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Table 3 Gene circuits linked to pathogenic phenotype. Gene symbols in the table indicate orthologs in the circuit, which are abundant in pathogenic but rarely found in nonpathogenic strains

From: Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity – a large-scale system analysis of decoded bacterial genomes

  Pathway Circuit Orthologs Genera
1 Two Component system Mg2+ starvation, antimicrobial peptide pagC, pagO, pagD, pagK, pgtE S. enterica*, B. aphidicola, E. coli*, P. ananatis, Y. pseudotuberculosis
2 Two Component system Hexose phosphate uptake uhpC, uhpA, uhpT C. trachomatis, E. coli*, S. enterica*, S. aureus, L. monocytogenes
3 Two Component system Competence Stimulating Peptide ABCC-BAC.COMA, comA, comB, comC, comD, comE S. pneumoniae, L. casei, L. rhamnosus, S. equi, L. plantarum
4 Two Component system Hypoxia,Oxygen, Nitrogen asssimilation devS, nreA, nreB, narT S. aureus*, M. tuberculosis, M. bovis, M. canettii, P. polymyxa
5 Two Component system Phosphpglycerate transport pgtC, pgtB, pgtA, pgtP S. enterica*, C. jejuni, V. cholerae, K. pneumoniae, E. coli
6 Biosynthesis of siderophore group nonribosomal peptides Yersiniabactin irp1, HMWP1, irp5, ybtE, irp3, ybtU E. coli* , Y. pestis, R. solanacearum, C. diphtheriae, K. pneumoniae
7 Biosynthesis of siderophore group nonribosomal peptides Pyochelin pchF, pchG, pchD, pchE P. aeruginosa, B. pseudomallei, B. cenocepacia, A. dieselolei, A. lipoferum
8 Bacterial secretion system Type III yscF, yscO, yscP, yscX, yscC, yscW C. trachomatis*, S. enterica, E. coli*, C. psittaci, P. aeruginosa
9 Bacterial secretion system Type V vacA, yadA, yadB_C H. pylori*, Y. pestis, Y. pseudotuberculosis, Y. enterocolitica, H. cetorum
10 Peptidoglycan biosynthesis Peptidoglycan branch sgtA, sgtB, femA, pbpA, femB, S. aureus, C. Arthromitus, E. sp., S.
11 Carotenoid biosynthesis Terpenpid backbone to Staphyloxanthin crtM, crtP, crtQ, K10212, crtO S. aureus*, B. megaterium, C. sp., S. lugdunensis, B. infantis
12 Salmonella infection Translocon sipB, ipaB, bipB, sipC, ipaC, bipC, sipD, ipaD, bipD, sseB, sseC, sseD S. enterica*, B. pseudomallei, E. coli*, S. baltica, B. mallei
13 Salmonella infection Type III secretion system/SPI-2 encoded sseJ, sifA, sseF, sseG, pipB2, sspH2, sseI, srfH, spvB S. enterica*, S. baltica, E. tarda, Y. enterocolitica, C. violaceum
14 Pentose phosphate pathway D-Glucosaminate metabolism dgaA-dgaE, PTS-Dga-EIIA, PTS-Dga-EIID, PTS-Dga-EIIB, PTS-Dga-EIIC S. enterica*, E. coli*, E. faecalis, C. difficile, L. casei
15 Bacterial invasion of epithelial cells ECM-receptor interaction pfbA, sfb1, fnbA, fnbB S. aureus, S. pyogenes, S. pneumoniae, S. dysgalactiae, S. equi
16 Phosphotransferase system Sorbose to Sorbose 1-phosphate PTS-Sor-EIIC, sorA, PTS-Sor-EIID, sorM, PTS-Sor-EIIA, sorF, PTS-Sor-EIIB, sorB E. coli*, K. pneumoniae, L. casei, L. rhamnosus, S. flexneri
17 Phosphotransferase system D-Glucosaminate to D-Glucosaminate 6-P PTS-Dga-EIIC, dgaA-dga-D, PTS-Dga-EIIA, PTS-Dga-EIID,, PTS-Dga-EIIB S. enterica*, E. coli*, E. faecalis, C. difficile, L. casei
18 Amino nucleotide sugar metabolism CMP-Pse metabolism pseC, pseH, pseF, UAP1 C. trachomatis, H. pylori*, C. jejuni, C. psittaci, P. acnes
19 Plant-pathogen interaction Bacterial secretion system hopAB, avrPtoB, avrPto1, avrRpm1, avrXccC, avrB P. syringae, _., X. campestris, _.
20 Bacterial invasion of epithelial cells Type III - Salmonella sipA-sipD, ipaA-ipaD, bipD, bipC, bipB, sopD, sptP, sopE, ipgD, sopB S. enterica, B. pseudomallei, E. coli, B. mallei, B. thailandensis
21 Bacterial invasion of epithelial cells Type III - Shigella sipC, ipaA-ipaC, bipC, sipB, bipB, ipgB1, espG, virA, ipgB2, ipgD, sopB S. enterica, E. coli, B. pseudomallei, B. mallei, B. thailandensis
22 Vibrio cholerae infection Type II secretion system ctxA, ctxB, ace, rtxA V. cholerae*, E. coli*, V. vulnificus, Y. enterocolitica, A. hydrophila
23 Vibrio cholerae infection Type IV pilus tcpA, tcpB, tcpC, tcpD, tcpE, tcpF V. cholerae*, C. rodentium, E. cloacae, R. aquatilis, R. sp.
24 Vibrio cholerae pathogenic cycle Quorum Sensing luxQ, luxU, qrr, tcpB, K10917, aphA, tcpH, tcpP V. cholerae*, V. vulnificus, V. fischeri, V. parahaemolyticus, V. sp.
25 Epithelial cell signaling in Helicobacter pylori infection Type IV secretion system cag1, cag2, cag1, cag2, cag3, virB11, lvhB11, cag7-cag25 H. pylori*, R. prowazekii, L. pneumophila, R. rickettsii, S. meliloti
26 Epithelial cell signaling in Helicobacter pylori infection Adhesins hopC, alpA, hopB, alpB, hopZ, K15846, hpaA, sdbA, sabA H. pylori*, L. pneumophila*, H. cetorum, H. acinonychis, H. bizzozeronii
27 Pathogenic Escherichia coli infection Intimate adhesion/Type III secretion system espG, virA, tir, espF, map, eae, nleA, nleH, espH, tccP, espG2 E. coli*, S. flexneri, S. sonnei, C. rodentium, S. boydii
28 Shigellosis Motility icsA, virG, espG, virA, icsB, bopA E. coli, B. pseudomallei, B. mallei, S. flexneri, S. sonnei
29 Shigellosis Type III Secretion/Downsteam ipgB1-2, ipaH9.8, ospE-G, espO, mkaD, sipA-D, ipaA-D, bipB-D, ipgD, sopB S. enterica*, E. coli*, B. pseudomallei*, B. mallei*, E. tarda
30 Salmonella infection Type III secretion system/SPI-1 encoded sipB, ipaB, bipB, sopE, ipgD, sopB, sipA, ipaA, sptP, yopJ S. enterica*, Y. pestis, B. pseudomallei, E. coli*, B. mallei*
31 Pertussis Type IV secretion system ptxD, ptxB, ptxE, ptxC, ptxA S. enterica*, B. pertussis, Y. enterocolitica, B. bronchiseptica, B. parapertussis
32 Legionellosis Adhesion/Cell entry sdeA, laiA, rtxA1, rtxA, enhC, lpnE L. pneumophila*, C. burnetii, L. longbeachae,
33 Legionellosis Dot/Icm secretion system ralF, lidA, sidC, legK1, lgt1_2_3, sidI,M, FlepB, vipA,D,E, sdbA, sdcA, drrA, lubX L. pneumophila*, L. longbeachae,
34 Staphylococcus aureus infection Colonization/MSCRMMs clfB, isdA, sdrC_D_E, sasG S. aureus*, C. pseudotuberculosis, S. epidermidis, S. pseudintermedius, E. casseliflavus
35 Staphylococcus aureus infection Surface proteins spa, sbi, clfA, sak, scn, scin, fib, efb, chp, chips, flr, flipr S. aureus*, S. lugdunensis*, S. pseudintermedius, B. thuringiensis, S. carnosus
  1. The symbol * identifies those genera for which the circuit shown was also linked to pathogenicity via within-genus comparison