ecf3) - - - - [8] (7) (5) 4
pO157_83 pO157 Absent Putative lipid A myristoyl transferase, MsbB2 (ecf4) - - - - [8] (7) (5) 4
  1. *Conservation of O157 Sakai virulence genes in four sequenced pathogenic E. coli strains was determined according to the results of homology search using the BLASTP program. The threshold for presence (+) or absence (-) determination was ≥90% sequence identity and ≥50% aligned length coverage of a query sequence. † Genes conserved in all strains are indicated by brackets in bold, and those absent only in one strain by parentheses in bold.
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