Table 1.
Genes higher transcribed in presence of sprouts in comparison to M9-glucose medium determined by RNA-seq analysis
| Category | Gene | Locus tag | Fold change | Function |
|---|---|---|---|---|
| Amino acid metabolism | argI | SENTW_4577 | 11.84 | Ornithine carbamoyltransferase 1 |
| speB | SENTW_3201 | 5.79 | Agmatinase | |
| speD | SENTW_0130 | 8.12 | S-adenosylmethionine decarboxylase | |
| putA | SENTW_1034 | 5.07 | Transcriptional repressor, proline oxidase | |
| putP | SENTW_1045 | 5.01 | Sodium/proline symporter | |
| ilvB | SENTW_3900 | 5.34 | Acetolactate synthase | |
| ilvN | SENTW_3899 | 8.33 | Acetolactate synthase small subunit | |
| avtA | SENTW_3763 | 4.67 | Valine pyruvate aminotransferase | |
| phnA | SENTW_4376 | 9.47 | Alkylphosphonate utilization operon protein | |
| hutH | SENTW_0770 | 8.68 | Histidine ammonia-lyase | |
| hutU | SENTW_0769 | 3.93 | Urocanate hydratase | |
| carA | SENTW_1700 | 9.47 | Carbamoyl-phosphate synthase small chain | |
| sbp | SENTW_4153 | 9.94 | Sulphate-binding protein | |
| cysM | SENTW_2618 | 4.46 | Cysteine synthase B | |
| cysI, cysJ | SENTW_3043-42 | 8.26 | Sulphite reductase | |
| cysH | SENTW_3041 | 8.47 | Sulphate reductase | |
| cysD | SENTW_3022 | 16.05 | Sulphate adenylsltransferase subunit | |
| cysC | SENTW_3020 | 15.37 | Adenosine 5′-phosphosulphate kinase | |
| cysN | SENTW_3021 | 15.37 | Sulphate adenylsltransferase subunit | |
| cysA, cysW, cysT, cysP | SENTW_2620-23 | 5.56 | Sulphate transporter | |
| metB | SENTW_4189 | 5.63 | Cystathionine gamma-synthase | |
| ST2 | SENTW_4354 | 5.43 | Sulphate transporter | |
| pphA | SENTW_1338 | 311.10 | Serine/threonine-protein phosphatase | |
| Pathogenicity island | sifA | SENTW_2029 | 8.68 | Secreted protein |
| (SPI-2) | ssaG, ssaH, ssaI | |||
| ssaJ, ssaK, ssaL | SENTW_1805-011 | 4.29 | Secretion apparatus | |
| ssaT, ssaU | SENTW_1794-95 | 7.22 | Secretion apparatus | |
| ssaM, ssaV | SENTW_1800-01 | 6.91 | Secretion apparatus | |
| sseE | SENTW_1812 | 5.93 | Effector protein | |
| sscB | SENTW_1811 | 23.57 | Chaperone | |
| ssaR | SENTW_1796 | 12.86 | Export apparatus | |
| sopD2 | SENTW_3040 | 5.99 | Effector protein | |
| pipB | SENTW_1007 | 4.01 | Effector protein | |
| sseL | SENTW_2415 | 5.46 | Deubiquitinase | |
| Motility | csgB | SENTW_2110 | 16.75 | Minor curli subunit |
| csgG | SENTW_2114 | 5.49 | Curli production assembly/transport component | |
| csgD | SENTW_2111 | 5.21 | Transcriptional regulator | |
| bcfE | SENTW_4730 | 4.81 | Fimbrin-like protein FimI | |
| spy | SENTW_1904 | 6.15 | Spheroplast protein | |
| Cofactors and energy production | thiC, thiE, thiF, thiS | SENTW_4269-72 | 12.48 | Thiamin phosphate pyrophosphorylase, Thiamine biosynthesis proteins |
| nuoI | SENTW_2443 | 6.82 | NADH dehydrogenase I (chain I) | |
| nuoE, nueF | SENTW_2449-50 | 3.30 | NADH dehydrogenase I (chains E and F) | |
| metF | SENTW_4195 | 6.17 | Methylenetrahydrofolate reductase | |
| atpG | SENTW_3971 | 4.42 | Membrane-bound ATP synthase | |
| Regulators | fis | SENTW_3516 | 37.55 | DNA binding protein |
| yiaG | SENTW_3750 | 13.86 | Transcriptional regulator | |
| metR | SENTW_4054 | 13.81 | Transcriptional regulator | |
| rcsA | SENTW_1101 | 9.30 | Regulator of capsular polysaccharide synthesis | |
| ydcI | SENTW_1576 | 6.26 | Probable RuBisCO transcriptional regulator | |
| ydhM | SENTW_1780 | 5.67 | HTH-type transcriptional repressor | |
| ydcN | SENTW_1600 | 4.29 | Uncharacterized HTH-type transcriptional regulator | |
| mntR | SENTW_0817 | 3.92 | Manganese transport regulator | |
| Stress response | pspA | SENTW_1509 | 15.49 | Phage shock protein |
| pspB, pspC | SENTW_1510-11 | 5.75 | Phage shock protein | |
| ibpA | SENTW_3916 | 5.86 | Heat shock protein | |
| osmY | SENTW_4668 | 9.81 | Osmotically-inducible protein | |
| Transporters | yehW | SENTW_1718 | 8.27 | Bicarbonate transport system permease |
| fliY | SENTW_1129 | 5.49 | Cysteine-binding periplasmic protein | |
| yliA | SENTW_0829 | 2.92 | Glutathione transporter | |
| corA | SENTW_4042 | 4.96 | Magnesium transporter protein | |
| dctA | SENTW_3716 | 4.87 | C4-dicarboxylate transport protein | |
| ybiR | SENTW_0818 | 2.58 | Inner membrane protein | |
| ydjN3 | SENTW_1892 | 12.28 | L-cystine uptake protein tcyP | |
| Protein export; Bacterial secretion system | yajC | SENTW_0393 | 4.06 | Preprotein translocase subunit YajC |
| uraA | SENTW_2680 | 14.89 | Uracil permease | |
| Lipid metabolism | glpK | SENTW_4175 | 12.90 | Glycerol kinase |
| glpT | SENTW_2411 | 12.82 | Glycerol-3-phosphate transporter | |
| glpF | SENTW_4176 | 7.58 | Glycerol uptake facilitator protein | |
| glpQ | SENTW_2410 | 6.15 | Glycerophosphodiester phosphodiesterase | |
| cdh1 | SENTW_4154 | 4.81 | CDP-diacylglycerol pyrophosphatase | |
| yjfO | SENTW_4482 | 13.03 | Lipoprotein | |
| ybaY | SENTW_0451 | 6.20 | Uncharacterized lipoprotein | |
| Fatty acid metabolism | fadB | SENTW_4073 | 6.14 | Enoyl-CoA hydratase |
| fadA | SENTW_4072 | 4.47 | Small (beta) subunit of the fatty acid-oxidizing multienzyme complex | |
| Post-transcriptional modification | queA | SENTW_0390 | 11.26 | Synthesis of queuine in tRNA |
| trmD | SENTW_2838 | 9.46 | tRNA methyltransferase | |
| yhdG | SENTW_3515 | 7.78 | tRNA-dihydrourindine synthase B | |
| rpoA | SENTW_3542 | 7.24 | DNA-dependent RNA polymerase | |
| Carbohydrate metabolism | aceB | SENTW_4287 | 10.86 | Malate synthase A |
| acs | SENTW_4361 | 8.99 | Acetyl-coenzyme A synthetase | |
| sdhC, sdhD, sdhA | SENTW_0709-11 | 5.39 | Succinate dehydrogenase | |
| sdhB | SENTW_0712 | 4.82 | Succinate dehydrogenase iron-sulphur protein | |
| sucC,sucD | SENTW_0716-17 | 2.63 | Succinyl-CoA synthetase | |
| prsA | SENTW_1416 | 5.20 | Ribose-Phosphate pyrophosphokinase | |
| cpsB, rfbK | SENTW_2210-11 | 3.06 | Mannose-1-phosphate guanylyltransferase; phosphomannomutase | |
| Nucleotide metabolism | upp | SENTW_2681 | 8.83 | Uracil phosporibosyltransferase |
| nrdA | SENTW_2405 | 4.66 | Ribonucleoside-diphosphate reductase alpha | |
| Genetic information processing – | ||||
| Replication and repair | priB | SENTW_4495 | 4.54 | Primosomal replication protein N |
| ruvC | SENTW_1185 | 4.31 | Cross-over junction endodeoxyribonuclease | |
| rplB | SENTW_3564 | 6.05 | 50S ribosomal protein L2 | |
| rplD, rplW | SENTW_3565-66 | 6.59 | 50S ribosomal protein L4; 50S ribosomal protein L23 | |
| rplF | SENTW_3552 | 7.62 | 50S ribosomal protein L6 | |
| rplI | SENTW_4497 | 5.45 | 50S ribosomal protein L9 | |
| rplJ | SENTW_4260 | 7.77 | 50S ribosomal protein L10 | |
| rplK | SENTW_4258 | 6.87 | 50S ribosomal protein L11 | |
| rplL | SENTW_4261 | 14.24 | 50S ribosomal protein L7/L12 | |
| rplO | SENTW_3548 | 4.54 | 50S ribosomal protein L15 | |
| rplP, rpmC, rpsQ | SENTW_3558-60 | 5.73 | 50S ribosomal protein L16; 50S ribosomal protein L29; 30S ribosomal protein S17 | |
| rplQ | SENTW_3541 | 5.94 | 50S ribosomal protein L17 | |
| rplS | SENTW_2837 | 12.01 | 50S ribosomal protein L19 | |
| rplU | SENTW_3432 | 4.42 | 50S ribosomal protein L21 | |
| rplV | SENTW_3562 | 6.73 | 50S ribosomal protein L22 | |
| rpmA | SENTW_3431 | 6.60 | 50S ribosomal protein L27 | |
| rpmB | SENTW_3829 | 5.06 | 50S ribosomal protein L28 | |
| rpmD | SENTW_3549 | 3.82 | 50S ribosomal protein L30 | |
| rpmF | SENTW_2062 | 6.82 | 50S ribosomal protein L32 | |
| rpmG | SENTW_3828 | 8.15 | 50S ribosomal protein L33 | |
| rpmJ | SENTW_3546 | 5.27 | 50S ribosomal subunit protein L36 | |
| rpsH | SENTW_3553 | 10.11 | 30S ribosomal protein S8 | |
| rpsI | SENTW_3473 | 6.06 | 30S ribosomal protein S9 | |
| rpsK | SENTW_3544 | 5.67 | 30S ribosomal protein S11 | |
| rpsR | SENTW_4496 | 12.63 | 30S ribosomal protein S18 | |
| rpsS | SENTW_3563 | 7.07 | 30S ribosomal protein S19 | |
| rpsT | SENTW_4750 | 6.53 | 30S ribosomal protein S20 | |
| rpsU | SENTW_3346 | 9.92 | 30S ribosomal protein S21 | |
| yfjA | SENTW_2839 | 5.16 | Ribosome maturation factor RimM | |
| Unclassified | yaiB | SENTW_0366 | 5.03 | Anti-adapter protein IraP |
| nusG | SENTW_4257 | 5.15 | Elongation factor | |
| rnt | SENTW_1783 | 4.24 | Ribonuclease T | |
| cesT | SENTW_2267 | 4.16 | Putative cytoplasmic protein | |
| sixA | SENTW_2511 | 4.02 | Phosphohistidine phosphatase | |
| rnpA, yidD | SENTW_3942-43 | 3.26 | RNase P, protein component | |
| era, rnc | SENTW_2769-70 | 2.63 | GTP-binding protein era homolog | |
| ntpA | SENTW_1183 | 6.70 | dATP pyrophosphohydrolase | |
| ydcF | SENTW_1578 | 8.27 | Putative esterase | |
| Hypothetical proteins | SENTW_0391 | 32.88 | Hypothetical protein | |
| ycdZ | SENTW_2115 | 5.11 | Hypothetical protein | |
| SENTW_1535 | 21.31 | Hypothetical protein | ||
| SENTW_1536 | 18.25 | Hypothetical protein | ||
| SENTW_1962 | 11.16 | Hypothetical protein | ||
| SENTW_1381 | 6.75 | Hypothetical protein | ||
| yeeI | SENTW_2127 | 4.43 | Hypothetical protein | |
| yibP | SENTW_3805 | 4.27 | Hypothetical protein | |
| yigM | SENTW_4053 | 4.01 | Hypothetical protein | |
| SENTW_0384 | 3.95 | Hypothetical protein | ||
| sopD | SENTW_0915 | 13.24 | Homologous to secreted protein SopD (T3SS) | |
| yahO | SENTW_0348 | 4.40 | Protein of unknown function | |
| yebV | SENTW_1340 | 15.38 | Uncharacterized protein | |
| yiaK | SENTW_3767 | 9.61 | Putative protein | |
| yciF | SENTW_1469 | 11.99 | Unknown function | |
| ygaT (csiD) | SENTW_2877 | 19.85 | Hypothetical protein | |
| tctA | SENTW_2876 | 10.62 | Unknown function | |
| yqeF | SENTW_3132 | 4.61 | Putative acyltransferase | |
| TPX | SENTW_1534 | 6.12 | Putative thiol peroxidase | |
| ybdL | SENTW_0580 | 4.55 | Putative aminotransferase | |
| yjgF | SENTW_4564 | 7.03 | Protein TdcF | |
| yiaL | SENTW_3768 | 7.86 | Protein YiaL | |
| ytfK | SENTW_4510 | 8.24 | Uncharacterized protein YtfK | |
| yhcN3 | SENTW_3490 | 5.82 | Protein YdgH | |
| ygaU | SENTW_2883 | 5.51 | Uncharacterized protein YgaU | |
| yggE | SENTW_3181 | 6.70 | Uncharacterized protein YggE | |
| yfeK | SENTW_2617 | 5.38 | Uncharacterized protein YfeK | |
| yjfN | SENTW_4481 | 6.70 | UPF0379 protein YjfN |