TABLE 1.
Salmonella genes required for in vitro and in vivo (enteric and systemic) fitness
| Categorya | Genesa,b | Conditions (in vitro, enteric, and systemic)c,d | COGc | Protein name |
|---|---|---|---|---|
| SPI genes | ||||
| SPI-1* | invA | Na, S, C, P, Ch, MΦ, SL | U | Needle complex export protein |
| invB | Na, S, C, P, Ch, MΦ, SL | U | Secretion chaperone | |
| invC | Na, S, C, P, MΦ, PM | NU | ATP synthase SpaL | |
| invE | Na, S, C, P, Ch, MΦ, SL | U | Invasion protein | |
| invI | Na, S, C, P, Ch, MΦ, SL | S | Needle complex assembly protein | |
| sicA | Na, S, C, P, Ch, MΦ, SL | S | Secretion chaperone | |
| sipA | Na, S, C, P, Ch, MΦ | D | Secreted effector protein | |
| sipB | Na, S, C, P, Ch, MΦ, SL | U | Translocation machinery component | |
| sipD | Na, S, C, P, Ch, MΦ | S | Translocation machinery component | |
| spaO | Na, S, C, P, Ch, MΦ, PM, SL | U | Surface presentation of antigens protein SpaO | |
| spaP | Na, S, C, P, Ch, MΦ, AM, SL | U | Surface presentation of antigens protein SpaP | |
| spaQ | Na, S, C, P, Ch, SL | U | Needle complex export protein | |
| spaR | Na, S, C, P, Ch, MΦ, PM, SL | U | Needle complex export protein | |
| spaS | Na, S, C, P, Ch, MΦ | U | Surface presentation of antigens protein SpaS | |
| SPI-2* | sseC | pH, S, C, P, Ch, MΦ, SL | S | Translocation machinery component |
| SPI-3 | marT | Na, C, P, Ch, PM | K | Putative transcriptional regulator |
| SPI-11 | envF | pH, C, Ch, MΦ | XX | Putative envelope lipoprotein |
| Non-SPI genes | ||||
| Two-component system | ompR* | B, S, C, P, MΦ, SL | T | Osmolality response regulator |
| phoQ* | B, S, dLB, C, Ch, AM, SL | E | Sensor protein PhoQ | |
| barA | pH, S, C, P, Ch, MΦ | T | Hybrid sensory histidine kinase BarA | |
| O antigen biosynthetic process | rfbB | B, S, C, P, Ch, AM, SL | M | dTDP-glucose-4,6-dehydratase |
| rfbP | B, S, L4, C, P, Ch, PM | M | Undecaprenol-phosphate galactosephosphotransferase/O-antigen transferase | |
| rfbN | B, S, C, P, Ch, SL | M | Rhamnosyl transferase | |
| ATP synthase genes* | atpA | PA, Na, pH, H2, S, C, P, Ch, SL | C | FoF1-ATP synthase subunit alpha |
| atpE | PA, Na, pH, H2, S, P, Ch, MΦ, SL | C | FoF1-ATP synthase subunit C | |
| atpF | PA, Na, pH, H2, S, C, Ch, MΦ | C | FoF1-ATP synthase subunit B | |
| Mismatch repair | dam* | pH, H2, S, C, P, Ch, AM, SL | L | DNA adenine methylase |
| Chromosome segregation | xerC* | PA, pH, H2, S, C, P, Ch, SL | L | Site-specific tyrosine recombinase XerC |
| Fructose and mannose metabolism | manA* | B, L4, dLB, C, P, Ch, SL | G | Mannose-6-phosphate isomerase |
| Carbon metabolism | rpe* | pH, H2, S, C, P, Ch, SL | G | Ribulose-phosphate 3-epimerase |
| Homologous recombination | recG | B, dLB, C, P, Ch, AM | L | ATP-dependent DNA helicase RecG |
| ABC transporter | pstB* | B, L4, S, dLB, C, P, Ch, SL | P | Phosphate transporter subunit |
| Translational elongation | lepA* | B, L4, S, dLB, C, P, Ch, MΦ, SL | M | GTP-binding protein LepA |
| Iron-sulfur cluster assembly | hscA | pH, H2, C, Ch, MΦ, SL | F | Chaperone protein HscA |
| Others | csgF* | pH, C, P, Ch, MΦ, PM | U | Curli assembly protein CsgF |
| rfaQ | B, L4, dLB, C, P, Ch, SL | M | Lipopolysaccharide core biosynthesis protein | |
| rfbI | B, S, dLB, C, P, Ch, MΦ | GM | CDP-6-deoxy-delta-3,4-glucoseen reductase | |
| trmE* | PA, H2, S, C, P, Ch, SL | S | tRNA modification GTPase TrmE | |
| Putative protein | STM14_1138 | pH, C, P, Ch, MΦ | E | Putative transcriptional regulator |
| STM14_3334 | pH, C, P, SL | S | Putative DNA/RNA helicase | |
| STM14_4825 | Na, C, P, Ch, MΦ | H | Coproporphyrinogen III oxidase | |
| STM_5184 | Na, C, P, Ch, SL | S | Putative inner membrane protein | |
a
Genes marked with an asterisk (*) have been implicated in vaccine development or drug targeting against a wide range of bacteria.
b
The genes listed are required for both in vitro and in vivo fitness (enteric and systemic infection) (i.e., conditions listed in Fig. 5 and 6).
c
COG, cluster of orthologous groups (same as Fig. 2); SPI, Salmonella pathogenicity island; Na, NaCl; H2, H2O2; S, starvation; C, cattle; P, pig; Ch, chicken; MΦ, macrophage; SL, Sp-Liv; pH, pH 3; B, bile; L4, LB42; AM, A-Mice; PM, P-Mice.
d
For conditions, italic font indicates in vitro, bold font indicates enteric, and underlining indicates systemic.