TABLE 2.
Transcription levels of genes involved in antibiotic tolerance and biofilm formation of S. epidermidis ΔvraSR
| Gene and locus | GenBank accession no. (location) | Description or predicted function | Expression ratio (mutant/WT) |
|
|---|---|---|---|---|
| RNA-Seq | qRT-PCRa | |||
| Genes involved in drug tolerance | ||||
| vraR | NC_002976.3 (1484739–1485368) | DNA-binding response regulator | 0.00 | 0.00001 |
| vraS | NC_002976.3 (1485358–1486404) | Two-component sensor histidine kinase | 0.00 | 0.00001 |
| pbp1 | NC_002976.3 (741901–744228) | Penicillin-binding protein 1 | 1.32 | 1.08 ± 0.10 |
| pbp2 | NC_002976.3 (1063849–1066080) | Penicillin-binding protein 2 | 1.01 | 1.06 ± 0.19 |
| pbp3 | NC_002976.3 (1155781–1157871) | Penicillin-binding protein 3 | 1.12 | ND |
| SERP_RS01330 | NC_002976.3 (235619–236599) | Penicillin-V acylase | 1.04 | ND |
| SERP1412(sgtB) | NC_002976.3 (1476585–1477394) | Monofunctional peptidoglycan glycosyltransferase | 0.73 | 0.85 ± 0.25 |
| SERP_RS06395 | NC_002976.3 (1340351-1341256) | Transglycosylase | 0.95 | ND |
| murAA | NC_002976.3 (1747152–1748417) | UDP-N-acetylglucosamine-1-carboxyvinyltransferase | 0.98 | 1.08 ± 0.13 |
| murE | NC_002976.3 (600125–601609) | UDP-N-acetylmuramoyl-l-alanyl-d-glutamate–l-lysine ligase | 1.17 | 0.99 ± 0.20 |
| pflA | NC_002976.3 (2411378–2412133) | Pyruvate formate lyase activating enzyme | 0.30 | 0.77 ± 0.23 |
| plfB | NC_002976.3 (2412155-2414401) | Formate C-acetyltransferase | 0.41 | ND |
| lrgA | NC_002976.3 (2047084–2047482) | Antiholin-like murein hydrolase modulator LrgA | 0.09 | 0.10 ± 0.11 |
| lrgB | NC_002976.3 (2047486–2048187) | Antiholin-like protein LrgB | 0.16 | ND |
| cidA | NC_002976.3 (2142373–2142765) | Holin-like protein, CidA/LrgA family protein | 2.20 | 4.60 ± 0.46 |
| Genes involved in biofilm formation | ||||
| icaA | NC_002976.3 (2334220–2335458) | Poly-beta-1,6-N-acetyl-d-glucosamine synthase | 0.55 | 0.17 ± 0.05 |
| icaR | NC_002976.3 (2333498–2334055) | icaADBC negative transcriptional regulator | 0.89 | 9.27 ± 4.4 |
| atlE | NC_002976.3 (627656-631663) | Bifunctional autolysin | 0.88 | 0.89 ± 0.10 |
| rsbU | NC_002976.3 (1724457–1725458) | Serine/threonine phosphatase | 1.48 | 0.84 ± 0.13 |
| sarA | NC_002976.3 (279424–279798) | Staphylococcal accessory regulator A | 0.88 | 0.89 ± 0.18 |
| aap | NC_002976.3 (2459164–2460687) | Accumulation-associated protein | 0.98 | 0.77 ± 0.12 |
| Genes involved in glycolysis/gluconeogenesis | ||||
| gntP | NC_002976.3 (2081933–2083291) | Gluconate transporter | 0.21 | ND |
| gntK | NC_002976.3 (2083341–2084882) | Gluconate kinase | 0.16 | 0.34 ± 0.19 |
| gntR | NC_002976.3 (2084906–2085586) | GntR family transcriptional regulator | 0.43 | ND |
| SERP_RS10290 | NC_002976.3 (2094468–2095742) | Glucarate transporter, MFS transporter | 0.33 | ND |
| SERP_RS11465 | NC_002976.3 (2371584–2372924) | Sugar porter family MFS transporter | 0.28 | ND |
| SERP_RS10325 | NC_002976.3 (2100973–2102937) | Fructose-1,6-bisphosphatase | 0.47 | ND |
| glpF | NC_002976.3 (879638–880462) | Glycerol transporter, aquaporin family protein | 0.22 | ND |
| glpK | NC_002976.3 (880616–882115) | Glycerol kinase | 0.20 | ND |
| glpD | NC_002976.3 (882292–883965) | Aerobic glycerol-3-phosphate dehydrogenase/oxidase | 0.09 | 0.38 ± 0.11 |
| larB | NC_002976.3 (261972–262748) | 1,5-Phosphoribosyl-5-amino-4-imidazole carboxylate carboxylase | 0.43 | ND |
| larE | NC_002976.3 (262763–263590) | ATP-dependent sacrificial sulfur transferase | 0.49 | ND |
| SERP_RS01465 | NC_002976.3 (263610–264878) | Nickel-dependent lactate racemase | 0.42 | ND |
| adhP | NC_002976.3 (265167–266189) | Zinc-dependent alcohol dehydrogenase | 0.43 | ND |
| SERP_RS01475 | NC_002976.3 (266272–266664) | Hypothetical protein | 0.43 | ND |
| pckA | NC_002976.3 (1409889–1411481) | Phosphoenolpyruvate carboxykinase (ATP) | 0.36 | ND |
| SERP_RS01910 | NC_002976.3 (355256–356014) | DeoR/GlpR family transcriptional regulator | 5.39 | ND |
| fruK | NC_002976.3 (356011–356931) | 1-Phosphofructokinase | 8.53 | 11.43 ± 2.99 |
| fruA | NC_002976.3 (356937–358889) | PTS fructose transporter subunit IIC | 5.91 | ND |
| pfkA | NC_002976.3 (1303827–1304795) | ATP-dependent 6-phosphofructokinase | 2.88 | ND |
| gapR | NC_002976.3 (445408–446421) | Sugar-binding transcriptional regulator | 4.59 | ND |
| gapA-1 | NC_002976.3 (446473–447483) | Type I glyceraldehyde-3-phosphate dehydrogenase | 2.67 | ND |
| pgk | NC_002976.3 (447677–448867) | Phosphoglycerate kinase | 2.99 | ND |
| pyk | NC_002976.3 (1302046–1303803) | Pyruvate kinase | 2.54 | ND |
| Genes involved in pentose phosphate pathway | ||||
| sucC | NC_002976.3 (815834–817000) | ADP-forming succinate-CoA ligase subunit beta | 0.46 | 0.31 ± 0.18 |
| sucD | NC_002976.3 (817022–817930) | Succinyl-CoA ligase subunit alpha | 0.38 | ND |
| SERP_RS03700 | NC_002976.3 (730806–732572) | Succinate dehydrogenase, flavoprotein subunit | 0.45 | ND |
| SERP_RS03705 | NC_002976.3 (732572–733414) | Succinate dehydrogenase iron-sulfur subunit | 0.39 | ND |
| SERP_RS04930 | NC_002976.3 (1001204–1002466) | Dihydrolipoyl lysine residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex | 0.21 | ND |
| SERP_RS04935 | NC_002976.3 (1002485–1005289) | 2-Oxoglutarate dehydrogenase subunit E1 component | 0.28 | ND |
| SERP_RS11420 | NC_002976.3 (2360269–2361546) | Acetoin dehydrogenase subunit E2 | 0.38 | 0.11 ± 0.08 |
| SERP_RS11425 | NC_002976.3 (2361560–2362600) | Acetoin dehydrogenase, E1 component, beta subunit | 0.16 | ND |
| SERP_RS11430 | NC_002976.3 (2362671–2363624) | Thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha | 0.35 | ND |
| sdhA | NC_002976.3 (2118833–2119732) | l-Serine dehydratase, iron-sulfur-dependent, subunit alpha | 0.31 | 0.65 ± 0.13 |
| sdhB | NC_002976.3 (2119745–2120425) | l-Serine ammonia-lyase, iron-sulfur-dependent, subunit beta | 0.46 | ND |
| mqo-3 | NC_002976.3 (2350001–2351497) | Malate quinone oxidoreductase | 2.29 | ND |
| icd | NC_002976.3 (1296195–1297463) | NADP-dependent isocitrate dehydrogenase | 0.43 | ND |
| gltA | NC_002976.3 (1297506–1298627) | Citrate synthase, catalyzes the formation of citrate from acetyl-CoA and oxaloacetate | 0.45 | ND |
| Genes involved in phosphate transport system | ||||
| SERP_RS10495 | NC_002976.3 (2137627–2139654) | PTS glucose EIICBA component | 0.14 | 0.48 ± 0.01 |
| SERP_RS11510 | NC_002976.3 (2389604–2389978) | PTS mannose transporter subunit IIA | 0.41 | ND |
| SERP_RS11515 | NC_002976.3 (2389982–2390557) | Dihydroxyacetone kinase subunit L | 0.46 | ND |
| SERP_RS11135 | NC_002976.3 (2289420–2291360) | PTS system, fructose-specific IIABC components | 0.27 | ND |
| SERP_RS09555 | NC_002976.3 (1928396–1929985) | PTS alpha-glucoside transporter subunit IIBC | 0.17 | ND |
| lacF | NC_002976.3 (1838149–1838463) | PTS system lactose-specific phosphotransferase IIA component | 0.40 | ND |
| lacD | NC_002976.3 (1838483–1839460) | Tagatose 1,6-diphosphate aldolase | 0.42 | ND |
| SERP_RS11820 | NC_002976.3 (2467765–2469144) | Hexose phosphate transporter, phosphoglycerate transporter family protein | 0.31 | ND |
| manA-2 | NC_002976.3 (2291376–2292326) | Mannose-6-phosphate isomerase class I | 0.11 | 0.14 ± 0.01 |
| malA | NC_002976.3 (1114441–1116096) | Alpha-glucosidase | 0.44 | ND |
| rbsK | NC_002976.3 (2124965–2125888) | Ribokinase | 0.17 | ND |
| rbsD | NC_002976.3 (2125942–2126346) | d-Ribose pyranase | 0.17 | ND |
| rbsU | NC_002976.3 (2126368–2127249) | Ribose transporter, membrane protein | 0.19 | ND |
| SERP_RS05175 | NC_002976.3 (1083213–1083662) | Nucleoside diphosphate kinase | 0.39 | ND |
| Genes involved in amino acid metabolism | ||||
| rocD | NC_002976.3 (529033–530223) | Ornithine oxoacid transaminase | 0.49 | ND |
| gluD | NC_002976.3 (530332–531576) | Glutamate dehydrogenase, NAD specific | 0.46 | ND |
| putA | NC_002976.3 (1385177–1386178) | Proline-dehydrogenase | 0.46 | ND |
| SERP_RS10565 | NC_002976.3 (2152253–2153797) | l-Glutamate gamma-semialdehyde dehydrogenase | 0.42 | ND |
| geh-1 | NC_002976.3 (2337843–2339909) | Lipase, YSIRK domain-containing triacylglycerol lipase GehC | 0.37 | ND |
| arcC | NC_002976.3 (2397500–2398432) | Carbamate kinase | 0.27 | ND |
| SERP_RS11560 | NC_002976.3 (2398606–2400162) | Membrane protein, YfcC family protein | 0.34 | ND |
a
qRT-PCR data are given as the means ± standard deviations of the results from three independent experiment. ND, not done.