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Table 2 S. lividans TK24 genes with (partially) known function with expression correlating to that of the OsdR regulatory protein, and significantly higher expression in a CelA-producing strain in exponential phase (Benjamini–Hochberg FDR 0.05)

From: Transcriptomic and fluxomic changes in Streptomyces lividans producing heterologous protein

Locus Function Expression [TPM] p-value
SLIV SCO Ref. CelA log2(FC)
01755 7511 Glyceraldehyde-3-phosphate dehydrogenase Gap3 52 323 2.65 2.8e−08
05195 6663 Transketolase 25 207 3.06 4.0e−13
05200 6662 Transaldolase 1 53 158 1.57 3.6e−04
05205 6661 Glucose-6-phosphate 1-dehydrogenase 40 110 1.46 1.9e−04
05215 6659 Glucose-6-phosphate isomerase 1 64 134 1.06 2.4e−03
05220 6658 6-phosphogluconate dehydrogenase 144 221 0.62 4.0e−02*
05225 6657 Membrane-associated oxidoreductase 26 33 0.32 3.9e−01*
18590 3946 CydB cytochrome d ubiquinol oxidase, subunit II 127 204 0.68 2.4e−02*
18595 3945 CydA cytochrome oxidase subunit I 250 892 1.83 2.0e−09
33310 0924 Cytochrome B subunit 45 273 2.59 5.9e−09
33315 0923 Fumarate dehydrogenase 17 96 2.50 3.9e−09
33320 0922 Fumarate dehydrogenase 26 78 1.59 3.1e−03
36805 0219 Respiratory nitrate reductase, gamma subunit 0 28 Inf 5.2e−07
36810 0218 Nitrate reductase subunit delta 0 36 Inf 2.0e−08
36815 0217 Nitrate reductase beta chain 0 111 8.23 1.0e−28
36820 0216 Nitrate reductase alpha subunit 2 192 6.86 3.5e−49
36825 0215 \(\hbox {Nitroreductase}^{\dagger }\) 1 82 7.14 4.0e−15
36830 0214 Pyridoxamine 5′-phosphate \(\hbox {oxidase}^{\dagger }\) 4 58 4.03 1.4e−04
36835 0213 Nitrate/nitrite transporter 3 114 5.46 1.0e−20
36845 0211 Two-component sensor 2 73 5.21 1.4e−08
36850 0209 Cystathionine \(\beta \)-\(\hbox {syntase}^{\dagger }\) 1 109 6.97 1.4e−20
36855 0208 Pyruvate, phosphate dikinase 1 65 5.90 5.4e−24
36865 0206 Putative pyruvate formate-lyase 0 74 Inf 3.1e−05
36867   Putative pyruvate formate-lyase-activating protein, N-terminal fragment, putative pseudogene 0 74 Inf 7.7e−06
36875 0204 Transcriptional regulatory protein OsdR 16 391 4.60 3.1e−25
36880 0203 Two-component sensor OsdK 23 56 1.30 4.2e−03*
36890 0201 Thiosulfate dehydrogenase (quinone)\(^{\dagger }\) 1 464 8.97 3.5e−37
36895 0200 Universal stress \(\hbox {protein}^{\dagger }\) 0 317 Inf 2.5e−04
36900 0199 Alcohol dehydrogenase 1 214 8.55 9.3e−26
36905 0198 Universal stress \(\hbox {protein}^{\dagger }\) 1 72 6.16 2.9e−11
36910 0197 Pyridoxamine 5′-phosphate \(\hbox {oxidase}^{\dagger }\) 6 97 4.07 3.1e−09
37035 0181 Universal stress \(\hbox {protein}^{\dagger }\) 2 175 6.76 4.0e−22
37040 0180 Universal stress \(\hbox {protein}^{\dagger }\) 0 69 Inf 2.7e−14
37045 0179 Zinc-containing dehydrogenase 4 293 6.37 6.9e−32
37050 0178 Universal stress \(\hbox {protein}^{\dagger }\) 8 28 1.72 1.2e−01
37060 0177 Membrane protein 2 112 6.22 2.5e−12
37070 0174 pyridoxamine 5′-phosphate \(\hbox {oxidase}^{\dagger }\) 1 232 8.50 6.0e−32
37075 0173 OsmC regulator of disulfide bond formation redox \(\hbox {protein}^{\dagger }\) 7 78 3.48 2.8e−06
37080 0172 Universal stress \(\hbox {protein}^{\dagger }\) 3 17 2.76 1.1e−01
37085 0171 Nicotinate phosphoribosyltransferase 0 56 Inf 3.5e−17
37095 0169 Cystathionine \(\beta \)-\(\hbox {synthase}^{\dagger }\) 10 398 5.29 4.0e−30
37100 0168 Regulator protein 10 625 5.94 5.1e−33
37105 0167 Universal stress \(\hbox {protein}^{\dagger }\) 4 297 6.35 8.5e−31
37130 0162 \(\hbox {Nitroreductase}^{\dagger }\) 0 91 8.28 3.5e−17
37090 0170 Cystathionine \(\beta \)-\(\hbox {synthase}^{\dagger }\) 6 252 5.44 1.2e−21
  1. A clustering algorithm was used for grouping nearby genes with similar expression patterns. When present, the corresponding ortholog of the model organism S. coelicolor is given
  2. * Genes included for completeness, but p-value does not satisfy FDR 0.05
  3. Function taken from [42]