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Table 1 Genes with (partially) known function that are significantly overexpressed in CelA-producing S. lividans TK24 with a Benjamini–Hochberg FDR 0.05, and that are only expressed in a CelA-producing strain

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

Locus Function Expression [TPM] p-value
SLIV SCO Ref. CelA log2(FC)
01700 7522 DNA ligase 2 6 36 2.50 7.9e−06
01705 7521 Beta-lactamase 2 12 2.88 3.1e−02
03875 7076 Two-component histidine kinase 5 30 2.72 4.5e−05
03880 7075 Response regulator 21 105 2.29 3.7e−05
04015 7047 Undecaprenyl-diphosphatase 1 7 53 2.87 7.6e−05
06835 6262 Helicase 9 36 1.95 1.5e−04
09765 5770 Regulatory protein RecX 36 172 2.24 5.3e−07
09770 5769 Recombinase RecA 314 1327 2.08 1.9e−11
09810 5761 ATP-dependent DNA helicase 6 19 1.58 7.4e−04
10645 5566 ATP-dependent DNAhelicase RecG 27 63 1.25 1.8e−03
10985 5504 Integral membrane protein 83 476 2.52 8.3e−09
11035 5494 DNA ligase 1 57 103 0.86 1.1e−02*
13140 5049 Putative NADHdehydrogenase/NAD(P)H nitroreductase 0 225 8.84 2.9e−24
13190 5039 Penicillin-binding protein 121 240 0.99 1.1e−03
13680 4938 ECF-sigma factor 1 20 4.99 2.5e−04
13690 4936 ABC transporter ATP-binding protein 3 244 6.16 2.5e−23
13695 4935 Integral membrane protein 2 238 7.25 4.1e−40
17590 4157 Protease HtrB 4 875 7.70 4.0e−63
17595 4156 Response regulator CssR 6 494 6.40 2.5e−37
17600 4155 Sensor histidine kinase CssS 2 101 5.98 1.0e−23
18305 4021 Two component system histidine kinase 1 81 5.82 3.6e−22
18310 4020 Putative transcriptional regulatory protein 16 493 4.95 3.5e−32
18435 3977 Protease HtrA3 62 204 1.71 5.8e−07
19310 3798 Chromosome condensation protein 9 260 4.82 1.5e−24
20575 3542 Integral membrane protein with kinase activity 45 61 0.43 2.7e−01*
20580 3541 DNA polymerase III subunit delta 59 88 0.57 1.1e−01*
20605 3434 DNA polymerase I 11 43 1.97 3.0e−04
21020 3351 DNA repair protein RadA 148 277 0.91 2.6e−03
26430 2258 ABC transporter 22 91 2.07 4.4e−05
26435 2257 Putative Daunorubicin/doxorubicin resistance ATP-binding protein 19 98 2.35 9.4e−06
27700 2003 DNA polymerase I 158 287 0.87 1.8e−03
27885 1966 UvrABC system protein B 59 190 1.69 2.1e−06
27925 1958 UvrABC system protein A 53 123 1.20 2.0e−04
28335 1876 RNA polymerase sigma factor 14 69 2.28 8.2e−03*
28340 1875 Penicillin binding protein 72 456 2.66 2.5e−14
28380 1867 Ectoine hydroxylase 100 778 2.95 7.8e−20
28385 1866 l-Ectoine synthase 221 2079 3.24 5.3e−21
28390 1865 Diaminobutyrate-2-oxoglutarate transaminase 24 169 2.81 1.9e−11
28395 1864 l-2,4-Diaminobutyric acid acetyltransferase 30 118 2.00 5.5e−04
31060 1343 Uracil-DNA glycosylase 2 Ung2 191 394 1.04 1.7e−03
  1. A clustering algorithm was used for grouping nearby genes with similar expression patterns. For all S. lividans genes, 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