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 4 S. lividans TK24 genes with (partially) known function with significantly lower expression in a CelA-producing strain compared to an empty plasmid-containing strain in early 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	Function	Ref.	CelA	log2(FC)	p-value
01030	7657	Secreted protein	1297	430	\(-\) 1.59	2.2e−04
01080	7647	Calcium-binding protein	251	54	\(-\) 2.22	1.7e−03
01125	7638	Enolase 2	197	40	\(-\) 2.30	4.4e−05
09410	5839	Peptidase	486	140	\(-\) 1.80	4.0e−04
09470	5827	Transmembrane transporter	227	47	\(-\) 2.28	3.7e−06
09475	5826	Putative membrane protein	396	124	\(-\) 1.67	3.0e−03
10950	5511	Membrane associated phosphodiesterase	232	75	\(-\) 1.62	4.1e−04
12120	5249	Nucleotide-binding protein	944	305	\(-\) 1.63	5.2e−04
12275	5218	Integral membrane protein	182	43	\(-\) 2.08	3.8e−04
12510	5174	Transferase	217	71	\(-\) 1.61	1.7e−03
14370	4798	Peptidase	125	37	\(-\) 1.75	2.3e−03
17195	4239	Small membrane protein	531	146	\(-\) 1.86	1.1e−03
17200	4238	Guanyltransferase	284	81	\(-\) 1.82	1.9e−03
18400	4002	Structural cell wall protein NepA	5745	1211	\(-\) 2.25	2.4e−07
18605	3943	Transcriptional regulator	285	88	\(-\) 1.70	1.9e−03
18635	3926	Sporulation control protein SsgA	175	30	\(-\) 2.55	2.1e−03
20395	3579	WhiB-family transcriptional regulator	1517	449	\(-\) 1.76	1.2e−04
20705	3413	HTH-type transcriptional activator TipA	435	14	\(-\) 4.97	5.3e−18
21025	3350	Alanine-rich protein	57	11	\(-\) 2.37	1.5e−03
21180	3323	ECF sigma factor BldN	1502	445	\(-\) 1.76	3.9e−05
23265	2884	Cytochrome P450	190	51	\(-\) 1.89	6.6e−04
24080	2718	Hydrophobic surface protein	170	20	\(-\) 3.06	6.7e−04
28720	1800	Hydrophobic surface protein	10,102	3979	\(-\) 1.34	1.3e−03
29370	1674	Hydrophobic surface protein	24,089	8481	\(-\) 1.51	4.1e−04
31930	1174	Putative aldehyde dehydrogenase	245	43	\(-\) 2.53	4.8e−07
32840	6393	Transposase	299	57	\(-\) 2.40	9.1e−07
34120	0762	Protease inhibitor protein	1495	485	\(-\) 1.62	1.1e−03
35005	0588	Sensor kinase	113	34	\(-\) 1.74	3.4e−03

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

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ISSN: 1475-2859

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