Table 1. Selection of down (log2 FC < -1.5, red)- and up (log2 FC > -1.5, green)-regulated Y. enterocolitica genes 12 h and 24 h p.i.
AMP, antimicrobial peptide; P, phosphate; PTS, phosphotransferase system; BCAA, branched-chain amino acid; dep., dependent; n.s., not significant.
| 12 h | 24 h | gene name | (predicted) function or product | COG | 12 h | 24 h | gene name | (predicted) function or product | COG | 12 h | 24 h | gene name | (predicted) function or product | COG | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| virulence factors, iron metabolism | virulence factors, iron metabolism | cell wall, membrane, and envelop biogenesis | ||||||||||||||
| n.s. | xaxB | α-xenorhabdolysin family binary toxin | R | n.s. | srfB | virulence factor SrfB | S | murPQ, anmK | anhydro-N-acetylmuramic acid utilization | G | ||||||
| hxuB | hemolysin secretion/activation | U | n.s. | cirA | iron-regulated outer virulence protein | P | ompD | outer membrane pore protein | M | |||||||
| n.s. | yqfA | hemolysin III | S | n.s. | shlB | hemolysin transporter/activator | U | galE | UDP-glucose 4-epimerase | M | ||||||
| n.s. | lktD | HlyD membrane-fusion protein of T1SS | M | n.s. | hxuB | hemolysin secretion/activation | U | n.s. | ftsI | cross-linking of the peptidoglycan cell wall | M | |||||
| n.s. | mgtAC | magnesium transporting P-type ATPase | S | n.s. | sodA | superoxide dismutase [Mn] | C | n.s. | rfaQ | lipopolysaccharide biosynthesis | M | |||||
| n.s. | tcaR1 (aaeR) | toxin complex gene repressor | K | /n.s. | tcaAB | insecticidal toxin complex subunits AB | K | agp | glucose-1-phosphatase | M | ||||||
| n.s. | fepDG | ferric enterobactin transport | P | n.s. | tcaR2 | toxin complex gene activator | K | emtA | lytic murein transglycosylase | M | ||||||
| dinI | virulence protein MsgA | S | tpd | high-affinity Fe2+ transport | P | n.s. | mliC | lysozyme inhibitor | M | |||||||
| amino acid metabolism and transport | ftnA | ferritin-1, iron-storgae | P | n.s. | glycosyltransferase | M | ||||||||||
| metABCFHIJLNQS | methionine biosynthesis/transport | E | sitABCD | chelated iron transport system | U | n.s. | lptD | oligogalacturonate-specific porin (KdgM) | M | |||||||
| mtnABCD | methionine biosynthesis/transport | E | sitCD | chelated iron transport system | U | n.s. | slyB | outer membrane lipoprotein Pcp | M | |||||||
| n.s. | map | methionine aminopeptidase | E | n.s. | fepA | ferric enterobactin receptor | M | n.s. | mppA | periplasmic murein peptide-binding protein | E | |||||
| ilvABDEGMN | isoleucine biosynthesis | E | n.s. | hemR | hemin receptor | P | signalling | |||||||||
| n.s. | livFGM | BCAA transport | U | foxA | ferrioxamine receptor | P | n.s. | cstA | carbon starvation protein A | T | ||||||
| n.s. | leuABCD | leucine biosynthesis | E | fbpA | Fe3+-binding periplasmic protein | P | n.s. | dksA | DnaK suppressor protein | T | ||||||
| n.s. | cysHIJM | cysteine biosynthesis from sulfate | EH | hasA | hemophore | C | cheV | two component signalling adaptor domain | T | |||||||
| n.s. | cysCDGN | assimilatory sulfate reduction | F | phlA | hemolysin secretion/phospholipase | IU | n.s. | lsrABCDGFKR | autoinducer 2 import/regulation/degradation | G | ||||||
| n.s. | cysAPTW | sulfate transport | P | amino acid metabolism and transport | n.s. | traI | acyl-homoserine-lactone synthase | H | ||||||||
| n.s. | hisDG | histidine biosynthesis | E | n.s. | metCIN | methionine metabolism and transport | E | n.s. | LuxR family transcription regulatory protein | K | ||||||
| /n.s. | trpEG/mtr | tryptophan biosynthesis/transport | EHU | n.s. | metE | homocysteine methyltransferase | E | resistance | ||||||||
| n.s. | gltBD | glutamate synthesis | E | metY | o-acetylhomoserine (thiol)-lyase | E | n.s. | crcB | reduces fluoride concentration in the cell | U | ||||||
| /n.s. | ddpABCDF; oppD | dipeptide transport | E | n.s. | putAPY | proline metabolism and transport | E | n.s. | tehB | tellurite resistance | PQ | |||||
| n.s. | hutU | histidine degradation | E | proX | glycine betaine-binding protein | E | n.s. | bleomycin resistance | S | |||||||
| cofactors | n.s. | gcvHPT | glycine degradation | E | yiiM | 6-N-hydroxylaminopurine resistance | S | |||||||||
| thiCEFGHIS | thiazole biosynthesis | H | n.s. | ureCDEFG | urease subunit/accessory proteins | E | n.s. | cusA/czcA | resistance-nodulation-cell division | P | ||||||
| n.s. | bioABCDF | biotin synthesis | H | ureAB | urease subunits | E | n.s. | ohr | organic hydroperoxide resistance | O | ||||||
| n.s. | birA | biotin-operon repressor | HK | n.s. | cysK | cysteine synthase | E | n.s. | bhsA | multiple stress resistance | S | |||||
| fthC | 5-formyltetrahydrofolate cyclo-ligase | H | tdcC | threonine/serine transporter | U | n.s. | cutC | copper homeostasis | P | |||||||
| n.s. | lipB | octanoyltransferase (lipoate-dep. enzymes) | H | n.s. | tdcB | threonine dehydratase | E | n.s. | copA | copper-exporting P-type ATPase | P | |||||
| n.s. | moaD | molybdopterin-convertion | H | n.s. | thrA | threonine synthesis | E | n.s. | yobA | copper resistance | S | |||||
| carbohydrate metabolism | n.s. | gltS | sodium/glutamate symport | P | n.s. | ampC | β-lactamase | V | ||||||||
| yadE | polysaccharide deacetylase | G | n.s. | gltJ | glutamate/aspartate transport system | E | n.s. | penP | β-lactamase | V | ||||||
| suhB | inositol-1-monophosphatase | G | gltI | glutamate/aspartate-binding protein | ET | carbohydrate metabolism and transport | ||||||||||
| ybbD | glycosyl hydrolase family | G | /n.s. | glnPQ | glutamine transport | E | n.s. | gpmA | phosphoglycerate mutase | G | ||||||
| cell wall, membrane, and envelop biogenesis | glnK | nitrogen regulatory protein P-II 2 | K | glpF | glycerol uptake facilitator | U | ||||||||||
| n.s. | lipid A biosynthetic process | M | glsA | glutaminase 2 | E | n.s. | glpDKQT | glycerol catabolism | G | |||||||
| ftsI | peptidoglycan synthetase | M | n.s. | aspA | aspartate ammonia-lyase | E | n.s. | sorBF | sorbose-specific PTS | G | ||||||
| n.s. | murDF | peptidoglycan synthesis | M | n.s. | hisHIJMPQU | histidine transport/degradation | ET | n.s. | agaCV | N-acetylgalactosamine permease | G | |||||
| mraY | peptidoglycan synthesis | M | n.s. | sdaABC | serine dehydratase/transporter | E | n.s. | celC | lactose-cellobiose-chitobiose-specific PTS | G | ||||||
| ftsW | cell division | D | n.s. | glyA | serine hydroxymethyltransferase | E | n.s. | ulaB | ascorbate-specific PTS subunit | G | ||||||
| n.s. | O-antigen biosynthesis | M | trpDEG | anthranilate phosphoribosyltransf./synthase | F | n.s. | cmtB | mannitol-specific cryptic PTS | G | |||||||
| ompC | outer membrane | M | n.s. | tnaA | tryptophanase | E | n.s. | uhpAC | regulation of hexose-P uptake | G | ||||||
| n.s. | lpxLM | lipid A biosynthesis | M | n.s. | argD | succinylornithine transaminase | H | /n.s. | xylFG | D-xylose import | G | |||||
| murJ | virulence factor mviN homolog | U | n.s. | acyG | subtilase | E | rbsB | D-ribose-binding periplasmic protein | G | |||||||
| n.s. | lnt | apolipoprotein N-acyltransferase | M | n.s. | aroFP | aromatic amino acid synthesis/transport | E | malEKMT | maltose operon (uptake and regulation) | S | ||||||
| ttgA | membrane fusion protein | M | n.s. | speF | ornithine decarboxylase | E | lamB | maltoporin (maltodextrin permease) | E | |||||||
| mltD | lytic murein transglycosylase D | M | n.s. | prtA | secreted protease | E | n.s. | iolABCDGET | inositol uptake and utilization | C | ||||||
| n.s. | tolA | cell envelope integrity | M | n.s. | pepD | dipeptidase | E | n.s. | dctA | C4-dicarboxylate transport | U | |||||
| degP | protease | M | n.s. | tesA | acyl-CoA thioesterase | E | n.s. | dcuAB | anaerobic C4-dicarboxylate transporter | U | ||||||
| n.s. | pgaBC | biofilm PGA synthesis | M | n.s. | ilvC | ketol-acid reductoisomerase | EH | n.s. | treBC | trehalose uptake and utilization | G | |||||
| n.s. | tolQR | outer membrane stability | U | n.s. | livK | BCAA-binding protein | E | /n.s. | srlAE | glucitol sorbitol-specific PTS | G | |||||
| signalling | n.s. | tauABCD | taurine transport and metabolism | P | n.s. | sorbitol-6-P-2-dehydrogenase | IQ | |||||||||
| n.s. | Lux regulon | K | cofactors | n.s. | mglABC | (methyl) galactoside/galactose transport | U | |||||||||
| n.s. | LuxR-family | KT | n.s. | kbl | 2-amino-3-ketobutyrate coenzyme A ligase | H | n.s. | nagBE | N-acetylglucosamine-transport/utilization | G | ||||||
| resistance | n.s. | wrbA | flavoprotein | H | fruB | multiphosphoryl transfer protein | G | |||||||||
| yoaE | heavy metal efflux pump | P | n.s. | yfiQ | CoA binding domain | H | n.s. | pehX | exo-poly-α-D-galacturonosidase | G | ||||||
| n.d. | tellurium-resistance | S | cell motility | n.s. | gmuD | 6-phospho-β-glucosidase gmuD | G | |||||||||
| /n.s. | cusA/czcA | resistance-nodulation-cell division | P | cheR | chemotaxis protein methyltransferase | H | n.s. | fbaA | fructose-bisP aldolase class 2 | G | ||||||
| n.s. | acrF | acriflavine resistance | V | cheD2 | methyl-accepting chemotaxis protein | NT | n.s. | fbp | fructose-1,6-bisP class 1 | G | ||||||
| mdlB | multidrug resistance | V | n.s. | tar | methyl-accepting chemotaxis protein | NT | n.s. | ptsG | glucose-specific PTS | G | ||||||
| /n.s. | arnT/arnB | resistance to polymyxin and cationic AMP | I | cheABWYZ | chemotaxis | KT | n.s. | glgP | glycogen phosphorylase | G | ||||||
| zntA | cadmium, zinc and mercury-transport | P | motAB | chemotaxis | N | n.s. | aglB | 6-phospho-α-glucosidase | G | |||||||
| n.s. | YPO2978 | chlorhexidine efflux transporter | S | flaA | flagellin | N | n.s. | gmhA | phosphoheptose isomerase | G | ||||||
| n.s. | mdtK | multidrug efflux pump | P | flgBCDEFGIKL | flagellar hook and basal-body | N | n.s. | scrK | fructokinase | G | ||||||
| n.s. | aaeB | p-hydroxybenzoic acid efflux pump | U | fliJLST | flagellar proteins | N | n.s. | gapA | glyceraldehyde-3-P dehydrogenase A | G | ||||||
| n.s. | metallo-β-lactamase | S | fliDEFGHMN | flagellar assembly, hook, basal body, M-ring | N | n.s. | fruK | 1-phosphofructokinase | H | |||||||
| n.s./ | flhCD | flagellar transcriptional activator | K | glgC | glucose-1-P adenylyltransferase | H | ||||||||||
| flhB | flagellar biosynthesis | N | n.s. | phnJ | synthesis of ADP-glucose | H | ||||||||||
| n.s. | mqsR | motility quorum-sensing regulator mqsR | K | n.s. | scrY | sucrose porin | M | |||||||||
| pckA | phosphoenolpyruvate carboxykinase | F | ||||||||||||||