Table 1.

Fold-changes of predicted and verified CtsR and HrcA regulon members ^a in the NZ3410 (Δ ctsR ), NZ3425 ^CM (Δ hrcA :: cat ), and NZ3423 ^CM (Δ ctsR Δ hrcA :: cat ) strains compared with the wild type

ID b	Name	Function	p -value c	28°C			40°C
				Δ ctsR	Δ hrcA	Δ ctsR Δ hrcA	Δ ctsR	Δ hrcA	Δ ctsR Δ hrcA
CtsR
lp_0786	clpP	Endopeptidase Clp, proteolytic subunit		2.42 d	−1.09	2.33	1.27	−1.29	1.12
lp_1269	clpE	ATP-dependent Clp protease, ATP-binding subunit ClpE	2.0·10-10	2.27	−1.02	2.12	−1.01	−1.20	−1.12
lp_1903	clpB	ATP-dependent Clp protease, ATP-binding subunit ClpB	5.0·10-10	7.01	1.00	6.92	4.24	−1.33	3.71
lp_1018	ctsR	transcription repressor of class III stress genes		−696	−1.15	−984	−526	−1.31	−161
lp_1019	clpC	ATP-dependent Clp protease, ATP-binding subunit ClpC		1.92	−1.09	1.84	1.76	−1.30	1.58
lp_0129	hsp1	Small heat shock protein	3.9·10-11	5.57	3.16	12.70	1.12	−1.38	1.21
lp_2945	lp_2945	Aromatic acid carboxylyase, subunit C (putative)	3.5·10-10	1.27	−1.08	1.57	1.21	1.20	1.46
lp_2451	lp_2451	Prophage P2a protein 6; endonuclease	4.9·10-7	1.05	1.11	1.12	1.03	1.40	1.32
lp_2926	lp_2926	Unknown	2.8·10-6	1.08	−1.08	−1.10	1.30	−1.19	1.05
lp_2426e	lp_2426	Prophage P2a protein 31; phage transcriptional regulator, ArpU family	2.8·10-6	−1.18	−1.56	−2.07	8.85	−1.87	1.31
lp_2540	lp_2540	Unknown	4.0·10-6	1.09	−1.31	4.11	−1.27	1.27	−1.14
lp_2541	lp_2541	ABC transporter, substrate binding protein	4.0·10-6	−1.15	−1.03	1.01	1.07	1.31	1.44
lp_2542	lp_2542	ABC transporter, permease protein (putative)	4.0·10-6	−1.03	−1.12	−1.06	−1.02	1.09	1.15
lp_2543	lp_2543	ABC transporter, ATP-binding protein	4.0·10-6	−1.18	1.02	1.27	−1.14	1.15	1.01
lp_3530	treP	Trehalose phosphorylase	4.0·10-6	−1.20	−1.25	−1.05	2.30	−1.32	−1.13
lp_2061	lp_2061	Unknown	4.0·10-6	1.38	1.53	1.47	−1.21	1.10	1.07
lp_2029	hrcA	Heat-inducible transcription repressor HrcA	5.8·10-6	−1.32	−241	−147	1.15	−176	−145
lp_2028	grpE	Heat shock protein GrpE	5.8·10-6	−1.04	1.48	1.23	−1.21	1.26	−1.27
lp_2027	dnaK	Chaperone, heat shock protein DnaK	5.8·10-6	−1.23	1.30	1.16	−1.28	1.09	−1.43
lp_2842	lp_2842	Transcription regulator, LysR family	6.7·10-6	1.08	1.14	−1.04	−1.17	−1.34	1.03
lp_1843	lp_1843	Aldose 1-epimerase family protein	9.8·10-6	−1.06	−1.14	1.06	1.50	1.19	1.20
lp_1845	hslU	ATP-dependent Hsl protease, ATP-binding subunit HslU	9.8·10-6	1.10	−1.02	1.23	1.65	1.08	1.44
lp_1846	hslV	ATP-dependent protease HslV	9.8·10-6	1.16	1.14	1.31	1.78	1.11	1.50
lp_1847	lp_1847	Integrase/recombinase, XerC/CodV family	9.8·10-6	1.22	1.22	1.36	1.73	1.11	1.36
HrcA
lp_0727	groEL	GroEL chaperonin	5.9·10-9	−1.19	2.00	1.59	−1.46	1.06	−1.50
lp_0728	groES	GroES co-chaperonin	5.9·10-9	−1.21	2.13	1.62	−1.55	1.14	−1.50
lp_2029	hrcA f	Heat-inducible transcription repressor HrcA	2.9·10-14	−1.32	−241	−147	1.15	−176	−145
lp_2028	grpE	Heat shock protein GrpE	2.9·10-14	−1.04	1.48	1.23	−1.21	1.26	−1.27
lp_2027	dnaK	Chaperone, heat shock protein DnaK	2.9·10-14	−1.23	1.30	1.16	−1.28	1.09	−1.43
lp_2026	dnaJ	Chaperone protein DnaJ		−1.13	1.05	1.17	−1.07	1.08	1.14
lp_0726	lp_0726	Membrane-bound protease, CAAX family	1.0·10-7	1.90	−1.07	1.56	2.26	−1.22	2.44
lp_0129	hsp1	Small heat shock protein		5.57	3.16	12.70	1.12	−1.38	1.21
lp_0413	plnQ	Plantaricin biosynthesis protein PlnQ	6.9·10-7	−1.03	1.23	1.51	−2.14	−1.16	1.16
lp_3578	kat	Catalase	1.0·10-6	1.02	1.02	1.03	1.28	−1.20	−1.13
lp_3617	tal3	Transaldolase	1.7·10-6	−1.19	−1.04	1.22	1.26	1.14	−1.28
lp_3618	pts37A	Sorbitol PTS, EIIA	1.7·10-6	1.03	1.02	1.33	4.51	1.33	1.26
lp_3619	pts37BC	Sorbitol PTS, EIIBC	1.7·10-6	2.15	1.31	2.50	2.68	−1.40	−1.23
lp_3620	pts37C	Sorbitol PTS, EIIC	1.7·10-6	1.00	−1.33	−1.10	1.88	1.19	1.46
lp_3621	srlM1	Sorbitol operon activator	1.7·10-6	1.39	1.17	2.13	2.22	1.08	1.40
lp_3622	srlR1	Sorbitol operon transcription antiterminator, BglG family	1.7·10-6	−1.36	−1.13	−1.05	2.17	1.01	1.30
lp_3623	srlD1	Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140)	1.7·10-6	−1.10	−1.35	−1.43	1.37	−1.16	1.88
lp_1268	lp_1268	Integrase/recombinase	3.7·10-6	−2.21	−1.10	−1.56	−3.07	1.49	−3.38
lp_0387	lp_0387	Unknown	2.4·10-6	1.18	1.04	1.25	1.06	−1.00	1.35
lp_1879	hbsU	DNA-binding protein	9.9·10-6	−1.14	1.04	−1.14	−1.23	1.04	−1.27
lp_1880	lp_1880	Unknown	9.9·10-6	−1.13	1.11	−1.14	−1.59	1.20	−1.71

^aAdapted from [1].

^bThe lp_number indicates gene number on L. plantarum WCFS1 chromosome [2].

^cp-value of the best match on the upstream sequence after comparing the canonical regulatory factor binding site. Values lower than 1.0·10^-5 were included.

^dFold-changes in bold are significant (FDR adjusted p-value < 0.05).

^eThe cis-element is predicted to be in front of this operon that contains lp_2426 until lp_2431, which all encode proteins of prophage P2a. Fold-changes are only given for lp_2426.

^fThe upstream region of hrcA contains two CIRCE elements. The second has a p-value of 8.3·10^-9.