Table 1.
Genes identified to be required for intracellular replication of L. monocytogenes within epithelial cells
| fold reduction | fold reduction | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| gene name or number | protein name, or protein homology/similarity to | polar effect | intrac. | invasion/adhesion | gene name or number | protein name, or protein homology/similarity to | polar effect | intrac. | invasion/adhesion |
| cell wall | protein modification | ||||||||
| 1lmo0441 | penicillin-binding protein (D-alanyl-D-alanine carboxypeptidase) | no | 9.4 | 6.1 | 5lmo0618 | protein kinase | no | 11.0 | 2.0 |
| 2,8lmo1085 | teichoic acid biosynthesis protein B | rf | 12.3 | 2 | 1lmo0763 | hypothetical Ser/Thr protein phosphatase family protein | possible | 5.5 | 2.0/5.0 |
| lmo1088 | teichoic acid biosynthesis protein B | rf | 26.2 | 1.9 | metabolism of amino acids and related molecules | ||||
| 7lmo1713 | actin-like ATPase involved in cell morphogenesis | no | 3.6 | 3.5 | lmo0594 | homoserine O-acetyltransferase | no | 7.7 | 3.9 |
| 3,5,7pbpB (lmo2039) | penicillin-binding protein 2B | rf | 3.8 | 2.6 | 6,8lmo1235 | aspartokinase II a subunit | no | 5.9 | nd |
| 1lmo2555 | Glycosyltransferase | rf | 8.1 | 3.9/5.0 | lmo1495 | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | possible | 6.2 | 1.0 |
| transport/binding proteins and lipoproteins | lmo1916 | peptidase | no | 7.0 | 2.4 | ||||
| 4lmo0135 (ctpA) | oligopeptide ABC transport system, substrate binding protein | rf | 13.6 | 2.2 | 8aroB (lmo1927) | 3-dehydroquinate synthase | rf | 2.8 | 1.4 |
| 4lmo0136 | oligopeptide ABC transport system, substrate binding protein | rf | 5.0 | 2.4 | 4,6ilvB (lmo1484) | acetolactate synthase (acetohydroxy-acid synthase) | rf | 5.5 | 1.8 |
| lmo0137 | oligopeptide ABC transport system, permease | no | 9.7 | 1.9 | 4,6ilvC (lmo1486) | ketol-acid reductoisomerase | no | 3.2 | 3 |
| 4lmo0195 | ABC-type antimicrobial peptide transport system, permease | no | 6.3 | nd | lmo2051 | weakly similar to proteases | no | 4.1 | 1 |
| lmo0495 | permease of the drug/metabolite transporter (DMT) superfamily | possible | 4.2 | 2.3 | lmo2694 | lysine decarboxylase | possible | 5.5 | 0 |
| 4lmo0584 | conserved hypothetical membrane protein, putative permease | no | 7.2 | 3.0 | lmo2770 | γ-glutamylcysteine synthetase and cyanophycin synthetase | no | 5.8 | 2.3 |
| lmo0645 | amino acid transporter | no | 4.9 | 1.5 | 6serC (lmo2825) | phosphoserine aminotransferase | possible | 5.7 | 3.5 |
| 5lmo0650 | conserved membrane protein | possible | 2.8 | 2.0 | metabolism of nucleotides and nucleic acids | ||||
| lmo0787 | amino acid transporter | no | 3.4 | 1.0 | 1,5purA (lmo0055) | adenylosuccinate synthetase | no | 14.9 | /4.0 |
| lmo0810 | spermidine/putrescine-binding protein | no | 7.4 | 3.1 | purQ (lmo1769) | phosphoribosylformylglycinamidine synthetase | rf | 12.0 | nd |
| 3lmo1003 | phosphotransferase system enzyme I | no | 3.4 | 1.0 | 8purS (lmo1771) | phosphoribosylformylglycinamidine synthetase | rf | 11.0 | 1.0 |
| gbuA (lmo1014) | glycine betaine ABC transporter, ATP-binding protein | rf | 10.0 | 4.0 | pyrE (lmo1831) | orotatephosphoribosyltransferase | no | 5.5 | 2.5 |
| 8lmo1416 | hypothetical transporter | no | 5.3 | 1.0 | metabolism of lipids | ||||
| 6opuCA (lmo1428) | glycine betaine/carnitine/choline ABC transporter, ATP-binding protein | rf | 15.7 | 1.7 | 5,8ispE (lmo0190) | CDP-ME synthase involved in isoprenoid biosynthesis | no | 4.7 | 2.3 |
| 5lmo1431 | ABC transporter, ATP binding protein | no | 4.8 | 3 | lmo1005 | 3-hydroxyisobutyrate dehydrogenase | no | 11.0 | 1.8 |
| lmo1506 | ABC-type antimicrobial peptide transport system, permease | rf | 6.2 | 2.3 | lmo1363 | geranyltransferase | no | 5.0 | 2.8 |
| lmo1739 | amino acid ABC transporter | rf | 5.5 | 2 | lmo2450 | carboxylesterase | possible | 4.2 | 3.0 |
| 3,5,7,8lmo1847 | ABC transporter specific for metal cations | no | 5.8 | 2.3 | metabolism of coenzymes and prosthetic groups | ||||
| lmo2124 | maltodextrin ABC transport system, permease | rf | 3.4 | 0 | 5lmo0221 | hypothetical type III pantothenate kinase | possible | 6.9 | 1.0 |
| 1,3oppF (lmo2192) | oligopeptide ABC-transporter, ATP-binding protein | no | 21.0 | 8.0/4.0 | 1,3pdxK (lmo0662) | pyridoxine kinase | no | 13.1 | 1/4.0 |
| lmo2227 | ABC transporter, ATP-binding protein | possible | 5.8 | 1.3 | lmo1043 | molybdopterin-guanine dinucleotide biosynthesis MobB | rf | 7.9 | 1.4 |
| lmo2249 | low-affinity inorganic phosphate transporter | no | 2.8 | 2.0 | lmo1932 | heptaprenyl diphosphate synthase component I | rf | 12.1 | 4.8 |
| lmo2353 | hypothetical Na+/H+ antiporter | no | 4.3 | 2.3 | nadB (lmo2023) | L-aspartate oxidase | rf | 3.4 | 0 |
| lmo2380 | protein involved in resistance to cholate/Na+ and in pH homeostasis | rf | 5.7 | 2.5 | 3lmo2102 | glutamine amidotransferase subunit PdxT (pyridoxine biosynthesis) | no | 4.0 | 3.3 |
| lmo2430 | B. subtilis ferrichrome ABC transporter FhuG, permease | rf | 75.6 | 5.0 | lmo2566 | biotin/lipoate A/B protein ligase family | possible | 6.2 | 2.0 |
| lmo2816 | transport protein | no | 6.3 | 2.0 | DNA restriction/modification and repair | ||||
| lmo2850 | sugar transport protein | rf | 16.5 | 0 | 5gyrB (lmo0006) | DNA gyrase subunit B | rf | 9.6 | nd |
| sensors | lmo0157 | ATP-dependent helicase | possible | 2.1 | 1.0 | ||||
| lmo0799 | oxygen/light sensor with PAS domain | no | 8.3 | 2.0 | mfd (lmo0214) | transcription-repair coupling factor | possible | 8.9 | 3.7 |
| lmo1508 | two-component sensor histidine kinase | no | 5.2 | 2.9 | lmo0588 | DNA photolyase | no | 9.6 | 2.0 |
| membrane bioenergetics | mutM (lmo1564) | formamidopyrimidine-DNA glycosylase | no | 5.2 | 1.1 | ||||
| lmo0091 | ATP synthase g chain, H+-transporting two-sector ATPase | rf | 5.7 | 2.0 | lmo1751 | hypothetical RNA methyltransferase | no | 6.2 | 2.0 |
| nifJ (lmo0829) | pyruvate-flavodoxin oxidoreductase | no | 6.4 | 3.6 | 8ansB (lmo1663) | asparaginyl-tRNA synthetases | no | 4.1 | 1.6 |
| 5atpA (lmo2531) | H+-transporting ATP synthase chain α | rf | 7.7 | 2.7 | lmo2050 | exconuclease ABC (subunit A) | no | 5.1 | 2.0 |
| atpB (lmo2535) | H+-transporting ATP synthase chain β | rf | 4.4 | 5.9 | DNA recombination | ||||
| mobility and chemotaxis | 6recN (lmo1368) | RecN | no | 14.8 | 1.9 | ||||
| lmo0680 | flagella-associated protein FlhA | rf | 7.0 | 3.1 | ruvB (lmo1532) | Holliday junction DNA helicase RuvB | possible | 9.4 | 3.9 |
| 6lmo0700 | flagellar motor switch protein FliY | rf | 5.8 | 1.7 | 8recS (lmo1942) | similar to ATP-dependent DNA helicase | no | 7.0 | 2.3 |
| cell surface proteins | regulation | ||||||||
| 1,2,6vip (lmo0320) | putative peptidoglycan bound protein with LPXTG motif | no | 6.4 | 4.5 | 3agrA (lmo0051) | 2-component response regulator protein | no | 3.4 | 1.0 |
| 8lmo0327 | protein with LPXTG motif, putative murein hydrolase activity | no | 6.9 | 3.0 | 6lmo0294 | transcription regulator, LysR-gltR family | no | 7.4 | 3.1 |
| 4lmo0514 | internalin-like protein with LPXTG motif | no | 6.4 | 1.4 | lmo0535 | transcription regulator, LacI family | no | 9.5 | 1.0 |
| 4lmo0576 | hypothetical cell wall associated protein | no | 4.2 | 1.5 | 3fur (lmo1956) | transcriptional regulator, Fur family | no | 5.5 | 1.0 |
| 2,8lmo1666 | peptidoglycan linked protein with LPXTG motif | no | 6.8 | 1.8 | lmo1994 | transcription regulators, LacI family | no | 9.0 | 1.4 |
| lmo2026 | hypothetical peptidoglycan bound protein with LPXTG motif | no | 8.7 | 1.4 | RNA modification | ||||
| 5lmo2504 | cell wall binding protein, peptidase-related enzyme | no | 4.8 | 2.0 | lmo0241 | hypothetical RNA methyltransferase, trmH family protein | rf | 4.1 | 1.0 |
| 1ami (lmo2558) | autolysin, N-acetylmuramoyl-L-alanine amidase | no | 3.8 | 5.3 | 1,3,5lmo1434 | RNA-metabolising metallo-β-lactamase | no | 9.6 | 3/22 |
| metabolism of carbohydrates and related molecules | miscellaneous | ||||||||
| glpQ (lmo0052) | transmembrane protein with phosphoesterase domain | possible | 4.1 | 2.0 | lmo0066 | toxin component of A/B toxin | rf | 2.8 | 1.0 |
| 8lmo0182 | α-xylosidase and α-glucosidase | rf | 7.9 | 1.3 | 4lmo0585 | secreted protein | no | 4.8 | 1.0 |
| lmo0261 | phospho-β-glucosidase | no | 3.4 | 0 | lmo0587 | secreted protein, YapH from Y. pestis, cell wall surface protein | no | 3.4 | 1.0 |
| 8lmo0271 | phospho-β-glucosidase | possible | 4.1 | 1.0 | unknown proteins | ||||
| lmo0517 | phosphoglycerate mutase | no | 13.8 | 2.3 | lmo0276 | hypothetical hydrolase, HAD superfamily | possible | 5.2 | 1.3 |
| 2lmo1031 | hypothetical L-fucose isomerase | rf | 11.1 | 2.1 | 2lmo0313 | hypothetical hydrolase, PHP superfamily | no | 2.8 | 1.0 |
| 2lmo1032 | Transketolase | rf | 14.4 | 4lmo0590 | hypothetical DAK2/DegV domain-containing protein | possible | 9.6 | 1.0 | |
| lmo1166 | NADPH-dependent butanol dehydrogenaseI | possible | 4.2 | 1.0 | lmo0765 | unknown protein | possible | 10.4 | 3.0 |
| 4glpD (lmo1293) | glycerol-3-phosphate dehydrogenase | no | 4.8 | 1.0 | 4,6,7lmo0794 | B. subtilis YwnB protein | no | 12.4 | 2.0 |
| 6lmo1244 | weakly similar to phosphoglycerate mutase 1 | no | 8.3 | 2.0 | lmo1379 | B. subtilis SpoIIIJ protein, hypothetical membrane protein | no | 4.8 | 3.0 |
| lmo2005 | Oxidoreductase | no | 7.4 | 3.9 | 3lmo1402 | B. subtilis YmcA protein | no | 2.1 | 2.0 |
| lmo2015 | α-mannosidase | no | 6.4 | 1.7 | lmo1575 | phosphoesterase, DHH superfamily | no | n.d. | 1.0 |
| lmo2134 | fructose-1,6-biphosphate aldolase type II | no | 5.2 | 2.4 | 6,8lmo1700 | unknown protein | no | 4.6 | 1.3 |
| lmo2172 | propionate CoA-transferase | possible | 5.3 | 1.3 | 4lmo1830 | short chain dehydrogenase | no | 11.7 | 2.0 |
| lmo2247 | Oxidoreductase | possible | 5.0 | 2.4 | lmo1866 | hypothetical phosphotransferase | possible | 7.1 | 2.2 |
| 8lmo2446 | Glycosidase | no | 9.9 | 2.5 | lmo1920 | unknown protein | 16.5 | 1.0 | |
| lmo2586 | formate dehydrogenase α-chain | possible | 2.4 | 2.2 | lmo2516 | conserved hypothetical protein | possible | 3.6 | 1.2 |
| 6lmo2660 | Transketolase | rf | 3.0 | 2.6 | lmo2639 | unknown protein, contains DUF1312 domain | possible | 5.5 | 1.0 |
| lmo2764 | xylose operon regulatory protein and to glucose kinase | rf | 3.6 | 2.1 | no similarity | ||||
| 2lmo2781 | β-glucosidase | rf | 6.5 | 2.0 | lmo0729 | no similarity | no | 4.8 | 1.0 |
| lmo2831 | Phosphoglucomutase | no | 5.3 | 2.8 | 2lmo1188 | no similarity | no | 5.1 | 3.5 |
| lmo1219 | no similarity | no | 4.8 | 2.0 | |||||
| lmo2129 | no similarity | no | 5.8 | 1.6 | |||||
1adhesion (seven genes) or invasion (four genes) defective as determined 35 min or 2 h post infection, respectively; 2genes without homologue in L. innocua; genes downregulated3 or upregulated4 during growth in macrophages [11]; genes downregulated5 or upregulated6 during growth in Caco-2 cells [12]; 7induced in vivo [23]; 8prfA binding box is located upstream [13]. Fold reduction of intracellular (intrac.) replication in comparison to a control group of >100 insertion mutants [12]. rf, related function of downstream genes. Four genes from categories which one gene only (1.6 protein secretion, 1.7 cell division, 1.10 transformation, and 3.7 protein synthesis) was assigned to are not shown. See also Additional file 6 for generation times.