Transcriptomic and fluxomic changes in Streptomyces lividans producing heterologous protein

Daniels, Wouter; Bouvin, Jeroen; Busche, Tobias; Rückert, Christian; Simoens, Kenneth; Karamanou, Spyridoula; Van Mellaert, Lieve; Friðjónsson, Ólafur H.; Nicolai, Bart; Economou, Anastassios; Kalinowski, Jörn; Anné, Jozef; Bernaerts, Kristel

doi:10.1186/s12934-018-1040-6

Microbial Cell Factories

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	Function	Ref.	CelA	log2(FC)	p-value
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

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
* Genes included for completeness, but p-value does not satisfy FDR 0.05

Back to article page

ISSN: 1475-2859

Contact us

Submission enquiries: journalsubmissions@springernature.com