Table 3.
The most downregulated genes in the ΔccpC strain compared to the levels in the wildtype F2365 strain.
| Gene id | Gene description | log2Fold change | p value |
|---|---|---|---|
| Internal and virulence factor | |||
| LMOf2365_0282 | Internalin-A: Bacterial adhesion/invasion protein N terminal (inlD) | −1.5 | 1.1E-02 |
| LMOf2365_0429 | Internalin-A: Bacterial adhesion/invasion protein N terminal (inlF) | −1.5 | 7.9E-03 |
| LMOf2365_0047 | Putative agmatine deiminase 1: Porphyromonas-type peptidyl-arginine deiminase | −1.6 | 1.7E-02 |
| LMOf2365_0281 | Internalin-A: Bacterial adhesion/invasion protein N terminal (inlC2) | −1.5 | 5.0E-02 |
| LMOf2365_0289 | Internalin-A: Leucine rich repeat | −1.7 | 2.4E-02 |
| LMOf2365_2418 | Internalin B(inlB) | −2.6 | 2.0E-03 |
| LMOf2365_0693 | Internalin-I | −1.9 | 4.3E-03 |
| LMOf2365_1812 | Internalin B: Bacterial adhesion/invasion protein N terminal (inlC) | −1.8 | 8.7E-03 |
| LMOf2365_0212 | 1-phosphatidylinositol phosphodiesterase, X domain (plcA) | −2.2 | 9.1E-03 |
| LMOf2365_0577 | Crp/Fnr family transcriptional regulator (crp/fnr) | −2.2 | 9.0E-03 |
| Propanediol dehydratase (PD) and ethanolamine and porphyrin metabolism | |||
| LMOf2365_1169 | Ethanolamine utilization protein: Cell division protein FtsA(eutJ) | −2.0 | 1.6E-02 |
| LMOf2365_1186 | Ethanolamine ammonia-lyase light chain (EutC) | −1.8 | 3.4E-02 |
| LMOf2365_1187 | Ethanolamine utilization protein: BMC domain (eutL) | −2.0 | 3.5E-02 |
| LMOf2365_1162 | Propanediol dehydratase medium subunit (pduD) | −2.8 | 1.4E-02 |
| LMOf2365_1173 | Ethanolamine utilization protein: Aldehyde dehydrogenase family (pduP) | −1.5 | 1.8E-02 |
| LMOf2365_1154 | Bifunctional adenosylcobalamin biosynthesis protein CobU (cobU) | −1.5 | 4.8E-02 |
| LMOf2365_1155 | Adenosylcobinamide-GDP ribazoletransferase (cobS) | −2.1 | 3.2E-02 |
| LMOf2365_1200 | Cobyrinate a,c-diamide synthase: CobQ/CobB/MinD/ParA nucleotide binding domain (cobB) | −2.6 | 6.2E-03 |
| LMOf2365_1201 | Cobalamin biosynthesis protein CobD: CobD/Cbib protein (cobD) | −2.2 | 3.9E-03 |
| LMOf2365_1202 | Cobalt-precorrin-8 methylmutase (cobH) | −2.7 | 6.0E-03 |
| LMOf2365_1208 | Probable cobalt-factor III C (17)-methyltransferas (cobJ) | −2.3 | 1.5E-03 |
| LMOf2365_1209 | Cobalt-precorrin-6A reductase (cobK) | −2.4 | 6.7E-03 |
| LMOf2365_1210 | Porphyrin biosynthesis protein: Uroporphyrinogen-III synthase HemD | −2.1 | 8.2E-03 |
| LMOf2365_1211 | Sirohydrochlorin cobaltochelatas: Cobalt chelatase (cbiK) | −2.0 | 2.2E-02 |
| LMOf2365_1212 | Cobalt-precorrin-2 C (20)-methyltransferase (cobI) | −2.9 | 2.4E-03 |
| LMOf2365_1213 | Cobalt uptake substrate-specific transmembrane region (cbiM) | −2.1 | 2.2E-02 |
| LMOf2365_1214 | Cobalt/nickel transport protein cobalt transport protein (cbiN) | −2.8 | 2.2E-02 |
| Sorbitol/glucitol metabolism | |||
| LMOf2365_0571 | PTS system glucitol/sorbitol-specific EIIA component (srlB) | −2.6 | 1.3E-02 |
| LMOf2365_0572 | PTS system glucitol/sorbitol-specific EIIB and C (srlE) | −2.0 | 7.3E-03 |
| LMOf2365_0574 | Glucitol operon activator (gutM) | −4.6 | 3.5E-02 |
| LMOf2365_0102 | Crp/Fnr family transcriptional regulator | −2.7 | 1.0E-04 |
| Phosphotransferase system (PTS) | |||
| LMOf2365_0024 | PTS system fructose-specific EIIA component | −2.7 | 1.9E-03 |
| LMOf2365_0026 | N-acetylgalactosamine permease IIC component | −3.3 | 7.2E-05 |
| LMOf2365_0044 | Glutamine--fructose-6-phosphate aminotransferase | −1.9 | 4.2E-03 |
| LMOf2365_0113 (manL) | PTS system mannose-specific EIIAB component fructose IIA component: PTS system sorbose subfamily IIB component | −1.6 | 1.0E-03 |
| LMOf2365_0114 | PTS system mannose-specific EIIC component | −2.4 | 9.5E-04 |
| LMOf2365_0115 | PTS system mannose-specific EIID component | −2.2 | 6.9E-03 |
| LMOf2365_0530 | Mannitol-specific cryptic phosphotransferase enzyme IIA: EIIA 2 | −1.6 | 1.4E-02 |
| LMOf2365_0532 | Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 | −1.8 | 3.6E-02 |
| LMOf2365_0659 | Transcriptional regulator MtlR: Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 | −1.8 | 5.6E-03 |
| LMOf2365_0662 | PTS system fructose-like EIIB component 2: PTS system, Lactose/Cellobiose specific IIB subunit | −2.2 | 1.7E-02 |
| LMOf2365_0892 | Ascorbate-specific PTS system EIIA component | −2.1 | 1.5E-03 |
| LMOf2365_0894 | PTS system cellobiose-specific: PTS system, Lactose/Cellobiose specific IIB subunit | −2.3 | 5.0E-02 |
| LMOf2365_0895 | Lichenan permease IIC component | −2.2 | 2.5E-03 |
| LMOf2365_2167 | D-tagatose-1,6-bisphosphate aldolase subunit: Fructose-bisphosphate aldolase class-II | −1.6 | 4.0E-02 |
| LMOf2365_2168 | D-tagatose-1,6-bisphosphate aldolase subunit: Fructose-bisphosphate aldolase class-II | −2.0 | 8.0E-03 |
| LMOf2365_2622 | Ascorbate-specific PTS system EIIB component | −1.9 | 1.5E-02 |
| LMOf2365_0192 | Bacterial extracellular solute-binding protein | −1.8 | 5.6E-03 |
| LMOf2365_0772 | YHCG_BACSU Uncharacterized ABC transporter ATP-binding protein | −2.3 | 4.2E-03 |
| LMOf2365_1214 | Cobalt transport protein | −2.8 | 2.2E-02 |
| LMOf2365_1754 | Putative binding protein (Bacterial extracellular solute-binding protein) | −1.6 | 1.6E-02 |
| LMOf2365_1756 | L-arabinose transport system permease protein | −1.6 | 1.3E-02 |
| LMOf2365_2032 | Probable ABC transporter permease protein | −2.7 | 3.7E-03 |
| LMOf2365_2157 | Maltodextrin transport system permease protein | −2.2 | 2.3E-03 |
| LMOf2365_2318 | L-cystine transport system permease protein | −2.7 | 1.1E-05 |
| LMOf2365_2553 | Putative hemin transport system permease protein: FtsX-like permease family | −1.7 | 4.3E-03 |
| LMOf2365_2828 | Inner membrane ABC transporter permease protein | −1.7 | 3.2E-02 |
| Pentose phosphate pathway (PPP) | |||
| LMOf2365_0363 | Fructose-6-phosphate aldolase | −2.1 | 8.2E-03 |
| LMOf2365_0379 | D-tagatose-1,6-bisphosphate aldolase class-II | −1.5 | 6.2E-03 |
| LMOf2365_0528 | Ribulose-phosphate 3 epimerase family | −2.1 | 9.3E-03 |
| LMOf2365_1054 | Putative transketolase C-terminal section | −1.7 | 1.0E-02 |
| LMOf2365_2167 | D-tagatose-1,6-bisphosphate aldolase subunit: Fructose-bisphosphate aldolase class-II | −1.6 | 4.0E-02 |
| LMOf2365_2168 | D-tagatose-1,6-bisphosphate aldolase subunit: Fructose-bisphosphate aldolase class-II | −2.0 | 8.0E-03 |
| LMOf2365_2641 | Ribulose-phosphate 3 epimerase family | −1.8 | 1.9E-02 |
| LMOf2365_0365 (rpiB1) | Ribose-5-P isomerase B | −1.9 | 1.4E-02 |
| Amino acids biosynthesis, 2-oxocarboxylic acid metabolism | |||
| LMOf2365_0363 | Probable transaldolase 2: Transaldolase | −2.1 | 8.2E-03 |
| LMOf2365_0395 | Probable triosephosphate isomerase 2 (tpiA-1) | −2.0 | 1.3E-02 |
| LMOf2365_0528 | Ribulose-phosphate 3 epimerase family | −2.1 | 9.3E-03 |
| LMOf2365_1654 | Anthranilate synthase component 2: Glutamine amidotransferase class-I (trpG) | −1.5 | 4.9E-02 |
| LMOf2365_1655 | Anthranilate synthase component 1, N terminal region (trpE) | −1.9 | 1.6E-03 |
| LMOf2365_2007 | Acetolactate synthase large subunit: Thiamine pyrophosphate enzyme, central domain(ilvB) | −1.4 | 3.3E-02 |
| LMOf2365_2008 | Acetolactate synthase small subunit: Small subunit of acetolactate synthase (ilvN) | −1.9 | 9.9E-03 |
| LMOf2365_2009 | Ketol-acid reductoisomerase [NADP (+): Acetohydroxy acid isomeroreductase, catalytic domain (ilvC)] | −1.9 | 1.5E-02 |
| LMOf2365_2010 | 2-isopropylmalate synthase (leuA) | −2.1 | 1.1E-03 |
| LMOf2365_2011 | 3-isopropylmalate dehydrogenase: Isocitrate/isopropylmalate dehydrogenase (leuB) | −2.3 | 1.9E-03 |
| LMOf2365_2012 | 3-isopropylmalate dehydratase large subunit: Aconitase family (leuC) | −2.3 | 3.9E-03 |
| LMOf2365_2013 | 3-isopropylmalate dehydratase small subunit: Aconitase C-terminal domain (leuD) | −2.2 | 5.8E-03 |
| LMOf2365_2014 | L-threonine dehydratase biosynthetic: Pyridoxal-phosphate dependent enzyme (ilvA) | −1.8 | 2.3E-02 |